Crystal structure of the YajQ-family protein XC_3703 from Xanthomonas campestris pv. campestris
In this study, the structure of XC_3703 was determined to 2.1   Å resolution using the molecular-replacement method. The structure of XC_3703 consists of two domains adopting the same topology, which is similar to that of the RNA-recognition motif (RRM). Arg65, which is conserved among the c-di-GMP-binding subfamily of the YajQ family of proteins, together with Phe80 in domain II, forms a putative c-di-GMP binding site. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - August 25, 2016 Category: Biochemistry Authors: Zhao, Z. Wu, Z. Zhang, J. Tags: XC_3703 YajQ c-di-GMP receptor research communications Source Type: research

Crystallization of and selenomethionine phasing strategy for a SETMAR – DNA complex
Transposable elements have played a critical role in the creation of new genes in all higher eukaryotes, including humans. Although the chimeric fusion protein SETMAR is no longer active as a transposase, it contains both the DNA-binding domain (DBD) and catalytic domain of the Hsmar1 transposase. The amino-acid sequence of the DBD has been virtually unchanged in 50 million years and, as a consequence, SETMAR retains its sequence-specific binding to the ancestral Hsmar1 terminal inverted repeat (TIR) sequence. Thus, the DNA-binding activity of SETMAR is likely to have an important biological function. To determine the stru...
Source: Acta Crystallographica Section F - August 25, 2016 Category: Biochemistry Authors: Chen, Q. Georgiadis, M. Tags: crystallization DNA-binding domain transposable element terminal inverted repeat Hsmar1 SETMAR research communications Source Type: research

The role of water molecules in the binding of class I and II peptides to the SH3 domain of the Fyn tyrosine kinase
Interactions of proline-rich motifs with SH3 domains are present in signal transduction and other important cell processes. Analysis of structural and thermodynamic data suggest a relevant role of water molecules in these protein – protein interactions. To determine whether or not the SH3 domain of the Fyn tyrosine kinase shows the same behaviour, the crystal structures of its complexes with two high-affinity synthetic peptides, VSL12 and APP12, which are class I and II peptides, respectively, have been solved. In the class I complexes two water molecules were found at the binding interface that were not present in t...
Source: Acta Crystallographica Section F - August 25, 2016 Category: Biochemistry Authors: Camara-Artigas, A. Ortiz-Salmeron, E. Andujar-S á nchez, M. Bacarizo, J. Martin-Garcia, J.M. Tags: SH3 domain X-ray crystal structure Fyn tyrosine kinase proline-rich motifs research communications Source Type: research

Crystal structure of pyruvate decarboxylase from Zymobacter palmae
Pyruvate decarboxylase (PDC; EC 4.1.1.1) is a thiamine pyrophosphate- and Mg2+ ion-dependent enzyme that catalyses the non-oxidative decarboxylation of pyruvate to acetaldehyde and carbon dioxide. It is rare in bacteria, but is a key enzyme in homofermentative metabolism, where ethanol is the major product. Here, the previously unreported crystal structure of the bacterial pyruvate decarboxylase from Zymobacter palmae is presented. The crystals were shown to diffract to 2.15   Å resolution. They belonged to space group P21, with unit-cell parameters a = 204.56, b = 177.39, c = 244.55   Å and Rr.i.m. = 0.175...
Source: Acta Crystallographica Section F - August 25, 2016 Category: Biochemistry Authors: Buddrus, L. Andrews, E.S.V. Leak, D.J. Danson, M.J. Arcus, V.L. Crennell, S.J. Tags: Zymobacter palmae pyruvate decarboxylase lyase crystal structure TPP-dependent enzyme research communications Source Type: research

Crystal structure of Halobacterium salinarum halorhodopsin with a partially depopulated primary chloride-binding site
In conclusion, the conformation of the chloride-free protein may not be compatible with this crystal form of HsHR despite a packing arrangement that hardly restrains helices E and F that presumably move during ion transport. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - August 25, 2016 Category: Biochemistry Authors: Schreiner, M. Schlesinger, R. Heberle, J. Niemann, H.H. Tags: halorhodopsin Halobacterium salinarum archaeal rhodopsin retinal protein light-driven ion pump post-crystallization treatment reaction intermediate research communications Source Type: research

Structural analysis of point mutations at the Vaccinia virus A20/D4 interface
This study confirms previous biochemical data and also points out the importance for stability of the restrained conformational space of Pro173. Moreover, these new structures will be useful for the design and rational improvement of known molecules targeting the D4/A20 interface. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - August 8, 2016 Category: Biochemistry Authors: Contesto-Richefeu, C. Tarbouriech, N. Brazzolotto, X. Burmeister, W.P. Peyrefitte, C.N. Iseni, F. Tags: Vaccinia virus DNA replication X-ray structure – π interaction protein protein interface research communications Source Type: research

The quorum-quenching lactonase from Geobacillus caldoxylosilyticus: purification, characterization, crystallization and crystallographic analysis
Lactonases are enzymes that are capable of hydrolyzing various lactones such as aliphatic lactones or acyl-homoserine lactones (AHLs), with the latter being used as chemical signaling molecules by numerous Gram-negative bacteria. Lactonases therefore have the ability to quench the chemical communication, also known as quorum sensing, of numerous bacteria, and in particular to inhibit behaviors that are regulated by this system, such as the expression of virulence factors or the production of biofilms. A novel representative from the metallo- β -lactamase superfamily, dubbed GcL, was isolated from the thermophilic bact...
Source: Acta Crystallographica Section F - August 8, 2016 Category: Biochemistry Authors: Bergonzi, C. Schwab, M. Elias, M. Tags: quorum sensing lactonase thermophile quorum quenching research communications Source Type: research

