Crystal structures of human Fabs targeting the Bexsero meningococcal vaccine antigen NHBA
This study also provides indirect evidence for the intrinsically disordered nature of two N-terminal regions of NHBA. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - May 25, 2017 Category: Biochemistry Authors: Maritan, M. Cozzi, R. Lo Surdo, P. Veggi, D. Bottomley, M.J. Malito, E. Tags: fragment antigen binding Fabs monoclonal antibodies mAbs NHBA Neisseria vaccine Bexsero research communications Source Type: research
Crystal structure of Rv1220c, a SAM-dependent O-methyltransferase from Mycobacterium tuberculosis
Rv1220c from Mycobacterium tuberculosis is annotated as an O-methyltransferase (MtbOMT). Currently, no structural information is available for this protein. Here, the crystal structure of MtbOMT refined to 2.0 Å resolution is described. The structure reveals the presence of a methyltransferase fold and shows clear electron density for one molecule of S-adenosylmethionine (SAM), which was apparently bound by the protein during its production in Escherichia coli. Although the overall structure of MtbOMT resembles the structures of O-methyltransferases from Cornybacterium glutamicum, Coxiella burnetti and Alfa alfa,...
Source: Acta Crystallographica Section F - May 11, 2017 Category: Biochemistry Authors: Yan, Q. Shaw, N. Qian, L. Jiang, D. Tags: S-adenosyl-l-methionine His – Asp pair crystal structure dihydroxycinnamic acid Mycobacterium tuberculosis Rv1220c research communications Source Type: research
Crystallization and biochemical characterization of an archaeal lectin from Methanococcus voltae A3
A lectin from Methanococcus voltae A3 has been cloned, expressed, purified and characterized. The lectin appears to be specific for complex sugars. The protein crystallized in a tetragonal space group, with around 16 subunits in the asymmetric unit. Sequence comparisons indicate the lectin to have a β -prism I fold, with poor homology to lectins of known three-dimensional structure. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - April 28, 2017 Category: Biochemistry Authors: Sivaji, N. Abhinav, K.V. Vijayan, M. Tags: archaeal lectins β -prism I fold X-ray studies Methanococcus voltae research communications Source Type: research
Crystal structure of CD27 in complex with a neutralizing noncompeting antibody
CD27 is a T-cell and B-cell co-stimulatory glycoprotein of the tumor necrosis factor (TNF) receptor superfamily that is dependent on the availability of the TNF-like ligand CD70. Therapeutic approaches to treating autoimmune diseases and cancers with antagonistic and agonistic anti-CD27 monoclonal antibodies (mAbs), respectively, have recently been developed. Mouse anti-human CD27 mAb 2177 shows potency in neutralizing CD70-induced signaling; however, it does not block the binding of soluble CD70. To provide insight into the mechanism of action of the mAb, the crystal structure of the CD27 extracellular domain in complex w...
Source: Acta Crystallographica Section F - April 26, 2017 Category: Biochemistry Authors: Teplyakov, A. Obmolova, G. Malia, T.J. Gilliland, G.L. Tags: CD27 cysteine-rich domain antibodies crystal structure epitopes tumor necrosis factor research communications Source Type: research
Camelid nanobodies used as crystallization chaperones for different constructs of PorM, a component of the type IX secretion system from Porphyromonas gingivalis
PorM is a membrane protein that is involved in the assembly of the type IX secretion system (T9SS) in Porphyromonas gingivalis, a major bacterial pathogen that is responsible for periodontal disease in humans. In the context of structural studies of PorM to better understand T9SS assembly, four camelid nanobodies were selected, produced and purified, and their specific interaction with the N-terminal or C-terminal part of the periplasmic domain of PorM was investigated. Diffracting crystals were also obtained, and the structures of the four nanobodies were solved by molecular replacement. Furthermore, two nanobodies were u...
Source: Acta Crystallographica Section F - April 26, 2017 Category: Biochemistry Authors: Duhoo, Y. Roche, J. Trinh, T.T.N. Desmyter, A. Gaubert, A. Kellenberger, C. Cambillau, C. Roussel, A. Leone, P. Tags: camelid nanobodies type IX secretion system crystallization chaperones PorM Porphyromonas gingivalis research communications Source Type: research
Transcription factor Rv0081 from Mycobacterium tuberculosis: purification, crystallization and initial crystallographic analysis
Because of its high infectivity and pathogenicity, Mycobacterium tuberculosis is a serious threat to human health. While the transcription-regulatory system of M. tuberculosis remains incompletely understood, Rv0081, an essential regulatory hub, is known to mediate the initial response to hypoxia in the long-term survival of M. tuberculosis. Here, the production, crystallization and initial X-ray crystallographic analysis of Rv0081 are reported. The crystals of Rv0081 belonged to space group P62, with unit-cell parameters a = 67.48, b = 67.48, c = 40.84 Å , γ = 120 ° . Th...
Source: Acta Crystallographica Section F - April 26, 2017 Category: Biochemistry Authors: Dong, S. Ding, Z. Wang, Y. Yang, Y. Mao, Y. Wang, Y. Tags: Rv0081 transcription factor Mycobacterium tuberculosis research communications Source Type: research
Crystal structure of the RNA 2 ′ ,3 ′ -cyclic phosphodiesterase from Deinococcus radiodurans
2 ′ ,3 ′ -Cyclic phosphodiesterase (CPDase) homologues have been found in all domains of life and are involved in diverse RNA and nucleotide metabolisms. The CPDase from Deinococcus radiodurans was crystallized and the crystals diffracted to 1.6 Å resolution, which is the highest resolution currently known for a CPDase structure. Structural comparisons revealed that the enzyme is in an open conformation in the absence of substrate. Nevertheless, the active site is well formed, and the representative motifs interact with sulfate ion, which suggests a conserved catalytic mechanism. (Source: Acta Crystal...
