Extension of resolution and oligomerization-state studies of 2,4′-dihydroxyacetophenone dioxygenase from Alcaligenes sp. 4HAP
The enzyme 2,4′-dihydroxyacetophenone dioxygenase (DAD) catalyses the conversion of 2,4′-dihydroxyacetophenone to 4-hydroxybenzoic acid and formic acid. This enzyme is a very unusual dioxygenase in that it cleaves a C—C bond in a substituent of the aromatic ring rather than within the ring itself. Whilst it has been shown that DAD is a tetramer in solution, the recently solved crystal structure of the Alcaligenes sp. 4HAP enzyme was in fact dimeric rather than tetrameric. Since the use of limited chymotrypsinolysis, which apparently results in removal of the first 20 or so N-terminal residues of DAD, was ...
Source: Acta Crystallographica Section F - September 23, 2015 Category: Biochemistry Authors: Guo, J.Erskine, P.Coker, A.R.Gor, J.Perkins, S.J.Wood, S.P.Cooper, J.B. Tags: 2,4 ′ -dihydroxyacetophenone dioxygenase protein X-ray structure oligomerization analytical ultracentrifugation gel filtration docking research communications Source Type: research

Structure of the HECT domain of human WWP2
WWP2 is a HECT-domain ubiquitin ligase of the Nedd4 family, which is involved in various important biological processes, such as protein degradation, membrane-protein sorting and transportation, the immune response, pluripotency of embryonic stem cells, tumourigenesis and metastasis. The HECT domain provides the intrinsic ubiquitin ligase activity of WWP2. Here, the expression, purification, crystallization and crystallographic analysis of the HECT domain of human WWP2 (HECTWWP2) are reported. HECTWWP2 has been crystallized and the crystals diffracted to 2.50 Å resolution. They belonged to space group P41212 and th...
Source: Acta Crystallographica Section F - September 23, 2015 Category: Biochemistry Authors: Gong, W.Zhang, X.Zhang, W.Li, J.Li, Z. Tags: crystal structure WWP2 HECT domain ubiquitin ligase research communications Source Type: research

Purification, crystallization and X-ray crystallographic analysis of human RAB11(S20V), a constitutively active GTP-binding form
In this study, the RAB11(S20V) mutant was overexpressed in Escherichia coli with an engineered C-terminal His tag. RAB11(S20V) was then purified to homogeneity and was crystallized at 293 K. X-ray diffraction data were collected to a resolution of 2.4 Å from a crystal belonging to space group I4, with unit-cell parameters a = 74.11, b = 74.11, c = 149.44 Å. The asymmetric unit was estimated to contain two molecules of RAB11(S20V). (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - September 23, 2015 Category: Biochemistry Authors: Kim, C.M.Choi, J.Y.Yoon, J. H.Park, H.H. Tags: small G protein RAB11 membrane trafficking crystallization diffraction research communications Source Type: research

Crystallization and initial crystallographic analysis of covalent DNA-cleavage complexes of Staphyloccocus aureus DNA gyrase with QPT-1, moxifloxacin and etoposide
Fluoroquinolone drugs such as moxifloxacin kill bacteria by stabilizing the normally transient double-stranded DNA breaks created by bacterial type IIA topoisomerases. Previous crystal structures of Staphylococcus aureus DNA gyrase with asymmetric DNAs have had static disorder (with the DNA duplex observed in two orientations related by the pseudo-twofold axis of the complex). Here, 20-base-pair DNA homoduplexes were used to obtain crystals of covalent DNA-cleavage complexes of S. aureus DNA gyrase. Crystals with QPT-1, moxifloxacin or etoposide diffracted to between 2.45 and 3.15 Å resolution. A G/T mismatch intro...
Source: Acta Crystallographica Section F - September 23, 2015 Category: Biochemistry Authors: Srikannathasan, V.Wohlkonig, A.Shillings, A.Singh, O.Chan, P.F.Huang, J.Gwynn, M.N.Fosberry, A.P.Homes, P.Hibbs, M.Theobald, A.J.Spitzfaden, C.Bax, B.D. Tags: fluoroquinolone topoisomerase DNA gyrase etoposide DNA complex research communications Source Type: research

Structure and binding properties of a cameloid nanobody raised against KDM5B
The histone demethylase KDM5B is considered to be a promising target for anticancer therapy. Single-chain antibodies from llama (nanobodies) have been raised to aid in crystallization and structure determination of this enzyme. The antigen-binding properties of 15 of these nanobodies have been characterized. The crystal structure of one of these (NB17) has been determined to a resolution of 1.85 Å. NB17 crystallizes in space group P4322 with six molecules in the asymmetric unit. The six molecules in the asymmetric unit pack as an entity with approximate D3 symmetry with interactions mediated by the CDR loops, which...
Source: Acta Crystallographica Section F - September 23, 2015 Category: Biochemistry Authors: Wiuf, A.Kristensen, L.H.Kristensen, O.Dorosz, J.Jensen, J.Gajhede, M. Tags: nanobody KDM5B research communications Source Type: research