Crystal structure of Plasmodium falciparum proplasmepsin IV: the plasticity of proplasmepsins
Plasmepsin IV from Plasmodium falciparum (PM IV) is a promising target for the development of novel antimalarial drugs. Here, the crystal structure of the truncated zymogen of PM IV (pPM IV), consisting of the mature enzyme plus a prosegment of 47 residues, has been determined at 1.5   Å resolution. pPM IV presents the fold previously described for studied proplasmepsins, displaying closer similarities to proplasmepin IV from P. vivax (pPvPM) than to the other two proplasmepsins from P. falciparum. The study and comparison of the pPM IV structure with the proplasmepsin structures described previously provide inform...
Source: Acta Crystallographica Section F - August 8, 2016 Category: Biochemistry Authors: Recacha, R. Jaudzems, K. Akopjana, I. Jirgensons, A. Tars, K. Tags: malaria proplasmepsin IV Plasmodium falciparum aspartic protease zymogen research communications Source Type: research

Surface-layer protein from Caulobacter crescentus: expression, purification and X-ray crystallographic analysis
Protein surface layers are self-assembling, paracrystalline lattices on the surface of many prokaryotes. Surface-layer proteins have not benefited from widespread structural analysis owing to their resistance to crystallization. Here, the successful expression of a truncated version of RsaA, the surface-layer protein from Caulobacter crescentus, from a Caulobacter protein-expression system is reported. The purification, crystallization and initial X-ray diffraction analysis of the truncated RsaA, the largest surface-layer protein studied to date and the first from a Gram-negative bacterium, are also reported. (Source: Acta...
Source: Acta Crystallographica Section F - August 8, 2016 Category: Biochemistry Authors: Jones, M.D. Chan, A.C.K. Nomellini, J.F. Murphy, M.E.P. Smit, J. Tags: S-layer surface-layer protein RTX motif phasing Gram-negative research communications Source Type: research

pHluorin-assisted expression, purification, crystallization and X-ray diffraction data analysis of the C-terminal domain of the HsdR subunit of the Escherichia coli type I restriction-modification system EcoR124I
The HsdR subunit of the type I restriction-modification system EcoR124I is responsible for the translocation as well as the restriction activity of the whole complex consisting of the HsdR, HsdM and HsdS subunits, and while crystal structures are available for the wild type and several mutants, the C-terminal domain comprising approximately 150 residues was not resolved in any of these structures. Here, three fusion constructs with the GFP variant pHluorin developed to overexpress, purify and crystallize the C-terminal domain of HsdR are reported. The shortest of the three encompassed HsdR residues 887 – 1038 and yie...
Source: Acta Crystallographica Section F - August 8, 2016 Category: Biochemistry Authors: Grinkevich, P. Iermak, I. Luedtke, N.A. Mesters, J.R. Ettrich, R. Ludwig, J. Tags: restriction-modification system EcoR124I HsdR pHluorin GFP Escherichia coli research communications Source Type: research

A putative siderophore-interacting protein from the marine bacterium Shewanella frigidimarina NCIMB 400: cloning, expression, purification, crystallization and X-ray diffraction analysis
Siderophore-binding proteins (SIPs) perform a key role in iron acquisition in multiple organisms. In the genome of the marine bacterium Shewanella frigidimarina NCIMB 400, the gene tagged as SFRI_RS12295 encodes a protein from this family. Here, the cloning, expression, purification and crystallization of this protein are reported, together with its preliminary X-ray crystallographic analysis to 1.35   Å resolution. The SIP crystals belonged to the monoclinic space group P21, with unit-cell parameters a = 48.04, b = 78.31, c = 67.71   Å , α = 90, β   =   99.94, γ = 90 ° , and ...
Source: Acta Crystallographica Section F - August 6, 2016 Category: Biochemistry Authors: Trindade, I.B. Fonseca, B.M. Matias, P.M. Louro, R.O. Moe, E. Tags: siderophore-interacting protein Shewanella frigidimarina crystallographic analysis research communications Source Type: research

Crystal structure of AibC, a reductase involved in alternative de novo isovaleryl coenzyme A biosynthesis in Myxococcus xanthus
Isovaleryl coenzyme A (IV-CoA) performs a crucial role during development and fruiting-body formation in myxobacteria, which is reflected in the existence of a de novo biosynthetic pathway that is highly upregulated when leucine, the common precursor of IV-CoA, is limited. The final step in de novo IV-CoA biosynthesis is catalyzed by AibC, a medium-chain dehydrogenase/reductase. Here, the crystal structure of AibC from Myxococcus xanthus refined to 2.55   Å resolution is presented. The protein adopts two different conformations in the crystal lattice, which is a consequence of partial interaction with the purificat...
Source: Acta Crystallographica Section F - July 28, 2016 Category: Biochemistry Authors: Bock, T. M ü ller, R. Blankenfeldt, W. Tags: alternative isovaleryl coenzyme A biosynthesis medium-chain dehydrogenase/reductase zinc-dependence hexahistidine tag TEV protease-recognition sequence Myxococcus xanthus research communications Source Type: research

Characterization of the NTPR and BD1 interacting domains of the human PICH – BEND3 complex
Chromosome integrity depends on DNA structure-specific processing complexes that resolve DNA entanglement between sister chromatids. If left unresolved, these entanglements can generate either chromatin bridging or ultrafine DNA bridging in the anaphase of mitosis. These bridge structures are defined by the presence of the PICH protein, which interacts with the BEND3 protein in mitosis. To obtain structural insights into PICH – BEND3 complex formation at the atomic level, their respective NTPR and BD1 domains were cloned, overexpressed and crystallized using 1.56   M ammonium sulfate as a precipitant at pH 7.0. The...
Source: Acta Crystallographica Section F - July 26, 2016 Category: Biochemistry Authors: Pitchai, G.P. Hickson, I.D. Streicher, W. Montoya, G. Mesa, P. Tags: crystallization protein complex – protein interaction biophysics data collection research communications Source Type: research