Source: Acta Crystallographica Section F - April 26, 2017 Category: Biochemistry Authors: Han, W. Cheng, J. Zhou, C. Hua, Y. Zhao, Y. Tags: RNA repair CPDase RNA 2 ′ ,3 -cyclic phosphodiesterase Deinococcus radiodurans research communications Source Type: research
Structural insights into the mechanism of the drastic changes in enzymatic activity of the cytochrome P450 vitamin D3 hydroxylase (CYP107BR1) caused by a mutation distant from the active site
Cytochromes P450 (P450s) are haem-containing enzymes that catalyze medically and industrially important oxidative reactions, and many P450s have been subjected to directed evolution and site-directed mutagenesis to improve their activity and substrate specificity. Nonetheless, in most cases the mechanism that leads to drastic changes in specific activity after the introduction of an amino-acid substitution distant from the active-site pocket is unclear. Here, two crystal structures of inactive mutants of the P450 vitamin D3 hydroxylase (Vdh), Vdh-F106V and Vdh-L348M, which were obtained in the course of protein-engineering...
Source: Acta Crystallographica Section F - April 26, 2017 Category: Biochemistry Authors: Yasutake, Y. Kameda, T. Tamura, T. Tags: crystal structure cytochrome P450 CYP vitamin D3 hydroxylase conformational changes research communications Source Type: research
Crystal structure of d(CCGGGGTACCCCGG)2 at 1.4 Å resolution
The X-ray crystal structure of the DNA tetradecamer sequence d(CCGGGGTACCCCGG)2 is reported at 1.4 Å resolution in the tetragonal space group P41212. The sequence was designed to fold as a four-way junction. However, it forms an A-type double helix in the presence of barium chloride. The metal ion could not be identified in the electron-density map. The crystallographic asymmetric unit consists of one A-type double helix with 12 base pairs per turn, in contrast to 11 base pairs per turn for canonical A-DNA. A large number of solvent molecules have been identified in both the grooves of the duplex and around the b...
Source: Acta Crystallographica Section F - April 26, 2017 Category: Biochemistry Authors: Karthik, S. Thirugnanasambandam, A. Mandal, P.K. Gautham, N. Tags: d(CCGGGGTACCCCGG)2 A-DNA duplex X-ray crystallography tetragonal space group research communications Source Type: research
Increasing the soluble expression and crystallization of the Escherichia coli quorum-sensing protein LsrK
LsrK is one of the key components of the luxS-regulated (lsr) operon in Escherichia coli and plays an important role during the quorum-sensing (QS) process mediated by autoinducer-2 (AI-2). The AI-2 molecule is imported into the cell by the LsrACB transporter and is subsequently phosphorylated (to AI-2-P) by LsrK. AI-2-P binds to the repressor protein of the lsr operon (LsrR) and triggers various cellular responses related to QS by dissociating LsrR from the DNA. Although a large amount of purified LsrK is required for structural studies, recombinant GST-LsrK was mostly expressed in an insoluble form. To enhance the solubl...
Source: Acta Crystallographica Section F - April 26, 2017 Category: Biochemistry Authors: Ha, J.-H. Eo, Y. Ahn, H.-C. Ryu, K.-S. Tags: chaperones heat shock LsrK complex LsrK crystal soluble expression of LsrK osmotic shock quorum sensing research communications Source Type: research
Structure of NADP+-bound 7 β -hydroxysteroid dehydrogenase reveals two cofactor-binding modes
In mammals, bile acids/salts and their glycine and taurine conjugates are effectively recycled through enterohepatic circulation. 7 β -Hydroxysteroid dehydrogenases (7 β -HSDHs; EC 188.8.131.52), including that from the intestinal microbe Collinsella aerofaciens, catalyse the NADPH-dependent reversible oxidation of secondary bile-acid products to avoid potential toxicity. Here, the first structure of NADP+ bound to dimeric 7 β -HSDH is presented. In one active site, NADP+ adopts a conventional binding mode similar to that displayed in related enzyme structures. However, in the other active site a unique binding...
Source: Acta Crystallographica Section F - April 26, 2017 Category: Biochemistry Authors: Wang, R. Wu, J. Jin, D.K. Chen, Y. Lv, Z. Chen, Q. Miao, Q. Huo, X. Wang, F. Tags: crystal structure NADP -bound 7 β -HSDH rational protein engineering research communications Source Type: research
Cryo-electron microscopy and X-ray crystallography: complementary approaches to structural biology and drug discovery
The invention of the electron microscope has greatly enhanced the view scientists have of small structural details. Since its implementation, this technology has undergone considerable evolution and the resolution that can be obtained for biological objects has been extended. In addition, the latest generation of cryo-electron microscopes equipped with direct electron detectors and software for the automated collection of images, in combination with the use of advanced image-analysis methods, has dramatically improved the performance of this technique in terms of resolution. While calculating a sub-10 Å resolutio...
Source: Acta Crystallographica Section F - March 30, 2017 Category: Biochemistry Authors: V é nien-Bryan, C. Li, Z. Vuillard, L. Boutin, J.A. Tags: cryo-electron microscopy cryo-EM structural biology high resolution conformational variability drug discovery topical reviews Source Type: research
X-ray diffraction analysis and in vitro characterization of the UAM2 protein from Oryza sativa
The role of seemingly non-enzymatic proteins in complexes interconverting UDP-arabinopyranose and UDP-arabinofuranose (UDP-arabinosemutases; UAMs) in the plant cytosol remains unknown. To shed light on their function, crystallographic and functional studies of the seemingly non-enzymatic UAM2 protein from Oryza sativa (OsUAM2) were undertaken. Here, X-ray diffraction data are reported, as well as analysis of the oligomeric state in the crystal and in solution. OsUAM2 crystallizes readily but forms highly radiation-sensitive crystals with limited diffraction power, requiring careful low-dose vector data acquisition. Using s...