Analysis of crystallization data in the Protein Data Bank
The Protein Data Bank (PDB) is the largest available repository of solved protein structures and contains a wealth of information on successful crystallization. Many centres have used their own experimental data to draw conclusions about proteins and the conditions in which they crystallize. Here, data from the PDB were used to reanalyse some of these results. The most successful crystallization reagents were identified, the link between solution pH and the isoelectric point of the protein was investigated and the possibility of predicting whether a protein will crystallize was explored. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - September 23, 2015 Category: Biochemistry Authors: Kirkwood, J.Hargreaves, D.O'Keefe, S.Wilson, J. Tags: crystallization pH isoelectric point PDB data statistics database proteins research communications Source Type: research

Purification, crystallization, crystallographic analysis and phasing of the CRISPR-associated protein Csm2 from Thermotoga maritima
The clusters of regularly interspaced short palindromic repeats (CRISPR)–CRISPR-associated proteins (Cas) system consists of an intriguing machinery of proteins that confer bacteria and archaea with immunity against phages and plasmids via an RNA-guided interference mechanism. Here, the cloning, recombinant expression in Escherichia coli BL21 (DE3), purification, crystallization and preliminary X-ray diffraction analysis of Csm2 from Thermotoga maritima are reported. Csm2 is thought to be a component of an important protein complex of the type IIIA CRISPR–Cas system, which is involved in the CRISPR–Cas RN...
Source: Acta Crystallographica Section F - September 23, 2015 Category: Biochemistry Authors: Gallo, G.Augusto, G.Rangel, G.Zelanis, A.Mori, M.A.Barbosa Campos, C.Würtele, M. Tags: RNA-guided interference CRISPR – Cas Csm2 Thermotoga maritima research communications Source Type: research

Structure of the response regulator RPA3017 involved in red-light signaling in Rhodopseudomonas palustris
Two-component signal transduction is the major signaling mechanism that enables bacteria to survive and thrive in complex environmental conditions. The photosynthetic bacterium R. palustris employs two tandem bacteriophytochromes, RpBphP2 and RpBphP3, to perceive red-light signals that regulate the synthesis of light-harvesting complexes under low-light conditions. Both RpBphP2 and RpBphP3 are photosensory histidine kinases coupled to the same response regulator RPA3017. Together, they constitute a two-component system that converts a red-light signal into a biological signal. In this work, the crystal structure of RPA3017...
Source: Acta Crystallographica Section F - September 23, 2015 Category: Biochemistry Authors: Yang, X.F.Zeng, X.Moffat, K.Yang, X. Tags: two-component signal transduction response regulator red-light signaling crystal structure phosphotransfer research communications Source Type: research

Crystallization and X-ray diffraction studies of a two-domain laccase from Streptomyces griseoflavus
Laccase (EC 1.10.3.2) is one of the most common copper-containing oxidases; it is found in many organisms and catalyzes the oxidation of primarily phenolic compounds by oxygen. Two-domain laccases have unusual thermostability, resistance to inhibitors and an alkaline optimum of activity. The causes of these properties in two-domain laccases are poorly understood. A recombinant two-domain laccase (SgfSL) was cloned from the genome of Streptomyces griseoflavus Ac-993, expressed in Escherichia coli and purified to homogeneity. The crystals of SgfSL belonged to the monoclinic space group P21, with unit-cell parameters a = 74.6...
Source: Acta Crystallographica Section F - August 25, 2015 Category: Biochemistry Authors: Tishchenko, S.Gabdulkhakov, A.Trubitsina, L.Lisov, A.Zakharova, M.Leontievsky, A. Tags: two-domain laccase Streptomyces griseoflavus research communications Source Type: research

Crystallization and X-ray diffraction analysis of a putative bacterial class I labdane-related diterpene synthase
Labdane-related diterpenoids are natural products with potential pharmaceutical applications that are rarely found in bacteria. Here, a putative class I labdane-related diterpene synthase (LrdC) identified by genome mining in a streptomycete was successfully crystallized using the microbatch method. Crystals of the LrdC enzyme were obtained in a holo form with its natural cofactor Mg2+ (LrdC-Mg2+) and in complex with inorganic pyrophosphate (PPi) (LrdC-Mg2+–PPi). Crystals of native LrdC-Mg2+ diffracted to 2.50 Å resolution and belonged to the trigonal space group P3221, with unit-cell parameters a = ...
Source: Acta Crystallographica Section F - August 25, 2015 Category: Biochemistry Authors: Serrano-Posada, H.Centeno-Leija, S.Rojas-Trejo, S.Stojanoff, V.Rodríguez-Sanoja, R.Rudiño-Piñera, E.Sánchez, S. Tags: diterpene synthase genome mining labdane-related diterpenoid Streptomyces research communications Source Type: research