Crystal structure of Rv3899c184 – 410, a hypothetical protein from Mycobacterium tuberculosis
Rv3899c is a hypothetical protein from Mycobacterium tuberculosis which is conserved across mycobacteria. It is predicted to be secreted and has been found in culture filtrates. It has been proposed as a potential vaccine candidate; however, its biological function is unknown. Here, the global structure of Rv3899c184 – 410, a fragment of Rv3899c, is reported. The structure resembles the shell of a sea snail, and its N- and C-termini form two relatively independent compact domains: an α / β / α sandwich folding domain and an α -helix bundle domain. There are no reported protein structures for an...
Source: Acta Crystallographica Section F - July 26, 2016 Category: Biochemistry Authors: Liu, Y. Gao, Y. Li, D. Fleming, J. Li, H. Bi, L. Tags: Mycobacterium tuberculosis Rv3899c184 – 410 crystal structure research communications Source Type: research

Crystal structure of the antigen-binding fragment of a monoclonal antibody specific for the multidrug-resistance-linked ABC transporter human P-glycoprotein
P-glycoprotein (P-gp) is a polyspecific ATP-dependent transporter linked to multidrug resistance in cancers that plays important roles in the pharmacokinetics of a large number of drugs. The drug-resistance phenotype of P-gp can be modulated by the monoclonal antibody UIC2, which specifically recognizes human P-gp in a conformation-dependent manner. Here, the purification, sequence determination and high-resolution structure of the Fab fragment of UIC2 (UIC2/Fab) are reported. Purified UIC2/Fab binds human P-gp with a 1:1 stoichiometry. Crystals of UIC2/Fab are triclinic (space group P1), with unit-cell parameters a = 40.6...
Source: Acta Crystallographica Section F - July 26, 2016 Category: Biochemistry Authors: Esser, L. Shukla, S. Zhou, F. Ambudkar, S.V. Xia, D. Tags: monoclonal antibodies UIC2/Fab multidrug resistance human ABC-dependent transporter P-glycoprotein research communications Source Type: research

Crystal structures of a subunit of the formylglycinamide ribonucleotide amidotransferase, PurS, from Thermus thermophilus, Sulfolobus tokodaii and Methanocaldococcus jannaschii
The crystal structures of a subunit of the formylglycinamide ribonucleotide amidotransferase, PurS, from Thermus thermophilus, Sulfolobus tokodaii and Methanocaldococcus jannaschii were determined and their structural characteristics were analyzed. For PurS from T. thermophilus, two structures were determined using two crystals that were grown in different conditions. The four structures in the dimeric form were almost identical to one another despite their relatively low sequence identities. This is also true for all PurS structures determined to date. A few residues were conserved among PurSs and these are located at the...
Source: Acta Crystallographica Section F - July 26, 2016 Category: Biochemistry Authors: Watanabe, Y. Yanai, H. Kanagawa, M. Suzuki, S. Tamura, S. Okada, K. Baba, S. Kumasaka, T. Agari, Y. Chen, L. Fu, Z.-Q. Chrzas, J. Wang, B.-C. Nakagawa, N. Ebihara, A. Masui, R. Kuramitsu, S. Yokoyama, S. Sampei, G. Kawai, G. Tags: purine nucleotide-biosynthetic pathway formylglycinamide ribonucleotide amidotransferase PurS crystal structure Thermus thermophilus Sulfolobus tokodaii Methanocaldococcus jannaschii research communications Source Type: research

Structural analysis of a function-associated loop mutant of the substrate-recognition domain of Fbs1 ubiquitin ligase
The SCF ubiquitin ligase comprises four components: Skp1, Cul1, Rbx1 and a variable-subunit F-box protein. The F-box protein Fbs1, which recognizes the N-linked glycoproteins, is involved in the endoplasmic reticulum-associated degradation pathway. Although FBG3, another F-box protein, shares 51% sequence identity with Fbs1, FBG3 does not bind glycoproteins. To investigate the sequence – structure relationship of the substrate-binding pocket, the crystal structure of a mutant substrate-binding domain of Fbs1 in which the six nonconserved regions ( β 1, β 2 – β 3, β 3 – β 4, β...
Source: Acta Crystallographica Section F - July 26, 2016 Category: Biochemistry Authors: Nishio, K. Yoshida, Y. Tanaka, K. Mizushima, T. Tags: SCF E3 ubiquitin ligase F-box protein glycoproteins sequence – structure relationship Fbs1 research communications Source Type: research

Structure of the lutein-binding domain of human StARD3 at 1.74   Å resolution and model of a complex with lutein
A crystal structure of the lutein-binding domain of human StARD3 (StAR-related lipid-transfer protein 3; also known as MLN64) has been refined to 1.74   Å resolution. A previous structure of the same protein determined to 2.2   Å resolution highlighted homology with StARD1 and shared cholesterol-binding character. StARD3 has since been recognized as a carotenoid-binding protein in the primate retina, where its biochemical function of binding lutein with specificity appears to be well suited to recruit this photoprotective molecule. The current and previous structures correspond closely to each other (r.m.s....
Source: Acta Crystallographica Section F - July 26, 2016 Category: Biochemistry Authors: Horvath, M.P. George, E.W. Tran, Q.T. Baumgardner, K. Zharov, G. Lee, S. Sharifzadeh, H. Shihab, S. Mattinson, T. Li, B. Bernstein, P.S. Tags: carotenoid-binding protein START domain StARD3 lutein protein tunnels and cavities research communications Source Type: research

Malonate in the nucleotide-binding site traps human AKAP18 γ / δ in a novel conformational state
A-kinase anchoring proteins (AKAPs) are a family of proteins that provide spatiotemporal resolution of protein kinase A (PKA) phosphorylation. In the myocardium, PKA and AKAP18 γ / δ are found in complex with sarcoendoplasmic reticulum Ca2+-ATPase 2 (SERCA2) and phospholamban (PLB). This macromolecular complex provides a means by which anchored PKA can dynamically regulate cytoplasmic Ca2+ release and re-uptake. For this reason, AKAP18 γ / δ presents an interesting drug target with therapeutic potential in cardiovascular disease. The crystal structure of the central domain of human AKAP18 γ ha...
Source: Acta Crystallographica Section F - July 12, 2016 Category: Biochemistry Authors: Bjerregaard-Andersen, K. Ø stensen, E. Scott, J.D. Task é n, K. Morth, J.P. Tags: A-kinase anchoring protein AKAP7 PKA phospholamban signalling drug design proton wire research communications Source Type: research