Source: Acta Crystallographica Section F - March 29, 2017 Category: Biochemistry Authors: Welner, D.H. Tsai, A.Y.-L. DeGiovanni, A.M. Scheller, H.V. Adams, P.D. Tags: reversibly glycosylated polypeptide limited proteolysis UDP-arabinopyranose mutase vector data collection research communications Source Type: research
Preliminary neutron diffraction analysis of challenging human manganese superoxide dismutase crystals
Superoxide dismutases (SODs) are enzymes that protect against oxidative stress by dismutation of superoxide into oxygen and hydrogen peroxide through cyclic reduction and oxidation of the active-site metal. The complete enzymatic mechanisms of SODs are unknown since data on the positions of hydrogen are limited. Here, methods are presented for large crystal growth and neutron data collection of human manganese SOD (MnSOD) using perdeuteration and the MaNDi beamline at Oak Ridge National Laboratory. The crystal from which the human MnSOD data set was obtained is the crystal with the largest unit-cell edge (240 Å )...
Source: Acta Crystallographica Section F - March 29, 2017 Category: Biochemistry Authors: Azadmanesh, J. Trickel, S.R. Weiss, K.L. Coates, L. Borgstahl, G.E.O. Tags: manganese superoxide dismutase neutron diffraction perdeuteration human large unit cell research communications Source Type: research
Crystal structure of enolase from Drosophila melanogaster
Enolase is an important enzyme in glycolysis and various biological processes. Its dysfunction is closely associated with diseases. Here, the enolase from Drosophila melanogaster (DmENO) was purified and crystallized. A crystal of DmENO diffracted to 2.0 Å resolution and belonged to space group R32. The structure was solved by molecular replacement. Like most enolases, DmENO forms a homodimer with conserved residues in the dimer interface. DmENO possesses an open conformation in this structure and contains conserved elements for catalytic activity. This work provides a structural basis for further functional and ...
Source: Acta Crystallographica Section F - March 22, 2017 Category: Biochemistry Authors: Sun, C. Xu, B. Liu, X. Zhang, Z. Su, Z. Tags: enolase crystal structure active site dimerization glycolysis Drosophila melanogaster research communications Source Type: research
Crystal structure of a small heat-shock protein from Xylella fastidiosa reveals a distinct high-order structure
Citrus variegated chlorosis is a disease that attacks economically important citrus plantations and is caused by the plant-pathogenic bacterium Xylella fastidiosa. In this work, the structure of a small heat-shock protein from X. fastidiosa (XfsHSP17.9) is reported. The high-order structures of small heat-shock proteins from other organisms are arranged in the forms of double-disc, hollow-sphere or spherical assemblies. Unexpectedly, the structure reported here reveals a high-order architecture forming a nearly square cavity. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - March 22, 2017 Category: Biochemistry Authors: Fonseca, E.M.B. Scorsato, V. dos Santos, M.L. J ú nior, A.T. Tada, S.F.S. dos Santos, C.A. de Toledo, M.A.S. de Souza, A.P. Polikarpov, I. Aparicio, R. Tags: small heat-shock protein Xylella fastidiosa α -crystallin domain citrus variegated chlorosis XfsHSP17.9 chaperones research communications Source Type: research
X-ray crystal structure of human calcium-bound S100A1
S100A1 is a member of the S100 family of Ca2+-binding proteins and regulates several cellular processes, including those involved in Ca2+ signaling and cardiac and skeletal muscle function. In Alzheimer's disease, brain S100A1 is overexpressed and gives rise to disease pathologies, making it a potential therapeutic target. The 2.25 Å resolution crystal structure of Ca2+-S100A1 is solved here and is compared with the structures of other S100 proteins, most notably S100B, which is a highly homologous S100-family member that is implicated in the progression of malignant melanoma. The observed structural differences ...
Source: Acta Crystallographica Section F - March 22, 2017 Category: Biochemistry Authors: Melville, Z. Aligholizadeh, E. McKnight, L.E. Weber, D.J. Pozharski, E. Weber, D.J. Tags: S100 S100A1 crystal structure calcium-binding proteins S100B Alzheimer's disease cardiomyopathy research communications Source Type: research
Crystal structure of the human heterogeneous ribonucleoprotein A18 RNA-recognition motif
The heterogeneous ribonucleoprotein A18 (hnRNP A18) is upregulated in hypoxic regions of various solid tumors and promotes tumor growth via the coordination of mRNA transcripts associated with pro-survival genes. Thus, hnRNP A18 represents an important therapeutic target in tumor cells. Presented here is the first X-ray crystal structure to be reported for the RNA-recognition motif of hnRNP A18. By comparing this structure with those of homologous RNA-binding proteins (i.e. hnRNP A1), three residues on one face of an antiparallel β -sheet (Arg48, Phe50 and Phe52) and one residue in an unstructured loop (Arg41) were id...
Source: Acta Crystallographica Section F - March 22, 2017 Category: Biochemistry Authors: Coburn, K. Melville, Z. Aligholizadeh, E. Roth, B.M. Varney, K.M. Carrier, F. Pozharski, E. Weber, D.J. Tags: crystal structure RNA-binding protein heterogeneous ribonucleoprotein A18 hnRNP A18 RNA-recognition motif tumor growth research communications Source Type: research
Crystallization and X-ray analysis of the extracellular adhesion domain of Helicobacter pylori adhesin A: the significance of the cation composition in the crystallization precipitant
In this study, two constructs were made for the production of truncated HpaA proteins comprising residues 31 – 260 and 53 – 260, respectively. The products of both constructs were crystallized, but only the protein from the shorter construct (residues 53 – 260) formed crystals that were capable of diffraction. In the subsequent optimization trials, crystals in different forms were unexpectedly obtained by using lithium sulfate and ammonium sulfate as the precipitant. An X-ray data set was collected to 1.95 Å resolution on beamline BL18U1 at SSRF using a crystal grown with 1.92 M lithium sulf...
Source: Acta Crystallographica Section F - March 22, 2017 Category: Biochemistry Authors: Guo, L. Zhang, J. Cui, L. Liu, D. Ma, B. Wang, S. Li, H. Wu, Y. Liu, W. Tags: Helicobacter pylori adhesin A HpaA adhesion domain crystallization cations research communications Source Type: research
Structure of the complex of phosphorylated liver kinase B1 and 14-3-3 ζ
The serine/threonine protein kinase liver kinase B1 (LKB1) is a tumour suppressor and plays important roles in development and metabolism. It phosphorylates AMPK and AMPK-related kinases to regulate multiple physiological processes. Mutations in LKB1 often occur in multiple cancers. LKB1 can be suppressed by 14-3-3 proteins in a phosphorylation-dependent manner. Previously, the structure of a 14-3-3 ζ – LKB1 fusion protein has been reported, revealing a phosphorylation-independent binding mode of LKB1 to 14-3-3 proteins. Here, the crystal structure of phosphorylated LKB1 peptide in complex with 14-3-3 ζ was...