Expression, purification, crystallization and X-ray diffraction studies of the molecular chaperone prefoldin from Homo sapiens
Proper protein folding is an essential process for all organisms. Prefoldin (PFD) is a molecular chaperone that assists protein folding by delivering non-native proteins to group II chaperonin. A heterohexamer of eukaryotic PFD has been shown to specifically recognize and deliver non-native actin and tubulin to chaperonin-containing TCP-1 (CCT), but the mechanism of specific recognition is still unclear. To determine its crystal structure, recombinant human PFD was reconstituted, purified and crystallized. X-ray diffraction data were collected to 4.7 Å resolution. The crystals belonged to space group P21212, with u...
Source: Acta Crystallographica Section F - August 25, 2015 Category: Biochemistry Authors: Aikawa, Y.Kida, H.Nishitani, Y.Miki, K. Tags: protein folding molecular chaperone prefoldin research communications Source Type: research

Structure of the SPRY domain of the human RNA helicase DDX1, a putative interaction platform within a DEAD-box protein
The human RNA helicase DDX1 in the DEAD-box family plays an important role in RNA processing and has been associated with HIV-1 replication and tumour progression. Whereas previously described DEAD-box proteins have a structurally conserved core, DDX1 shows a unique structural feature: a large SPRY-domain insertion in its RecA-like consensus fold. SPRY domains are known to function as protein–protein interaction platforms. Here, the crystal structure of the SPRY domain of human DDX1 (hDSPRY) is reported at 2.0 Å resolution. The structure reveals two layers of concave, antiparallel β-sheets that stack ont...
Source: Acta Crystallographica Section F - August 25, 2015 Category: Biochemistry Authors: Kellner, J.N.Meinhart, A. Tags: DEAD-box proteins SPRY domains RNA processing – protein interaction research communications Source Type: research

Structure of the N-terminal dimerization domain of CEACAM7
CEACAM7 is a human cellular adhesion protein that is expressed on the surface of colon and rectum epithelial cells and is downregulated in colorectal cancers. It achieves cell adhesion through dimerization of the N-terminal IgV domain. The crystal structure of the N-terminal dimerization domain of CEACAM has been determined at 1.47 Å resolution. The overall fold of CEACAM7 is similar to those of CEACAM1 and CEACAM5; however, there are differences, the most notable of which is an insertion that causes the C′′ strand to buckle, leading to the creation of a hydrogen bond in the dimerization interface. The ...
Source: Acta Crystallographica Section F - August 25, 2015 Category: Biochemistry Authors: Bonsor, D.A.Beckett, D.Sundberg, E.J. Tags: cell adhesion CEACAM7 research communications Source Type: research

Crystals of the Arp2/3 complex in two new space groups with structural information about actin-related protein 2 and potential WASP binding sites
Co-crystals of the bovine Arp2/3 complex with the CA motif from N-WASP in two new space groups were analyzed by X-ray diffraction. The crystals in the orthorhombic space group P212121 contained one complex per asymmetric unit, with unit-cell parameters a = 105.48, b = 156.71, c = 177.84 Å, and diffracted to 3.9 Å resolution. The crystals in the tetragonal space group P41 contained two complexes per asymmetric unit, with unit-cell parameters a = b = 149.93, c = 265.91 Å, and diffracted to 5.0 Å resolution. The electron-density maps of both new crystal forms had densities for small s...
Source: Acta Crystallographica Section F - August 25, 2015 Category: Biochemistry Authors: Jurgenson, C.T.Pollard, T.D. Tags: Arp2/3 Wiskott – Aldrich syndrome actin research communications Source Type: research

Crystallization and preliminary X-ray crystallographic analysis of a nonstructural protein 15 mutant from Human coronavirus 229E
Nonstructural protein 15 (nsp15), also called endoribonuclease, is a gene product of open reading frame 1b (ORF 1b) in coronaviruses. It is an important enzyme in the transcription/replication process involved in discontinuous negative-strand RNA synthesis. In this work, mutants of nsp15 from Human coronavirus 229E (HCoV-229E) were made based on structural analysis of the homologous nsp15s in Severe acute respiratory syndrome coronavirus (SARS-CoV) and Mouse hepatitis virus (MHV). The I26A/N52A mutant of nsp15 was overexpressed, purified and crystallized, and this mutant led to a trimeric form rather than hexamers or monom...
Source: Acta Crystallographica Section F - August 25, 2015 Category: Biochemistry Authors: Huo, T.Liu, X. Tags: coronaviruses Human coronavirus 229E nonstructural protein 15 endoribonuclease trimeric form research communications Source Type: research

Cleavage of nicotinamide adenine dinucleotide by the ribosome-inactivating protein from Momordica charantia
The interaction of momordin, a type 1 ribosome-inactivating protein from Momordica charantia, with NADP+ and NADPH has been investigated by X-ray diffraction analysis of complexes generated by co-crystallization and crystal soaking. It is known that the proteins of this family readily cleave the adenine–ribose bond of adenosine and related nucleotides in the crystal, leaving the product, adenine, bound to the enzyme active site. Surprisingly, the nicotinamide–ribose bond of oxidized NADP+ is cleaved, leaving nicotinamide bound in the active site in the same position but in a slightly different orientation to th...
Source: Acta Crystallographica Section F - August 25, 2015 Category: Biochemistry Authors: Vinkovic, M.Dunn, G.Wood, G.E.Husain, J.Wood, S.P.Gill, R. Tags: ribosome-inactivating protein N-glycosidase nicotinamide crystal structure momordin research communications Source Type: research