Crystallization and X-ray diffraction analysis of an l-arabinonate dehydratase from Rhizobium leguminosarum bv. trifolii and a d-xylonate dehydratase from Caulobacter crescentus
In this study, recombinant l-arabinonate dehydratase from Rhizobium leguminosarum bv. trifolii (RlArDHT) and d-xylonate dehydratase from Caulobacter crescentus (CcXyDHT) were heterologously expressed in Escherichia coli and purified by the use of affinity chromatography followed by gel-filtration chromatography. The purified proteins were crystallized using the hanging-drop vapour-diffusion method at 293 K. Crystals of RlArDHT that diffracted to 2.40 Å resolution were obtained using sodium formate as a precipitating agent. They belonged to space group P21, with unit-cell parameters a = 106.07, b = 208.6...
Source: Acta Crystallographica Section F - July 12, 2016 Category: Biochemistry Authors: Rahman, M.M.Andberg, M.Koivula, A.Rouvinen, J.Hakulinen, N. Tags: l-arabinonate dehydratase d-xylonate dehydratase IlvD/EDD enzymes [Fe – S] cluster Rhizobium leguminosarum bv. trifolii Caulobacter crescentus research communications Source Type: research

Structure of the human DNA-repair protein RAD52 containing surface mutations
The Rad52 protein is a eukaryotic single-strand DNA-annealing protein that is involved in the homologous recombinational repair of DNA double-strand breaks. The isolated N-terminal half of the human RAD52 protein (RAD521–212) forms an undecameric ring structure with a surface that is mostly positively charged. In the present study, it was found that RAD521–212 containing alanine mutations of the charged surface residues (Lys102, Lys133 and Glu202) is highly amenable to crystallization. The structure of the mutant RAD521–212 was solved at 2.4 Å resolution. The structure revealed an association betw...
Source: Acta Crystallographica Section F - July 12, 2016 Category: Biochemistry Authors: Saotome, M.Saito, K.Onodera, K.Kurumizaka, H.Kagawa, W. Tags: ssDNA-binding protein single-strand annealing proteins homologous recombinational repair surface-entropy reduction higher order interaction RAD52 research communications Source Type: research

Malonate in the nucleotide-binding site traps human AKAP18γ/δ in a novel conformational state
A-kinase anchoring proteins (AKAPs) are a family of proteins that provide spatiotemporal resolution of protein kinase A (PKA) phosphorylation. In the myocardium, PKA and AKAP18γ/δ are found in complex with sarcoplasmatic reticulum Ca2+-ATPase 2 (SERCA2) and phospholamban (PLB). This macromolecular complex provides a means by which anchored PKA can dynamically regulate cytoplasmic Ca2+ release and re-uptake. For this reason, AKAP18γ/δ presents an interesting drug target with therapeutic potential in cardiovascular disease. The crystal structure of the central domain of human AKAP18γ has been de...
Source: Acta Crystallographica Section F - July 12, 2016 Category: Biochemistry Authors: Bjerregaard-Andersen, K.Østensen, E.Scott, J.D.Taskén, K.Morth, J.P. Tags: A-kinase anchoring protein AKAP7 PKA phospholamban signalling drug design proton wire research communications Source Type: research

Envelope protein VP24 from White spot syndrome virus: expression, purification and crystallization
White spot syndrome virus (WSSV) is a major shrimp pathogen known to infect penaeid shrimp and other crustaceans. VP24 is one of the major envelope proteins of WSSV. In order to facilitate purification, crystallization and structure determination, the predicted N-terminal transmembrane region of approximately 26 amino acids was truncated from VP24 and several mutants were prepared to increase the proportion of selenomethionine (SeMet) residues for subsequent structural determination using the SAD method. Truncated VP24, its mutants and the corresponding SeMet-labelled proteins were purified, and the native and SeMet protei...
Source: Acta Crystallographica Section F - July 12, 2016 Category: Biochemistry Authors: Sun, L.Wu, Y. Tags: White spot syndrome virus WSSV VP24 envelope protein purification crystallization research communications Source Type: research

Crystal structure of the PAS domain of the hEAG potassium channel
KCNH voltage-gated potassium channels play critical roles in regulating cellular functions. The channel is composed of four subunits, each of which contains six transmembrane helices forming the central pore. The cytoplasmic parts of the subunits present a Per–Arnt–Sim (PAS) domain at the N-terminus and a cyclic nucleotide-binding homology domain at the C-terminus. PAS domains are conserved from prokaryotes to eukaryotes and are involved in sensing signals and cellular responses. To better understand the functional roles of PAS domains in KCNH channels, the structure of this domain from the human ether-à...
Source: Acta Crystallographica Section F - July 11, 2016 Category: Biochemistry Authors: Tang, X.Shao, J.Qin, X. Tags: KCNH channels PAS domain ether- à -go-go channel hEAG potassium chanels research communications Source Type: research

Cryoannealing-induced space-group transition of crystals of the carbonic anhydrase psCA3
Cryoannealing has been demonstrated to improve the diffraction quality and resolution of crystals of the β-carbonic anhydrase psCA3 concomitant with a change in space group. After initial flash-cooling in a liquid-nitrogen cryostream an X-ray diffraction data set from a psCA3 crystal was indexed in space group P21212 and was scaled to 2.6 Å resolution, but subsequent cryoannealing studies revealed induced protein rearrangements in the crystal contacts, which transformed the space group to I222, with a corresponding improvement of 0.7 Å in resolution. Although the change in diffraction resolution was si...
Source: Acta Crystallographica Section F - June 27, 2016 Category: Biochemistry Authors: Pinard, M.A.Kurian, J.J.Aggarwal, M.Agbandje-McKenna, M.McKenna, R. Tags: β -carbonic anhydrase Pseudomonas aeruginosa cryoannealing crystal packing research communications Source Type: research