Source: Acta Crystallographica Section F - March 22, 2017 Category: Biochemistry Authors: Lu, Y. Ding, S. Zhou, R. Wu, J. Tags: liver kinase B1 14-3-3 proteins phosphorylation complexes crystal structure Peutz – Jeghers syndrome tumour suppression research communications Source Type: research
The hidden treasure in your data: phasing with unexpected weak anomalous scatterers from routine data sets
Single-wavelength anomalous dispersion (SAD) utilizing anomalous signal from native S atoms, or other atoms with Z ≤ 20, generally requires highly redundant data collected using relatively long-wavelength X-rays. Here, the results from two proteins are presented where the anomalous signal from serendipitously acquired surface-bound Ca atoms with an anomalous data multiplicity of around 10 was utilized to drive de novo structure determination. In both cases, the Ca atoms were acquired from the crystallization solution, and the data-collection strategy was not optimized to exploit the anomalous signal from these scatterer...
Source: Acta Crystallographica Section F - March 22, 2017 Category: Biochemistry Authors: Hegde, R.P. Fedorov, A.A. Sauder, J.M. Burley, S.K. Almo, S.C. Ramagopal, U.A. Tags: SAD phasing weak anomalous signal research communications Source Type: research
Crystal structure of the type IV secretion system component CagX from Helicobacter pylori
Helicobacter pylori, a Gram-negative bacterial pathogen prevalent in the human population, is the causative agent of severe gastric diseases. An H. pylori type IV secretion (T4S) system encoded by the cytotoxin-associated gene pathogenicity island (cagPAI) is responsible for communication with host cells. As a component of the cagPAI T4S system core complex, CagX plays an important role in virulence-protein translocation into the host cells. In this work, the crystal structure of the C-terminal domain of CagX (CagXct), which is a homologue of the VirB9 protein from the VirB/D4 T4S system, is presented. CagXct is only the s...
Source: Acta Crystallographica Section F - February 28, 2017 Category: Biochemistry Authors: Zhang, J. Fan, F. Zhao, Y. Sun, L. Liu, Y. Keegan, R.M. Isupov, M.N. Wu, Y. Tags: Helicobacter pylori cytotoxin-associated gene pathogenicity island cagPAI type IV secretion system CagX crystal structure X-ray diffraction research communications Source Type: research
New molecular packing in a crystal of pseudoazurin from Alcaligenes faecalis: a double-helical arrangement of blue copper
Pseudoazurin from the denitrifying bacterium Alcaligenes faecalis (AfPAz) is a blue copper protein and functions as an electron donor to copper-containing nitrite reductase (CuNIR). Conventionally, AfPAz has been crystallized using highly concentrated ammonium sulfate as a precipitant. Here, a needle-like crystal of AfPAz grown in a solution containing a macromolecular precipitant, polyethylene glycol 8000 (PEG 8000), is reported. The crystal belonged to space group P61, with unit-cell parameters a = b = 68.7, c = 94.2 Å . The structure has been determined and refined at 2.6 Å resolution. The asymmetric...
Source: Acta Crystallographica Section F - February 28, 2017 Category: Biochemistry Authors: Fukuda, Y. Mizohata, E. Inoue, T. Tags: pseudoazurin blue copper protein macromolecular crowding effect molecular packing Alcaligenes faecalis research communications Source Type: research
The crystal structure of mouse LC3B in complex with the FYCO1 LIR reveals the importance of the flanking region of the LIR motif
FYVE and coiled-coil domain-containing protein 1 (FYCO1), a multidomain autophagy adaptor protein, mediates microtubule plus-end-directed autophagosome transport by interacting with kinesin motor proteins and with the autophagosomal membrane components microtubule-associated protein 1 light chain 3 (LC3), Rab7 and phosphatidylinositol 3-phosphate (PI3P). To establish the structural basis for the recognition of FYCO1 by LC3, the crystal structure of mouse LC3B in complex with the FYCO1 LC3-interacting region (LIR) motif peptide was determined. Structural analysis showed that the flanking sequences N-terminal and C-terminal ...
Source: Acta Crystallographica Section F - February 22, 2017 Category: Biochemistry Authors: Sakurai, S. Tomita, T. Shimizu, T. Ohto, U. Tags: autophagy FYCO1 LC3 LC3-interacting region (LIR) motif research communications Source Type: research
The hyperthermophilic cystathionine γ -synthase from the aerobic crenarchaeon Sulfolobus tokodaii: expression, purification, crystallization and structural insights
Cystathionine γ -synthase (CGS; EC 184.108.40.206), a pyridoxal 5 ′ -phosphate (PLP)-dependent enzyme, catalyzes the formation of cystathionine from an l-homoserine derivative and l-cysteine in the first step of the transsulfuration pathway. Recombinant CGS from the thermoacidophilic archaeon Sulfolobus tokodaii (StCGS) was overexpressed in Escherichia coli and purified to homogeneity by heat treatment followed by hydroxyapatite and gel-filtration column chromatography. The purified enzyme shows higher enzymatic activity at 353 K under basic pH conditions compared with that at 293 K. Crystallization trials yi...
Source: Acta Crystallographica Section F - February 21, 2017 Category: Biochemistry Authors: Sato, D. Shiba, T. Mizuno, S. Kawamura, A. Hanada, S. Yamada, T. Shinozaki, M. Yanagitani, M. Tamura, T. Inagaki, K. Harada, S. Tags: transsulfuration hyperthermophilic enzyme pyridoxal 5 ′ -phosphate methionine biosynthesis Sulfolobus tokodaii cystathionine γ -synthase research communications Source Type: research
Similarities in the structure of the transcriptional repressor AmtR in two different space groups suggest a model for the interaction with GlnK
AmtR belongs to the TetR family of transcription regulators and is a global nitrogen regulator that is induced under nitrogen-starvation conditions in Corynebacterium glutamicum. AmtR regulates the expression of transporters and enzymes for the assimilation of ammonium and alternative nitrogen sources, for example urea, amino acids etc. The recognition of operator DNA by homodimeric AmtR is not regulated by small-molecule effectors as in other TetR-family members but by a trimeric adenylylated PII-type signal transduction protein named GlnK. The crystal structure of ligand-free AmtR (AmtRorth) has been solved at a resoluti...