The structure of Tim50(164–361) suggests the mechanism by which Tim50 receives mitochondrial presequences
Mitochondrial preproteins are transported through the translocase of the outer membrane (TOM) complex. Tim50 and Tim23 then transfer preproteins with N-terminal targeting presequences through the intermembrane space (IMS) across the inner membrane. The crystal structure of the IMS domain of Tim50 [Tim50(164–361)] has previously been determined to 1.83 Å resolution. Here, the crystal structure of Tim50(164–361) at 2.67 Å resolution that was crystallized using a different condition is reported. Compared with the previously determined Tim50(164–361) structure, significant conformational chang...
Source: Acta Crystallographica Section F - August 25, 2015 Category: Biochemistry Authors: Li, J.Sha, B. Tags: Tim50 preprotein transport IMS domain research communications Source Type: research

Cloning, expression, purification and crystallization of a pair of novel virulence factors, SghA and SghR, from Agrobacterium tumefaciens
Two proteins, SghA and SghR, which were recently identified and characterized as novel bacterial virulence factors regulating the infection of plant hosts by Agrobacterium, were cloned, overexpressed and purified with high yield. Both SghA and SghR form dimers in solution. The purified SghA and SghR were crystallized and the crystals diffracted to 1.9 and 2.1 Å resolution, respectively. Data were collected and processed, and the crystallographic parameters were within acceptable ranges. These results will help in the determination of their structures in order to uncover the molecular mechanism of how these two prot...
Source: Acta Crystallographica Section F - August 25, 2015 Category: Biochemistry Authors: Ye, F.Wang, C.Fu, Q.Zhang, L.Gao, Y.G. Tags: SghA SghR crystallization virulence factor Agrobacterium plant – microbe interaction salicylic acid lacI chemical signal glucosidase research communications Source Type: research

Crystallization and crystallographic studies of kallistatin
Kallistatin is a serine protease inhibitor (serpin) which specifically inhibits human tissue kallikrein; however, its inhibitory activity is inhibited by heparin. In order to elucidate the underlying mechanism, recombinant human kallistatin was prepared in Escherichia coli and the protein was crystallized by the sitting-drop vapour-diffusion method. X-ray diffraction data were collected to 1.9 Å resolution. The crystals were found to belong to space group P61, with unit-cell parameters a = 113.51, b = 113.51, c = 76.17 Å. Initial analysis indicated that the crystallized kallistatin was in a relaxed conforma...
Source: Acta Crystallographica Section F - August 25, 2015 Category: Biochemistry Authors: Lin, F.Zhou, A.Wei, Z. Tags: kallistatin tissue kallikrein crystallization serpins heparin research communications Source Type: research

X-ray crystallographic studies of the middle part of the human synaptonemal complex protein 1 coiled-coil domain
In this study, the short form of the coiled-coil domain of SYCP1 was overexpressed in Escherichia coli with an engineered C-terminal His tag. The short form of the coiled-coil domain of SYCP1 was then purified to homogeneity and crystallized at 293 K. X-ray diffraction data were collected to a resolution of 3.0 Å from a crystal belonging to space group I4, with unit-cell parameters a = 41.95, b = 41.95, c = 318.78 Å. The asymmetric unit was estimated to contain two molecules. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - August 25, 2015 Category: Biochemistry Authors: Park, H.H. Tags: meiosis syneptonemal complex SYCP1 coiled-coil domain crystallization research communications Source Type: research

Structure of RizA, an l-amino-acid ligase from Bacillus subtilis
RizA is an l-amino-acid ligase from Bacillus subtilis that participates in the biosynthesis of rhizocticin, an oligopeptide antibiotic. The substrate-free form of RizA has been crystallized and the structure was solved at 2.8 Å resolution. The amino-acid-binding site appears to be capable of accommodating multiple amino acids, consistent with previous biochemical studies. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - August 25, 2015 Category: Biochemistry Authors: Kagawa, W.Arai, T.Ishikura, S.Kino, K.Kurumizaka, H. Tags: l-amino-acid ligase ATP-grasp fold rhizocticin dipeptide synthesis research communications Source Type: research

Crystallographic studies of the structured core domain of Knr4 from Saccharomyces cerevisiae
The potentially structured core domain of the intrinsically disordered protein Knr4 from Saccharomyces cerevisiae, comprising residues 80–340, was expressed in Escherichia coli and crystallized using the hanging-drop vapour-diffusion method. Selenomethionine-containing (SeMet) protein was also purified and crystallized. Crystals of both proteins belonged to space group P6522, with unit-cell parameters a = b = 112.44, c = 265.21 Å for the native protein and a = b = 112.49, c = 262.21 Å for the SeMet protein, and diffracted to 3.50 and 3.60 Å resolution, respectively. There a...
Source: Acta Crystallographica Section F - August 25, 2015 Category: Biochemistry Authors: Julien, S.Tondl, P.Durand, F.Dagkessamanskaia, A.van Tilbeurgh, H.François, J.M.Mourey, L.Zerbib, D.Martin-Yken, H.Maveyraud, L. Tags: intrinsically disordered proteins hub proteins Saccharomyces cerevisiae cell-wall biogenesis regulation research communications Source Type: research