Crystallographic analysis of a subcomplex of the transsulfursome with tRNA for Cys-tRNACys synthesis
In this study, a subcomplex of the transsulfursome with tRNACys (SepCysS–SepCysE–tRNACys), which is involved in the second reaction step of the indirect pathway, was constructed and then crystallized. The crystals diffracted X-rays to a resolution of 2.6 Å and belonged to space group P6522, with unit-cell parameters a = b = 107.2, c = 551.1 Å. The structure determined by molecular replacement showed that the complex consists of a SepCysS dimer, a SepCysE dimer and one tRNACys in the asymmetric unit. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - June 27, 2016 Category: Biochemistry Authors: Chen, M.Nakazawa, Y.Kubo, Y.Asano, N.Kato, K.Tanaka, I.Yao, M. Tags: Cys-tRNACys SepRS SepCysS SepCysE transsulfursome research communications Source Type: research

The galactoside 2-α-l-fucosyltransferase FUT1 from Arabidopsis thaliana: crystallization and experimental MAD phasing
The plant cell wall is a complex network of polysaccharides made up of cellulose, hemicelluloses and pectins. Xyloglucan (XyG), which is the main hemicellulosic component of dicotyledonous plants, has attracted much attention for its role in plant development and for its many industrial applications. The XyG-specific fucosyltransferase (FUT1) adds a fucose residue from GDP-fucose to the 2-O position of the terminal galactosyl residues on XyG side chains. Recombinant FUT1 from Arabidopsis thaliana was crystallized in two different crystal forms, with the best diffracting crystals (up to 1.95 Å resolution) belonging ...
Source: Acta Crystallographica Section F - June 27, 2016 Category: Biochemistry Authors: Rocha, J.Cicéron, F.Lerouxel, O.Breton, C.de Sanctis, D. Tags: plant cell walls fucosyltransferase xyloglucan MAD tantalum bromide Arabidopsis thaliana research communications Source Type: research

Exogenous acetate ion reaches the type II copper centre in CueO through the water-excretion channel and potentially affects the enzymatic activity
The acetate-bound form of the type II copper was found in the X-ray structure of the multicopper oxidase CueO crystallized in acetate buffer in addition to the conventional OH−-bound form as the major resting form. The acetate ion was retained bound to the type II copper even after prolonged exposure of a CueO crystal to X-ray radiation, which led to the stepwise reduction of the Cu centres. However, in this study, when CueO was crystallized in citrate buffer the OH−-bound form was present exclusively. This fact shows that an exogenous acetate ion reaches the type II Cu centre through the water channel construc...
Source: Acta Crystallographica Section F - June 21, 2016 Category: Biochemistry Authors: Komori, H.Kataoka, K.Tanaka, S.Matsuda, N.Higuchi, Y.Sakurai, T. Tags: bioinorganic chemistry enzyme catalysis metalloproteins CueO multicopper oxidase research communications Source Type: research

LCP crystallization and X-ray diffraction analysis of VcmN, a MATE transporter from Vibrio cholerae
Multidrug and toxic compound extrusion (MATE) transporters, one of the multidrug exporter families, efflux xenobiotics towards the extracellular side of the membrane. Since MATE transporters expressed in bacterial pathogens contribute to multidrug resistance, they are important therapeutic targets. Here, a MATE-transporter homologue from Vibrio cholerae, VcmN, was overexpressed in Escherichia coli, purified and crystallized in lipidic cubic phase (LCP). X-ray diffraction data were collected to 2.5 Å resolution from a single crystal obtained in a sandwich plate. The crystal belonged to space group P212121, with unit...
Source: Acta Crystallographica Section F - June 21, 2016 Category: Biochemistry Authors: Kusakizako, T.Tanaka, Y.Hipolito, C.J.Kuroda, T.Ishitani, R.Suga, H.Nureki, O. Tags: MATE transporter multidrug resistance lipidic cubic phase LCP research communications Source Type: research

Structure of a double hexamer of the Pyrococcus furiosus minichromosome maintenance protein N-terminal domain
The crystal structure of the N-terminal domain of the Pyrococcus furiosus minichromosome maintenance (MCM) protein as a double hexamer is described. The MCM complex is a ring-shaped helicase that unwinds DNA at the replication fork of eukaryotes and archaea. Prior to replication initiation, the MCM complex assembles as an inactive double hexamer at specific sites of DNA. The presented structure is highly consistent with previous MCM double-hexamer structures and shows two MCM hexamers with a head-to-head interaction mediated by the N-terminal domain. Minor differences include a diminished head-to-head interaction and a sli...
Source: Acta Crystallographica Section F - June 21, 2016 Category: Biochemistry Authors: Meagher, M.Enemark, E.J. Tags: DNA replication helicase MCM minichromosome maintenance Pyrococcus furiosus research communications Source Type: research

Crystal structure of a thiolase from Escherichia coli at 1.8 Å resolution
Thiolases catalyze the Claisen condensation of two acetyl-CoA molecules to give acetoacetyl-CoA, as well as the reverse degradative reaction. Four genes coding for thiolases or thiolase-like proteins are found in the Escherichia coli genome. In this communication, the successful cloning, purification, crystallization and structure determination at 1.8 Å resolution of a homotetrameric E. coli thiolase are reported. The structure of E. coli thiolase co-crystallized with acetyl-CoA at 1.9 Å resolution is also reported. As observed in other tetrameric thiolases, the present E. coli thiolase is a dimer of t...
Source: Acta Crystallographica Section F - June 21, 2016 Category: Biochemistry Authors: Ithayaraja, M.Janardan, N.Wierenga, R.K.Savithri, H.S.Murthy, M.R.N. Tags: Escherichia coli thiolase fatty-acid metabolism degradative enzyme active-site geometry asymmetry research communications Source Type: research