Source: Acta Crystallographica Section F - February 21, 2017 Category: Biochemistry Authors: Sevvana, M. Hasselt, K. Grau, F.C. Burkovski, A. Muller, Y.A. Tags: nitrogen regulation Corynebacterium glutamicum transcription regulator effector complex AmtR adenylylated GlnK complex stoichiometry crystal-packing comparison research communications Source Type: research
Proteolysis of truncated hemolysin A yields a stable dimerization interface
Wild-type and variant forms of HpmA265 (truncated hemolysin A) from Proteus mirabilis reveal a right-handed, parallel β -helix capped and flanked by segments of antiparallel β -strands. The low-salt crystal structures form a dimeric structure via the implementation of on-edge main-chain hydrogen bonds donated by residues 243 – 263 of adjacent monomers. Surprisingly, in the high-salt structures of two variants, Y134A and Q125A-Y134A, a new dimeric interface is formed via main-chain hydrogen bonds donated by residues 203 – 215 of adjacent monomers, and a previously unobserved tetramer is formed. In addi...
Source: Acta Crystallographica Section F - February 21, 2017 Category: Biochemistry Authors: Novak, W.R.P. Bhattacharyya, B. Grilley, D.P. Weaver, T.M. Tags: hemolysin A two-partner secretion alternate crystal forms proteolysis β -helix Proteus mirabilis research communications Source Type: research
Crystal structure of full-length Zika virus NS5 protein reveals a conformation similar to Japanese encephalitis virus NS5
The rapid spread of the recent Zika virus (ZIKV) epidemic across various countries in the American continent poses a major health hazard for the unborn fetuses of pregnant women. To date, there is no effective medical intervention. The nonstructural protein 5 of Zika virus (ZIKV-NS5) is critical for ZIKV replication through the 5 ′ -RNA capping and RNA polymerase activities present in its N-terminal methyltransferase (MTase) and C-terminal RNA-dependent RNA polymerase (RdRp) domains, respectively. The crystal structure of the full-length ZIKV-NS5 protein has been determined at 3.05 Å resolution from a cryst...
Source: Acta Crystallographica Section F - February 21, 2017 Category: Biochemistry Authors: Upadhyay, A.K. Cyr, M. Longenecker, K. Tripathi, R. Sun, C. Kempf, D.J. Tags: Zika virus NS5 nonstructural protein 5 research communications Source Type: research
Crystallization of FcpA from Leptospira, a novel flagellar protein that is essential for pathogenesis
The protein FcpA is a unique component of the flagellar filament of spirochete bacteria belonging to the genus Leptospira. Although it plays an essential role in translational motility and pathogenicity, no structures of FcpA homologues are currently available in the PDB. Its three-dimensional structure will unveil the novel motility mechanisms that render pathogenic Leptospira particularly efficient at invading and disseminating within their hosts, causing leptospirosis in humans and animals. FcpA from L. interrogans was purified and crystallized, but despite laborious attempts no useful X ray diffraction data could be ob...
Source: Acta Crystallographica Section F - February 21, 2017 Category: Biochemistry Authors: San Martin, F. Mechaly, A.E. Larrieux, N. Wunder, E.A. Ko, A.I. Picardeau, M. Trajtenberg, F. Buschiazzo, A. Tags: spirochetes motility flagella SAD phasing Leptospira interrogans Leptospira biflexa FcpA leptospirosis research communications Source Type: research
Crystallization and X-ray crystallographic analysis of recombinant TylP, a putative γ -butyrolactone receptor protein from Streptomyces fradiae
In this report, N-terminally His-tagged recombinant TylP protein (rTylP) was overproduced in Escherichia coli and purified to homogeneity. The rTylP protein was crystallized from a reservoir solution comprising 34%(v/v) ethylene glycol and 5%(v/v) glycerol. The protein crystals diffracted X-rays to 3.05 Å resolution and belonged to the trigonal space group P3121, with unit-cell parameters a = b = 126.62, c = 95.63 Å . (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - January 31, 2017 Category: Biochemistry Authors: Mohd-Sharif, N. Shaibullah, S. Givajothi, V. Tan, C.-S. Ho, K.L. Teh, A.-H. Baharum, S.N. Waterman, J. Ng, C.L. Tags: Streptomyces fradiae recombinant TylP protein γ -butyrolactone GBL transcription factors tylosin research communications Source Type: research
The crystal structure of PD1, a Haemophilus surface fibril domain
The Haemophilus surface fibril (Hsf) is an unusually large trimeric autotransporter adhesin (TAA) expressed by the most virulent strains of H. influenzae. Hsf is known to mediate adhesion between pathogen and host, allowing the establishment of potentially deadly diseases such as epiglottitis, meningitis and pneumonia. While recent research has suggested that this TAA might adopt a novel `hairpin-like' architecture, the characterization of Hsf has been limited to in silico modelling and electron micrographs, with no high-resolution structural data available. Here, the crystal structure of Hsf putative domain 1 (PD1) is rep...
Source: Acta Crystallographica Section F - January 31, 2017 Category: Biochemistry Authors: Wright, J. Thomsen, M. Kolodziejczyk, R. Ridley, J. Sinclair, J. Carrington, G. Singh, B. Riesbeck, K. Goldman, A. Tags: Hsf putative domain 1 trimeric autotransporter Haemophilus influenzae adhesin cell adhesion Haemophilus surface fibril research communications Source Type: research
A natural, single-residue substitution yields a less active peptaibiotic: the structure of bergofungin A at atomic resolution
Bergofungin is a peptide antibiotic that is produced by the ascomycetous fungus Emericellopsis donezkii HKI 0059 and belongs to peptaibol subfamily 2. The crystal structure of bergofungin A has been determined and refined to 0.84 Å resolution. This is the second crystal structure of a natural 15-residue peptaibol, after that of samarosporin I. The amino-terminal phenylalanine residue in samarosporin I is exchanged to a valine residue in bergofungin A. According to agar diffusion tests, this results in a nearly inactive antibiotic peptide compared with the moderately active samarosporin I. Crystals were obtained f...