Structure of the 14-3-3ζ–LKB1 fusion protein provides insight into a novel ligand-binding mode of 14-3-3
The 14-3-3 proteins are a family of highly conserved proteins that play key roles in many cellular processes. The tumour suppressor LKB1 regulates cell polarity, cell growth and energy metabolism. 14-3-3 proteins bind to LKB1 and suppress its functions. Previously, preliminary crystallographic data for the 14-3-3ζ–LKB1 fusion protein have been reported. Here, the crystal structure of this fusion protein was solved and a novel potential binding mode of 14-3-3 to its ligands was found. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - August 25, 2015 Category: Biochemistry Authors: Ding, S.Zhou, R.Zhu, Y. Tags: LKB1 tumour supressors 14-3-3 ζ crystal structure research communications Source Type: research

Crystallization and crystallographic analysis of branching enzymes from Cyanothece sp. ATCC 51142
Several cyanobacterial species, including Cyanothece sp. ATCC 51142, remarkably have four isoforms of α-glucan branching enzymes (BEs). Based on their primary structures, they are classified into glycoside hydrolase (GH) family 13 (BE1, BE2 and BE3) or family 57 (GH57 BE). In the present study, GH13-type BEs from Cyanothece sp. ATCC 51142 (BE1, BE2 and BE3) have been overexpressed in Escherichia coli and biochemically characterized. The recombinant BE1 was crystallized by the hanging-drop vapour-diffusion method. Crystals of BE1 were obtained at 293 K in the presence of 0.2 M Mg2+, 7–10%(w/v) ethanol, 0.1...
Source: Acta Crystallographica Section F - July 29, 2015 Category: Biochemistry Authors: Hayashi, M.Suzuki, R.Colleoni, C.Ball, S.G.Fujita, N.Suzuki, E. Tags: cyanobacteria Cyanothece glycogen amylopectin branching enzyme research communications Source Type: research

Structural analysis of Clostridium acetobutylicum ATCC 824 glycoside hydrolase from CAZy family GH105
Clostridium acetobutylicum ATCC 824 gene CA_C0359 encodes a putative unsaturated rhamnogalacturonyl hydrolase (URH) with distant amino-acid sequence homology to YteR of Bacillus subtilis strain 168. YteR, like other URHs, has core structural homology to unsaturated glucuronyl hydrolases, but hydrolyzes the unsaturated disaccharide derivative of rhamnogalacturonan I. The crystal structure of the recombinant CA_C0359 protein was solved to 1.6 Å resolution by molecular replacement using the phase information of the previously reported structure of YteR (PDB entry 1nc5) from Bacillus subtilis strain 168. The YteR-like ...
Source: Acta Crystallographica Section F - July 29, 2015 Category: Biochemistry Authors: Germane, K.L.Servinsky, M.D.Gerlach, E.S.Sund, C.J.Hurley, M.M. Tags: Clostridium acetobutylicum pectin unsaturated rhamnogalacturonyl hydrolase glycoside hydrolase GH105 research communications Source Type: research

Structure of GUN4 from Chlamydomonas reinhardtii
The genomes uncoupled 4 (GUN4) protein stimulates chlorophyll biosynthesis by increasing the activity of Mg-chelatase, the enzyme that inserts magnesium into protoporphyrin IX (PPIX) in the chlorophyll biosynthesis pathway. One of the roles of GUN4 is in binding PPIX and Mg-PPIX. In eukaryotes, GUN4 also participates in plastid-to-nucleus signalling, although the mechanism for this is unclear. Here, the first crystal structure of a eukaryotic GUN4, from Chlamydomonas reinhardtii, is presented. The structure is in broad agreement with those of previously solved cyanobacterial structures. Most interestingly, conformational d...
Source: Acta Crystallographica Section F - July 29, 2015 Category: Biochemistry Authors: Tarahi Tabrizi, S.Langley, D.B.Harrop, S.J.Duff, A.P.Willows, R.D. Tags: genomes uncoupled chlorophyll biosynthesis plastid signalling magnesium chelatase protoporphyrin research communications Source Type: research

High-resolution crystal structure of cAMP-dependent protein kinase from Cricetulus griseus
Protein kinases (PKs) are dynamic regulators of numerous cellular processes. Their phosphorylation activity is determined by the conserved kinase core structure, which is maintained by the interaction and dynamics with associated domains or interacting proteins. The prototype enzyme for investigations to understand the activity and regulation of PKs is the catalytic subunit of cAMP-dependent protein kinase (PKAc). Major effects of functional regulation and ligand binding are driven by only minor structural modulations in protein–protein interactions. In order to resolve such minor structural differences, very high re...
Source: Acta Crystallographica Section F - July 29, 2015 Category: Biochemistry Authors: Kudlinzki, D.Linhard, V.L.Saxena, K.Sreeramulu, S.Gande, S.Schieborr, U.Dreyer, M.Schwalbe, H. Tags: PKA kinase serine/threonine protein kinase transferase NTP binding cAMP nucleotide binding ATP binding research communications Source Type: research