Crystal structure of truncated aspartate transcarbamoylase from Plasmodium falciparum
The de novo pyrimidine-biosynthesis pathway of Plasmodium falciparum is a promising target for antimalarial drug discovery. The parasite requires a supply of purines and pyrimidines for growth and proliferation and is unable to take up pyrimidines from the host. Direct (or indirect) inhibition of de novo pyrimidine biosynthesis via dihydroorotate dehydrogenase (PfDHODH), the fourth enzyme of the pathway, has already been shown to be lethal to the parasite. In the second step of the plasmodial pyrimidine-synthesis pathway, aspartate and carbamoyl phosphate are condensed to N-carbamoyl-l-aspartate and inorganic phosphate by ...
Source: Acta Crystallographica Section F - June 21, 2016 Category: Biochemistry Authors: Lunev, S.Bosch, S.S.Batista, F.A.Wrenger, C.Groves, M.R. Tags: aspartate transcarbamoylase X-ray structure pyrimidine biosynthesis Plasmodium falciparum malaria antimalarial drugs research communications Source Type: research

Crystal structure of the cyan fluorescent protein Cerulean-S175G
In this study, Cerulean-S175G was revealed to adopt only the Cerulean conformation, while Cerulean has been reported to adopt both the ECFP and the Cerulean conformations in its crystal structures. Sharing the same S175G mutation with SCFP3A, Cerulean-S175G showed a slightly increased quantum yield, like SCFP3A, but did not adopt the ECFP conformation adopted by SCFP3A. Detailed comparison of Cerulean-S175G and other ECFP variants revealed that the notable conformational changes in ECFP variants can be understood mainly in terms of the interaction between the Trp66 residue of the chromophore and residues 145–148 of &...
Source: Acta Crystallographica Section F - June 21, 2016 Category: Biochemistry Authors: Park, S.Kang, S.Yoon, T.-S. Tags: Cerulean-S175G enhanced cyan fluorescent protein fluorophores fluorescence resonance energy transfer fluorescence lifetime imaging microscopy research communications Source Type: research

Structural insights into the catalytic reaction trigger and inhibition of d-3-hydroxybutyrate dehydrogenase
d-3-Hydroxybutyrate dehydrogenase catalyzes the reversible conversion of acetoacetate and d-3-hydroxybutyrate. These ketone bodies are both energy-storage forms of acetyl-CoA. In order to clarify the structural mechanisms of the catalytic reaction with the cognate substrate d-3-hydroxybutyrate and of the inhibition of the reaction by inhibitors, the enzyme from Alcaligenes faecalis has been analyzed by X-ray crystallography in liganded states with the substrate and with two types of inhibitor: malonate and methylmalonate. In each subunit of the tetrameric enzyme, the substrate is trapped on the nicotinamide plane of the bo...
Source: Acta Crystallographica Section F - June 21, 2016 Category: Biochemistry Authors: Kanazawa, H.Hoque, Md.M.Tsunoda, M.Suzuki, K.Yamamoto, T.Kawai, G.Kondo, J.Takénaka, A. Tags: X-ray crystal structure d-3-hydroxybutyrate dehydrogenase substrate inhibitor catalytic reaction trigger ketone bodies acetyl-CoA research communications Source Type: research

High-resolution NMR structures of the domains of Saccharomyces cerevisiae Tho1
In this study, high-resolution structures of both the N-terminal DNA-binding SAP domain and C-terminal RNA-binding domain have been determined. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - May 22, 2016 Category: Biochemistry Authors: Jacobsen, J.O.B.Allen, M.D.Freund, S.M.V.Bycroft, M. Tags: SAP Tho1 RNA research communications Source Type: research

Crystal structures of two monomeric triosephosphate isomerase variants identified via a directed-evolution protocol selecting for l-arabinose isomerase activity
The crystal structures are described of two variants of A-TIM: Ma18 (2.7 Å resolution) and Ma21 (1.55 Å resolution). A-TIM is a monomeric loop-deletion variant of triosephosphate isomerase (TIM) which has lost the TIM catalytic properties. Ma18 and Ma21 were identified after extensive directed-evolution selection experiments using an Escherichia coli l-arabinose isomerase knockout strain expressing a randomly mutated A-TIM gene. These variants facilitate better growth of the Escherichia coli selection strain in medium supplemented with 40 mM l-arabinose. Ma18 and Ma21 differ from A-TIM by four and one poi...
Source: Acta Crystallographica Section F - May 22, 2016 Category: Biochemistry Authors: Krause, M.Kiema, T.-R.Neubauer, P.Wierenga, R.K. Tags: enzyme engineering non-natural enzymes triosephosphate isomerase structure-based rational design TIM barrel research communications Source Type: research

The VapBC1 toxin–antitoxin complex from Mycobacterium tuberculosis: purification, crystallization and X-ray diffraction analysis
Mycobacterium tuberculosis, a major human pathogen, encodes at least 88 toxin–antitoxin (TA) systems. Remarkably, more than half of these modules belong to the VapBC family. Under normal growth conditions, the toxicity of the toxin VapC is neutralized by the protein antitoxin VapB. When bacteria face an unfavourable environment, the antitoxin is degraded and the free toxin VapC targets important cellular processes in order to inhibit cell growth. TA systems function in many biological processes, such as in the stringent response, in biofilm formation and in drug tolerance. To explore the structure of the VapBC1 compl...
Source: Acta Crystallographica Section F - May 22, 2016 Category: Biochemistry Authors: Lu, Z.Wang, H.Zhang, A.Tan, Y. Tags: VapBC toxin – antitoxin system Mycobacterium tuberculosis drug target research communications Source Type: research