Source: Acta Crystallographica Section F - January 27, 2017 Category: Biochemistry Authors: Gessmann, R. Axford, D. Br ü ckner, H. Berg, A. Petratos, K. Tags: crystal structure Emericellopsis donezkii hydrogen bond peptaibols peptide antibiotics 310-helix α research communications Source Type: research
Structure of Methylobacterium extorquens malyl-CoA lyase: CoA-substrate binding correlates with domain shift
Malyl-CoA lyase (MCL) is an Mg2+-dependent enzyme that catalyzes the reversible cleavage of (2S)-4-malyl-CoA to yield acetyl-CoA and glyoxylate. MCL enzymes, which are found in a variety of bacteria, are members of the citrate lyase-like family and are involved in the assimilation of one- and two-carbon compounds. Here, the 1.56 Å resolution X-ray crystal structure of MCL from Methylobacterium extorquens AM1 with bound Mg2+ is presented. Structural alignment with the closely related Rhodobacter sphaeroides malyl-CoA lyase complexed with Mg2+, oxalate and CoA allows a detailed analysis of the domain motion of the ...
Source: Acta Crystallographica Section F - January 27, 2017 Category: Biochemistry Authors: Gonz á lez, J.M. Marti-Arbona, R. Chen, J.C.-H. Unkefer, C.J. Tags: biofuels metabolic engineering methanol malyl-CoA lyase Methylobacterium extorquens research communications Source Type: research
Expression and crystallographic studies of d-glycero- β -d-manno-heptose-1-phosphate adenylyltransferase from Burkholderia pseudomallei
In this study, HldC from B. pseudomallei has been cloned, expressed, purified and crystallized. Synchrotron X-ray data from a selenomethionine-substituted HldC crystal were also collected to 2.8 Å resolution. The crystal belonged to the primitive triclinic space group P1, with unit-cell parameters a = 74.0, b = 74.0, c = 74.9 Å , α = 108.4, β = 108.4, γ = 108.0 ° . Eight protomers are present in the unit cell and three out of five selenomethionines were found in each protomer using the PHENIX software suite. A full structural determination is in progress to elucidate the structure &...
Source: Acta Crystallographica Section F - January 19, 2017 Category: Biochemistry Authors: Park, J. Kim, H. Kim, S. Lee, D. Shin, D.H. Tags: Burkholderia pseudomallei heptose biosynthesis pathway melioidosis d-glycero- β -d-manno-heptose-1-phosphate adenylyltransferase HldC research communications Source Type: research
Crystallization and X-ray analysis of d-threonine aldolase from Chlamydomonas reinhardtii
d-Threonine aldolase from the green alga Chlamydomonas reinhardtii (CrDTA) catalyzes the interconversion of several β -hydroxy-d-amino acids (e.g. d-threonine) and glycine plus the corresponding aldehydes. Recombinant CrDTA was overexpressed in Escherichia coli and purified to homogeneity; it was subsequently crystallized using the hanging-drop vapour-diffusion method at 295 K. Data were collected and processed at 1.85 Å resolution. Analysis of the diffraction pattern showed that the crystal belonged to space group P1, with unit-cell parameters a = 64.79, b = 74.10, c = 89.94 Å , α = 77.0...
Source: Acta Crystallographica Section F - January 19, 2017 Category: Biochemistry Authors: Hirato, Y. Goto, M. Tokuhisa, M. Tanigawa, M. Nishimura, K. Tags: d-threonine aldolase Chlamydomonas reinhardtii d-amino acids crystallization research communications Source Type: research
Crystal structure of the N-terminal anticodon-binding domain of the nondiscriminating aspartyl-tRNA synthetase from Helicobacter pylori
The N-terminal anticodon-binding domain of the nondiscriminating aspartyl-tRNA synthetase (ND-AspRS) plays a crucial role in the recognition of both tRNAAsp and tRNAAsn. Here, the first X-ray crystal structure of the N-terminal domain of this enzyme (ND-AspRS1 – 104) from the human-pathogenic bacterium Helicobacter pylori is reported at 2.0 Å resolution. The apo form of H. pylori ND-AspRS1 – 104 shares high structural similarity with the N-terminal anticodon-binding domains of the discriminating aspartyl-tRNA synthetase (D-AspRS) from Escherichia coli and ND-AspRS from Pseudomonas aeruginosa, allowing...
Source: Acta Crystallographica Section F - January 19, 2017 Category: Biochemistry Authors: Songsiriritthigul, C. Suebka, S. Chen, C.-J. Fuengfuloy, P. Chuawong, P. Tags: nondiscriminating aspartyl-tRNA synthetase anticodon-binding domain Helicobacter pylori crystal structure research communications Source Type: research
Crystallization of a fungal lytic polysaccharide monooxygenase expressed from glycoengineered Pichia pastoris for X-ray and neutron diffraction
Lytic polysaccharide monooxygenases (LPMOs) are carbohydrate-disrupting enzymes secreted by bacteria and fungi that break glycosidic bonds via an oxidative mechanism. Fungal LPMOs typically act on cellulose and can enhance the efficiency of cellulose-hydrolyzing enzymes that release soluble sugars for bioethanol production or other industrial uses. The enzyme PMO-2 from Neurospora crassa (NcPMO-2) was heterologously expressed in Pichia pastoris to facilitate crystallographic studies of the fungal LPMO mechanism. Diffraction resolution and crystal morphology were improved by expressing NcPMO-2 from a glycoengineered strain ...