Crystallographic analysis of archaeal ribosomal protein L11
Ribosomal protein L11 is an important part of the GTPase-associated centre in ribosomes of all organisms. L11 is a highly conserved two-domain ribosomal protein. The C-terminal domain of L11 is an RNA-binding domain that binds to a fragment of 23S rRNA and stabilizes its structure. The complex between L11 and 23S rRNA is involved in the GTPase activity of the translation elongation and release factors. Bacterial and archaeal L11–rRNA complexes are targets for peptide antibiotics of the thiazole class. To date, there is no complete structure of archaeal L11 owing to the mobility of the N-terminal domain of the protein...
Source: Acta Crystallographica Section F - July 29, 2015 Category: Biochemistry Authors: Mitroshin, I.Garber, M.Gabdulkhakov, A. Tags: ribosome archaea L11 ribosomal stalk research communications Source Type: research

Expression, purification, crystallization and X-ray crystallographic analysis of the periplasmic binding protein VatD from Vibrio vulnificus M2799
Vibrio vulnificus is a halophilic marine microorganism which causes gastroenteritis and primary septicaemia in humans. An important factor that determines the survival of V. vulnificus in the human body is its ability to acquire iron. VatD is a periplasmic siderophore-binding protein from V. vulnificus M2799. The current study reports the expression, purification and crystallization of VatD. Crystals of both apo VatD and a VatD–desferrioxamine B–Fe3+ (VatD–FOB) complex were obtained. The crystal of apo VatD belonged to space group P6422, while the crystal of the VatD–FOB complex belonged to space gr...
Source: Acta Crystallographica Section F - July 29, 2015 Category: Biochemistry Authors: Miyano, N.Igarashi, T.Kawano, H.Miyamoto, K.Tsuchiya, T.Tomoo, K.Tsujibo, H. Tags: Vibrio vulnificus periplasmic binding protein siderophore iron desferrioxamine B research communications Source Type: research

Crystallization, neutron data collection, initial structure refinement and analysis of a xyloglucan heptamer bound to an engineered carbohydrate-binding module from xylanase
Carbohydrate-binding modules (CBMs) are discrete parts of carbohydrate-hydrolyzing enzymes that bind specific types of carbohydrates. Ultra high-resolution X-ray crystallographic studies of CBMs have helped to decipher the basis for specificity in carbohydrate–protein interactions. However, additional studies are needed to better understand which structural determinants confer which carbohydrate-binding properties. To address these issues, neutron crystallographic studies were initiated on one experimentally engineered CBM derived from a xylanase, X-2 L110F, a protein that is able to bind several different plant carb...
Source: Acta Crystallographica Section F - July 29, 2015 Category: Biochemistry Authors: Ohlin, M.von Schantz, L.Schrader, T.E.Ostermann, A.Logan, D.T.Fisher, S.Z. Tags: carbohydrate-binding module neutron crystallography hydrogen bond research communications Source Type: research

Structure of GTP-specific succinyl-CoA synthetase in complex with CoA
Pig GTP-specific succinyl-CoA synthetase is an αβ-heterodimer. The crystal structure of the complex with the substrate CoA was determined at 2.1 Å resolution. The structure shows CoA bound to the amino-terminal domain of the α-subunit, with the free thiol extending from the adenine portion into the site where the catalytic histidine residue resides. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - July 29, 2015 Category: Biochemistry Authors: Huang, J.Malhi, M.Deneke, J.Fraser, M.E. Tags: ligase ATP-grasp fold research communications Source Type: research

Crystallographic analysis of RsmA, a ribosomal RNA small subunit methyltransferase A from Staphylococcus aureus
In this study, RsmA from Staphylococcus aureus was cloned, expressed, purified and crystallized. The crystal belonged to space group C2, with unit-cell parameters a = 84.38, b = 157.76, c = 96.50 Å, β = 95.04°. X-ray diffraction data were collected to a resolution of 3.2 Å. The self-rotation function and the Matthews coefficient suggested the presence of two molecules in the asymmetric unit. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - July 29, 2015 Category: Biochemistry Authors: Liu, Y.Zhu, Y.Teng, M.Li, X. Tags: methyltransferase RsmA RNA methylation research communications Source Type: research

Structure of BbKI, a disulfide-free plasma kallikrein inhibitor
A serine protease inhibitor from Bauhinia bauhinioides (BbKI) belongs to the Kunitz family of plant inhibitors, which are common in plant seeds. BbKI does not contain any disulfides, unlike most other members of this family. It is a potent inhibitor of plasma kallikrein, in addition to other serine proteases, and thus exhibits antithrombotic activity. A high-resolution crystal structure of recombinantly expressed BbKI was determined (at 1.4 Å resolution) and was compared with the structures of other members of the family. Modeling of a complex of BbKI with plasma kallikrein indicates that changes in the local struc...
Source: Acta Crystallographica Section F - July 29, 2015 Category: Biochemistry Authors: Zhou, D.Hansen, D.Shabalin, I.G.Gustchina, A.Vieira, D.F.de Brito, M.V.Araújo, A.P.U.Oliva, M.L.V.Wlodawer, A. Tags: β -trefoil Kunitz inhibitor kallikrein crystal structure research communications Source Type: research