Plant-specific DUF1110 protein from Oryza sativa: expression, purification and crystallization
In this study, the Os01T0156300 protein was crystallized using the hanging-drop vapour-diffusion method. X-ray diffraction data were collected to 1.84 Å resolution. The crystal belonged to space group P21, with unit-cell parameters a = 89.9, b = 89.8, c = 107.1 Å, β = 106.6°. The asymmetric unit was estimated to contain 6–11 molecules. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - May 22, 2016 Category: Biochemistry Authors: Harada, K.Yamashita, E.Inoue, K.Yamaguchi, K.Fujiwara, T.Nakagawa, A.Kawasaki, T.Kojima, C. Tags: plant-specific protein PAMP-triggered immunity interactor for OsPUB44 Os01T0156300 Oryza sativa DUF1110 research communications Source Type: research

Structure of the I-SceI nuclease complexed with its dsDNA target and three catalytic metal ions
Homing endonucleases are highly specific DNA-cleaving enzymes that recognize and cleave long stretches of DNA. The engineering of these enzymes provides instruments for genome modification in a wide range of fields, including gene targeting. The homing endonuclease I-SceI from the yeast Saccharomyces cerevisiae has been purified after overexpression in Escherichia coli and its crystal structure has been determined in complex with its target DNA. In order to evaluate the number of ions that are involved in the cleavage process, thus determining the catalytic mechanism, crystallization experiments were performed in the prese...
Source: Acta Crystallographica Section F - May 22, 2016 Category: Biochemistry Authors: Prieto, J.Redondo, P.Merino, N.Villate, M.Montoya, G.Blanco, F.J.Molina, R. Tags: gene targeting protein – DNA interaction genetics I-SceI homing endonuclease DNA cleavage Saccharomyces cerevisiae research communications Source Type: research

Structure of an ABC transporter solute-binding protein specific for the amino sugars glucosamine and galactosamine
The uptake of exogenous solutes by prokaryotes is mediated by transport systems embedded in the plasma membrane. In many cases, a solute-binding protein (SBP) is utilized to bind ligands with high affinity and deliver them to the membrane-bound components responsible for translocation into the cytoplasm. In the present study, Avi_5305, an Agrobacterium vitis SBP belonging to Pfam13407, was screened by differential scanning fluorimetry (DSF) and found to be stabilized by d-glucosamine and d-galactosamine. Avi_5305 is the first protein from Pfam13407 shown to be specific for amino sugars, and co-crystallization resulted in s...
Source: Acta Crystallographica Section F - May 22, 2016 Category: Biochemistry Authors: Yadava, U.Vetting, M.W.Al Obaidi, N.Carter, M.S.Gerlt, J.A.Almo, S.C. Tags: solute-binding protein differential scanning fluorimetry Thermofluor Agrobacterium vitis Avi_5305 Pfam13407 research communications Source Type: research

Crystal structure of a chimaeric bacterial glutamate dehydrogenase
Glutamate dehydrogenases (EC 1.4.1.2–4) catalyse the oxidative deamination of l-glutamate to α-ketoglutarate using NAD(P)+ as a cofactor. The bacterial enzymes are hexameric, arranged with 32 symmetry, and each polypeptide consists of an N-terminal substrate-binding segment (domain I) followed by a C-terminal cofactor-binding segment (domain II). The catalytic reaction takes place in the cleft formed at the junction of the two domains. Distinct signature sequences in the nucleotide-binding domain have been linked to the binding of NAD+ versus NADP+, but they are not unambiguous predictors of cofactor preference...
Source: Acta Crystallographica Section F - May 22, 2016 Category: Biochemistry Authors: Oliveira, T.Sharkey, M.A.Engel, P.C.Khan, A.R. Tags: glutamate dehydrogenase chimaera enzyme NADP -binding domain catalysis research communications Source Type: research

The SecB-like chaperone Rv1957 from Mycobacterium tuberculosis: crystallization and X-ray crystallographic analysis
Protein export is important in all bacteria, and bacteria have evolved specialized export machineries to fulfil this task. In Mycobacterium tuberculosis, the causative agent of tuberculosis, the general secretion pathway (Sec pathway) is conserved and is essential in performing the export of proteins. The bacterial Sec pathway post-translationally exports unfolded proteins out of the cytoplasm, and the core of the Sec pathway is composed of a heterotrimeric membrane-embedded channel, SecYEG, and two cytosolic components, SecA and SecB. SecB functions by stabilizing unfolded proteins, maintaining them in an export-competent...
Source: Acta Crystallographica Section F - May 22, 2016 Category: Biochemistry Authors: Lu, Z.Wang, H.Yu, T. Tags: SecB Rv1957 Mycobacterium tuberculosis Sec pathway toxin – antitoxin system research communications Source Type: research

Crystal structure of glutamate-1-semialdehyde-2,1-aminomutase from Arabidopsis thaliana
Glutamate-1-semialdehyde-2,1-aminomutase (GSAM) catalyzes the isomerization of glutamate-1-semialdehyde (GSA) to 5-aminolevulinate (ALA) and is distributed in archaea, most bacteria and plants. Although structures of GSAM from archaea and bacteria have been resolved, a GSAM structure from a higher plant is not available, preventing further structure–function analysis. Here, the structure of GSAM from Arabidopsis thaliana (AtGSA1) obtained by X-ray crystallography is reported at 1.25 Å resolution. AtGSA1 forms an asymmetric dimer and displays asymmetry in cofactor binding as well as in the gating-loop orientat...
Source: Acta Crystallographica Section F - May 22, 2016 Category: Biochemistry Authors: Song, Y.Pu, H.Jiang, T.Zhang, L.Ouyang, M. Tags: X-ray crystallography asymmetry pyridoxamine 5 ′ -phosphate pyridoxal 5 gating loop glutamate-1-semialdehyde-2,1-aminomutase Arabidopsis thaliana research communications Source Type: research