Source: Acta Crystallographica Section F - January 19, 2017 Category: Biochemistry Authors: O'Dell, W.B. Swartz, P.D. Weiss, K.L. Meilleur, F. Tags: lytic polysaccharide monooxygenases Pichia pastoris glycoengineering neutron protein crystallography research communications Source Type: research
Structural characterization of the Streptococcus pneumoniae carbohydrate substrate-binding protein SP0092
Streptococcus pneumoniae is an opportunistic respiratory pathogen that remains a major cause of morbidity and mortality globally, with infants and the elderly at the highest risk. S. pneumoniae relies entirely on carbohydrates as a source of carbon and dedicates a third of all uptake systems to carbohydrate import. The structure of the carbohydrate-free substrate-binding protein SP0092 at 1.61 Å resolution reveals it to belong to the newly proposed subclass G of substrate-binding proteins, with a ligand-binding pocket that is large enough to accommodate complex oligosaccharides. SP0092 is a dimer in solution and ...
Source: Acta Crystallographica Section F - December 24, 2016 Category: Biochemistry Authors: Culurgioni, S. Tang, M. Walsh, M.A. Tags: Streptococcus pneumoniae substrate-binding protein SP0092 ABC transporters carbohydrate uptake research communications Source Type: research
Expression, purification and crystallization of a protein resulting from the inversion of the amino-acid sequence of a helical bundle
Earlier studies have found that the occurrence of inverse sequence identity in proteins is not indicative of three-dimensional similarity, but rather leads to different folds or unfolded proteins. Short helices, however, frequently keep their conformations when their sequences are inverted. To explore the impact of sequence inversion on long helices, revRM6, with the inverse amino-acid sequence relative to RM6, a highly stable variant of the ColE1 Rop protein, was engineered. RM6 is a highly regular four- α -helical bundle that serves as a model system for protein-folding studies. Here, the crystallization and prelim...
Source: Acta Crystallographica Section F - December 24, 2016 Category: Biochemistry Authors: Kefala, A. Kotsifaki, D. Providaki, M. Amprazi, M. Kokkinidis, M. Tags: Rop protein heptad repeat protein folding sequence – structure relationship hyperthermophilic protein research communications Source Type: research
Recombinant hepatocyte growth factor activator inhibitor 1: expression in Drosophila S2 cells, purification and crystallization
Hepatocyte growth factor activator inhibitor 1 (HAI-1) is a multi-domain membrane-associated protease inhibitor that potently inhibits a variety of serine proteases such as hepatocyte growth factor activator and matriptase. Different truncates of HAI-1 show varying potencies for inhibition of target proteases, suggesting that the domain organization of HAI-1 plays a critical role in its function. Here, the soluble full-length extracellular part of HAI-1 (sHAI-1) was expressed using the Drosophila S2 insect-cell expression system. Diffraction-quality crystals of sHAI-1 were produced using ammonium sulfate as precipitant. Th...
Source: Acta Crystallographica Section F - December 24, 2016 Category: Biochemistry Authors: Liu, M. Yuan, C. Jiang, Y. Jiang, L. Huang, M. Tags: HAI-1 hepatocyte growth factor activator inhibitor Drosophila expression purification crystallization research communications Source Type: research
Structure of a fungal form of aspartate-semialdehyde dehydrogenase from Aspergillus fumigatus
Aspartate-semialdehyde dehydrogenase (ASADH) functions at a critical junction in the aspartate biosynthetic pathway and represents a validated target for antimicrobial drug design. This enzyme catalyzes the NADPH-dependent reductive dephosphorylation of β -aspartyl phosphate to produce the key intermediate aspartate semialdehyde. The absence of this entire pathway in humans and other mammals will allow the selective targeting of pathogenic microorganisms for antimicrobial development. Here, the X-ray structure of a new form of ASADH from the pathogenic fungal species Aspergillus fumigatus has been determined. The over...
Source: Acta Crystallographica Section F - December 24, 2016 Category: Biochemistry Authors: Dahal, G.P. Viola, R.E. Tags: aspartate-semialdehyde dehydrogenase Aspergillus fumigatus pathogenic fungi oligomeric arrangement structural comparison research communications Source Type: research
Crystal structure of a putrescine aminotransferase from Pseudomonas sp. strain AAC
The putrescine aminotransferase KES24511 from Pseudomonas sp. strain AAC was previously identified as an industrially relevant enzyme based on the discovery that it is able to promiscuously catalyse the transamination of 12-aminododecanoic acid. Here, the cloning, heterologous expression, purification and successful crystallization of the KES24511 protein are reported, which ultimately generated crystals adopting space group I2. The crystals diffracted X-rays to 2.07 Å resolution and data were collected using the microfocus beamline of the Australian Synchrotron. The structure was solved using molecular replaceme...
Source: Acta Crystallographica Section F - December 24, 2016 Category: Biochemistry Authors: Wilding, M. Scott, C. Newman, J. Peat, T.S. Tags: aminotransferases 12-aminododecanoic acid transaminase PLP-dependent research communications Source Type: research
X-ray crystal structure of a malonate-semialdehyde dehydrogenase from Pseudomonas sp. strain AAC
The NAD-dependent malonate-semialdehyde dehydrogenase KES23460 from Pseudomonas sp. strain AAC makes up half of a bicistronic operon responsible for β -alanine catabolism to produce acetyl-CoA. The KES23460 protein has been heterologously expressed, purified and used to generate crystals suitable for X-ray diffraction studies. The crystals belonged to space group P212121 and diffracted X-rays to beyond 3 Å resolution using the microfocus beamline of the Australian Synchrotron. The structure was solved using molecular replacement, with a monomer from PDB entry 4zz7 as the search model. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - December 24, 2016 Category: Biochemistry Authors: Wilding, M. Scott, C. Peat, T.S. Newman, J. Tags: malonate-semialdehyde dehydrogenase β -alanine catabolism Pseudomonas sp. strain AAC research communications Source Type: research
Crystal structure of an IclR homologue from Microbacterium sp. strain HM58-2
The bacterial transcription factor IclR (isocitrate lyase regulator) is a member of a one-component signal transduction system, which shares the common motif of a helix – turn – helix (HTH)-type DNA-binding domain (DBD) connected to a substrate-binding domain (SBD). Here, the crystal structure of an IclR homologue (Mi-IclR) from Microbacterium sp. strain HM58-2, which catabolizes acylhydrazide as the sole carbon source, is reported. Mi-IclR is expected to regulate an operon responsible for acylhydrazide degradation as an initial step. Native single-wavelength anomalous diffraction (SAD) experiments were perform...