Structure of human Roquin-2 and its complex with constitutive-decay element RNA
Roquin mediates mRNA degradation by recognizing the constitutive-decay element (CDE) in the 3′ untranslated region of the target gene followed by recruitment of the deadenylation machinery. Deficiency or dysfunction of Roquin has been associated with autoimmunity and inflammation. To establish the structural basis for the recognition of CDE RNA by Roquin, the crystal structure of the ROQ domain of human Roquin-2 was determined in ligand-free and CDE-derived RNA-bound forms. The ROQ domain of Roquin-2 folded into a winged-helix structure in which the wing region showed structural flexibility and acted as a lid for RNA...
Source: Acta Crystallographica Section F - July 29, 2015 Category: Biochemistry Authors: Sakurai, S.Ohto, U.Shimizu, T. Tags: Roquin mRNA degradation winged-helix motif stem-loop structure research communications Source Type: research

Crystal structure analysis of c4763, a uropathogenic Escherichia coli-specific protein
Urinary-tract infections (UTIs), which are some of the most common infectious diseases in humans, can cause sepsis and death without proper treatment. Therefore, it is necessary to understand their pathogenicity for proper diagnosis and therapeutics. Uropathogenic Escherichia coli, the major causative agents of UTIs, contain several genes that are absent in nonpathogenic strains and are therefore considered to be relevant to UTI pathogenicity. c4763 is one of the uropathogenic E. coli-specific proteins, but its function is unknown. To investigate the function of c4763 and its possible role in UTI pathogenicity, its crystal...
Source: Acta Crystallographica Section F - July 29, 2015 Category: Biochemistry Authors: Kim, H.Choi, J.Kim, D.Kim, K.K. Tags: uropathogenic bacteria crystal allophanate hydrolase urea urinary-tract infection research communications Source Type: research

In vivo protein crystallization in combination with highly brilliant radiation sources offers novel opportunities for the structural analysis of post-translationally modified eukaryotic proteins
During the last decade, the number of three-dimensional structures solved by X-ray crystallography has increased dramatically. By 2014, it had crossed the landmark of 100 000 biomolecular structures deposited in the Protein Data Bank. This tremendous increase in successfully crystallized proteins is primarily owing to improvements in cloning strategies, the automation of the crystallization process and new innovative approaches to monitor crystallization. However, these improvements are mainly restricted to soluble proteins, while the crystallization and structural analysis of membrane proteins or proteins that undergo m...
Source: Acta Crystallographica Section F - July 28, 2015 Category: Biochemistry Authors: Duszenko, M.Redecke, L.Mudogo, C.N.Sommer, B.P.Mogk, S.Oberthuer, D.Betzel, C. Tags: in vivo crystallization serial femtosecond crystallography X-ray free-electron laser expression systems research communications Source Type: research

Crystallographic studies of SarV, a global regulator from Staphylococcus aureus
In this study, SarV from S. aureus was successfully cloned, expressed, purified and crystallized. X-ray diffraction data were collected to 2.10 Å resolution. The crystals of SarV belonged to the monoclinic space group P21, with unit-cell parameters a = 36.40, b = 119.64, c = 66.80 Å, α = γ = 90, β = 98.75°. The Matthews coefficient and the solvent content were estimated to be 2.57 Å3 Da−1 and 52%, respectively, suggesting the presence of four molecules in the asymmetric unit. The results of size-exclusion chromatography (SEC) indicated that S. aureus SarV exists as a hom...
Source: Acta Crystallographica Section F - July 28, 2015 Category: Biochemistry Authors: Song, Y.Zhang, F.Li, X.Zang, J.Zhang, X. Tags: SarV global regulator Staphylococcus aureus autolysis crystallographic study research communications Source Type: research

Crystallographic analysis of NosA, which catalyzes terminal amide formation in the biosynthesis of nosiheptide
Nosiheptide is a member of the thiopeptide family of antibiotics which demonstrates potent activities against various bacterial pathogens. The formation of its C-terminal amide is catalysed by NosA in an unusual strategy for maturating certain thiopeptides by processing precursor peptides featuring a serine extension. Here, a recombinant C-terminally truncated selenomethionine-derivatized NosA1–111 variant from Streptomyces actuosus consisting of residues 1–111, named SeMet NosA1–111, was crystallized using the sitting-drop vapour-diffusion method. Diffraction data were collected to 2.40 Å resolut...
Source: Acta Crystallographica Section F - July 28, 2015 Category: Biochemistry Authors: Wang, Y.Liu, S.Yao, P.Yu, Y.Zhang, Y.Lan, W.Wang, C.Ding, J.Liu, W.Cao, C. Tags: nosiheptide NosA catalysis crystallization research communications Source Type: research