Putative thioredoxin Trx1 from Thermosipho africanus strain TCF52B: expression, purification and structural determination using S-SAD
Thioredoxin is a small ubiquitous protein that plays a role in many biological processes. A putative thioredoxin, Trx1, from Thermosipho africanus strain TCF52B, which has low sequence identity to its closest homologues, was successfully cloned, overexpressed and purified. The protein was crystallized using the microbatch-under-oil technique at 289 K in a variety of conditions; crystals grown in 0.2 M MgCl2, 0.1 M bis-tris pH 6.5, 25%(w/v) PEG 3350, which grew as irregular trapezoids to maximum dimensions of 1.2 × 1.5 × 0.80 mm, were used for sulfur single-wavelength anomalous dispersion analysis. The a...
Source: Acta Crystallographica Section F - May 22, 2016 Category: Biochemistry Authors: Sahtout, N.Kuttiyatveetil, J.R.A.Fodje, M.Sanders, D.A.R. Tags: thioredoxin Thermosipho africanus thermophile sulfur SAD research communications Source Type: research

Cyclization strategies of meditopes: affinity and diffraction studies of meditope–Fab complexes
Recently, a unique binding site for a cyclic 12-residue peptide was discovered within a cavity formed by the light and heavy chains of the cetuximab Fab domain. In order to better understand the interactions that drive this unique complex, a number of variants including the residues within the meditope peptide and the antibody, as well as the cyclization region of the meditope peptide, were created. Here, multiple crystal structures of meditope peptides incorporating different cyclization strategies bound to the central cavity of the cetuximab Fab domain are presented. The affinity of each cyclic derivative for the Fab was...
Source: Acta Crystallographica Section F - May 22, 2016 Category: Biochemistry Authors: Bzymek, K.P.Ma, Y.Avery, K.A.Horne, D.A.Williams, J.C. Tags: meditope monoclonal antibody X-ray crystallography surface plasmon resonance research communications Source Type: research

Crystal structure of the TK2203 protein from Thermococcus kodakarensis, a putative extradiol dioxygenase
The TK2203 protein from the hyperthermophilic archaeon Thermococcus kodakarensis KOD1 (262 residues, 29 kDa) is a putative extradiol dioxygenase catalyzing the cleavage of C–C bonds in catechol derivatives. It contains three metal-binding residues, but has no significant sequence similarity to proteins for which structures have been determined. Here, the first crystal structure of the TK2203 protein was determined at 1.41 Å resolution to investigate its functional role. Structure analysis reveals that this protein shares the same fold and catalytic residues as other extradiol dioxygenases, strongly suggesti...
Source: Acta Crystallographica Section F - May 22, 2016 Category: Biochemistry Authors: Nishitani, Y.Simons, J.-R.Kanai, T.Atomi, H.Miki, K. Tags: aromatic compound degradation nonhaem iron archaea SIRAS homodimer TK2203 Thermococcus kodakarensis research communications Source Type: research

Structural basis for DNA recognition by the transcription regulator MetR
MetR, a LysR-type transcriptional regulator (LTTR), has been extensively studied owing to its role in the control of methionine biosynthesis in proteobacteria. A MetR homodimer binds to a 24-base-pair operator region of the met genes and specifically recognizes the interrupted palindromic sequence 5′-TGAA-N5-TTCA-3′. Mechanistic details underlying the interaction of MetR with its target DNA at the molecular level remain unknown. In this work, the crystal structure of the DNA-binding domain (DBD) of MetR was determined at 2.16 Å resolution. MetR-DBD adopts a winged-helix–turn–helix (wHTH) mot...
Source: Acta Crystallographica Section F - May 22, 2016 Category: Biochemistry Authors: Punekar, A.S.Porter, J.Carr, S.B.Phillips, S.E.V. Tags: methionine biosynthesis MetR LysR-type transcriptional regulator DNA recognition helix – turn molecular replacement phasing phenix.mr_rosetta HADDOCK DNA binding research communications Source Type: research

Structural analysis of the spliceosomal RNA helicase Prp28 from the thermophilic eukaryote Chaetomium thermophilum
Prp28 (pre-mRNA-splicing ATP-dependent RNA helicase 28) is a spliceosomal DEAD-box helicase which is involved in two steps of spliceosome assembly. It is required for the formation of commitment complex 2 in an ATP-independent manner as well as for the formation of the pre-catalytic spliceosome, which in contrast is ATP-dependent. During the latter step, Prp28 is crucial for the integration of the U4/U6·U5 tri-snRNP since it displaces the U1 snRNP and allows the U6 snRNP to base-pair with the 5′-splice site. Here, the crystal structure of Prp28 from the thermophilic fungus Chaetomium thermophilum is reported a...
Source: Acta Crystallographica Section F - April 21, 2016 Category: Biochemistry Authors: Tauchert, M.J.Ficner, R. Tags: spliceosome RNA helicase DEAD-box protein U5-100kD DDX23 research communications Source Type: research

1.2 Å resolution crystal structure of the periplasmic aminotransferase PvdN from Pseudomonas aeruginosa
This study reports the high-resolution structure of PvdN bound to a PLP cofactor solved by multi-wavelength anomalous dispersion (MAD). The PvdN model shows high structural homology to type I aspartate aminotransferases and also contains positive density that suggests an uncharacterized external aldimine. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - April 21, 2016 Category: Biochemistry Authors: Drake, E.J.Gulick, A.M. Tags: PvdN pyoverdine nonribosomal peptide synthetase Pseudomonas aeruginosa research communications Source Type: research

RRM domain of human RBM7: purification, crystallization and structure determination
RNA decay is an important process that is essential for controlling the abundance, quality and maturation of transcripts. In eukaryotes, RNA decay in the 3′–5′ direction is carried out by the exosome, an RNA-degradation machine that is conserved from yeast to humans. A range of cofactors stimulate the enzymatic activity of the exosome and serve as adapters for the many RNA substrates. In human cells, the exosome associates with the heterotrimeric nuclear exosome targeting (NEXT) complex consisting of the DExH-box helicase hMTR4, the zinc-finger protein hZCCHC8 and the RRM-type protein hRBM7. Here, the 2.5...
Source: Acta Crystallographica Section F - April 21, 2016 Category: Biochemistry Authors: Sofos, N.Winkler, M.B.L.Brodersen, D.E. Tags: RNA degradation human NEXT complex RRM domain X-ray crystallography research communications Source Type: research