Source: Acta Crystallographica Section F - December 16, 2016 Category: Biochemistry Authors: Akiyama, T. Yamada, Y. Takaya, N. Ito, S. Sasaki, Y. Yajima, S. Tags: isocitrate lyase regulator transcription factor Microbacterium hydrazide one-component system research communications Source Type: research
Crystal structure of the ATPase-C domain of the chromatin remodeller Fun30 from Saccharomyces cerevisiae
Fun30 (Function unknown now 30) is a chromatin remodeller belonging to the Snf2 family. It has previously been reported to be a regulator of several cellular activities, including DNA repair, gene silencing and maintenance of chromatin structure. Here, the crystal structure of the Fun30 ATPase-C domain (the C-lobe of the ATPase domain) is reported at 1.95 Å resolution. Although the structure displays overall similarities to those of other Snf2 family members, a new structural module was found to be specific to the Fun30 subfamily. Fun30 ATPase-C was shown be monomeric in solution and showed no detectable affinity...
Source: Acta Crystallographica Section F - December 16, 2016 Category: Biochemistry Authors: Liu, L. Jiang, T. Tags: Fun30 Snf2 structure remodeller ATPase research communications Source Type: research
Crystal structure of truncated human coatomer protein complex subunit ζ 1 (Cop ζ 1)
The majority of modern anticancer approaches target DNA/protein targets involved in tumour-cell proliferation. Such approaches have a major drawback, as nonproliferating cancer cells remain unaffected and may cause relapse or remission. Human coatomer protein complex I (COPI) subunit ζ (Cop ζ ), a component of the coat protein involved in cell apoptosis and intracellular trafficking, has recently been proposed as a potential anticancer drug target. Previous studies have shown that two different isoforms of the Cop ζ subunit exist in mammalian cells. While normal cells express both Cop ζ 1 and Cop ζ...
Source: Acta Crystallographica Section F - December 15, 2016 Category: Biochemistry Authors: Lunev, S. Semmelink, M.F.W. Xian, J.L. Ma, K.Y. Leenders, A.J.A. D ö mling, A.S.S. Shtutman, M. Groves, M.R. Tags: cancer dormant cells human COPI crystal structure ζ 1 2 research communications Source Type: research
Protein production, crystallization and preliminary crystallographic analysis of the four N-terminal immunoglobulin domains of Down syndrome cell adhesion molecule 1. Corrigendum
An extra author is added to the article by Chen et al. [(2015), Acta Cryst. F71, 775 – 778]. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - November 30, 2016 Category: Biochemistry Authors: Cheng, L. Li, S.-A. Wang, J. Yu, Y. Chen, Q. Tags: Dscam1 RNA splicing homophilic dimer horseshoe configuration crystallization corrigendum addenda and errata Source Type: research
Characterization and 1.57 Å resolution structure of the key fire blight phosphatase AmsI from Erwinia amylovora
AmsI is a low-molecular-weight protein tyrosine phosphatase that regulates the production of amylovoran in the Gram-negative bacterium Erwinia amylovora, a specific pathogen of rosaceous plants such as apple, pear and quince. Amylovoran is an exopolysaccharide that is necessary for successful infection. In order to shed light on AmsI, its structure was solved at 1.57 Å resolution at the same pH as its highest measured activity (pH 5.5). In the active site, a water molecule, bridging between the catalytic Arg15 and the reaction-product analogue sulfate, might be representative of the water molecule attacking the p...
Source: Acta Crystallographica Section F - November 30, 2016 Category: Biochemistry Authors: Salomone-Stagni, M. Musiani, F. Benini, S. Tags: hydrolases amylovoran low-molecular-weight protein tyrosine phosphatase kinetics fire blight Enterobacteriaceae Erwinia amylovora research communications Source Type: research
Overcoming a hemihedral twinning problem in tetrahydrofolate-dependent O-demethylase crystals by the microseeding method
A tetrahydrofolate-dependent O-demethylase, LigM, from Sphingobium sp. SYK-6 was crystallized by the hanging-drop vapour-diffusion method. However, the obtained P3121 or P3221 crystals, which diffracted to 2.5 – 3.3 Å resolution, were hemihedrally twinned. To overcome the twinning problem, microseeding using P3121/P3221 crystals as microseeds was performed with optimization of the reservoir conditions. As a result, another crystal form was obtained. The newly obtained crystal diffracted to 2.5 – 3.0 Å resolution and belonged to space group P21212, with unit-cell parameters a = 102.0, b = 117...
Source: Acta Crystallographica Section F - November 30, 2016 Category: Biochemistry Authors: Harada, A. Sato, Y. Kamimura, N. Venugopalan, N. Masai, E. Senda, T. Tags: hemihedral twinning microseeding cryoprotectant tetrahydrofolate Sphingobium sp. SYK-6 O-demethylase research communications Source Type: research
Purification, crystallization and characterization of the Pseudomonas outer membrane protein FapF, a functional amyloid transporter
Bacteria often produce extracellular amyloid fibres via a multi-component secretion system. Aggregation-prone, unstructured subunits cross the periplasm and are secreted through the outer membrane, after which they self-assemble. Here, significant progress is presented towards solving the high-resolution crystal structure of the novel amyloid transporter FapF from Pseudomonas, which facilitates the secretion of the amyloid-forming polypeptide FapC across the bacterial outer membrane. This represents the first step towards obtaining structural insight into the products of the Pseudomonas fap operon. Initial attempts at crys...
Source: Acta Crystallographica Section F - November 30, 2016 Category: Biochemistry Authors: Rouse, S.L. Hawthorne, W.J. Lambert, S. Morgan, M.L. Hare, S.A. Matthews, S. Tags: amyloid transporter bacterial outer membrane FapF Pseudomonas C8E4 research communications Source Type: research