Overproduction, crystallization and X-ray diffraction data analysis of ectoine synthase from the cold-adapted marine bacterium Sphingopyxis alaskensis
Ectoine biosynthetic genes (ectABC) are widely distributed in bacteria. Microorganisms that carry them make copious amounts of ectoine as a cell protectant in response to high-osmolarity challenges. Ectoine synthase (EctC; EC 4.2.1.108) is the key enzyme for the production of this compatible solute and mediates the last step of ectoine biosynthesis. It catalyzes the ring closure of the cyclic ectoine molecule. A codon-optimized version of ectC from Sphingopyxis alaskensis (Sa) was used for overproduction of SaEctC protein carrying a Strep-tag II peptide at its carboxy-terminus. The recombinant SaEctC-Strep-tag II protein w...
Source: Acta Crystallographica Section F - July 28, 2015 Category: Biochemistry Authors: Kobus, S.Widderich, N.Hoeppner, A.Bremer, E.Smits, S.H.J. Tags: compatible solute osmostress protectant chemical chaperone enzyme ectoine synthesis cupin X-ray analysis research communications Source Type: research

Structures of Pseudomonas aeruginosa β-ketoacyl-(acyl-carrier-protein) synthase II (FabF) and a C164Q mutant provide templates for antibacterial drug discovery and identify a buried potassium ion and a ligand-binding site that is an artefact of the crystal form
Bacterial infections remain a serious health concern, in particular causing life-threatening infections of hospitalized and immunocompromised patients. The situation is exacerbated by the rise in antibacterial drug resistance, and new treatments are urgently sought. In this endeavour, accurate structures of molecular targets can support early-stage drug discovery. Here, crystal structures, in three distinct forms, of recombinant Pseudomonas aeruginosa β-ketoacyl-(acyl-carrier-protein) synthase II (FabF) are presented. This enzyme, which is involved in fatty-acid biosynthesis, has been validated by genetic and chemical...
Source: Acta Crystallographica Section F - July 28, 2015 Category: Biochemistry Authors: Baum, B.Lecker, L.S.M.Zoltner, M.Jaenicke, E.Schnell, R.Hunter, W.N.Brenk, R. Tags: fatty-acid biosynthesis FabF Gram-negative bacteria potassium binding Pseudomonas aeruginosa structure-based drug discovery research communications Source Type: research

Crystallographic analysis of FAD-dependent glucose dehydrogenase
An FAD-dependent glucose dehydrogenase (GDH) from Aspergillus terreus was purified and crystallized at 293 K using the sitting-drop vapour-diffusion method. A data set was collected to a resolution of 1.6 Å from a single crystal at 100 K using a rotating-anode X-ray source. The crystal belonged to space group P21, with unit-cell parameters a = 56.56, b = 135.74, c = 74.13 Å, β = 90.37°. The asymmetric unit contained two molecules of GDH. The Matthews coefficient was calculated to be 2.2 Å3 Da−1 and the solvent content was estimated to be 44%. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - July 28, 2015 Category: Biochemistry Authors: Komori, H.Inaka, K.Furubayashi, N.Honda, M.Higuchi, Y. Tags: glucose dehydrogenase FAD glucose sensor research communications Source Type: research

Crystallographic studies of aspartate racemase from Lactobacillus sakei NBRC 15893
Aspartate racemase catalyzes the interconversion between l-aspartate and d-aspartate and belongs to the PLP-independent racemases. The enzyme from the lactic acid bacterium Lactobacillus sakei NBRC 15893, isolated from kimoto, is considered to be involved in d-aspartate synthesis during the brewing process of Japanese sake at low temperatures. The enzyme was crystallized at 293 K by the sitting-drop vapour-diffusion method using 25%(v/v) PEG MME 550, 5%(v/v) 2-propanol. The crystal belonged to space group P3121, with unit-cell parameters a = b = 104.68, c = 97.29 Å, and diffracted to 2.6 Å resolution. Str...
Source: Acta Crystallographica Section F - July 28, 2015 Category: Biochemistry Authors: Fujii, T.Yamauchi, T.Ishiyama, M.Gogami, Y.Oikawa, T.Hata, Y. Tags: aspartate racemase Lactobacillus sakei d-amino acid crystallization research communications Source Type: research

Structure of α-carbonic anhydrase from the human pathogen Helicobacter pylori
The crystal structure of α-carbonic anhydrase, an enzyme present in the periplasm of Helicobacter pylori, a bacterium that affects humans and that is responsible for several gastric pathologies, is described. Two enzyme monomers are present in the asymmetric unit of the monoclinic space group P21, forming a dimer in the crystal. Despite the similarity of the enzyme structure to those of orthologues from other species, the H. pylori protein has adopted peculiar features in order to allow the bacterium to survive in the difficult environment of the human stomach. In particular, the crystal structure shows how the bacte...
Source: Acta Crystallographica Section F - July 28, 2015 Category: Biochemistry Authors: Compostella, M.E.Berto, P.Vallese, F.Zanotti, G. Tags: Helicobacter pylori carbonic anhydrase metalloproteins periplasmic protein research communications Source Type: research

Phormidium phycoerythrin forms hexamers in crystals: a crystallographic study
The crystallographic analysis of a marine cyanobacterium (Phormidium sp. A09DM) phycoerythrin (PE) that shows distinct sequence features compared with known PE structures from cyanobacteria and red algae is reported. Phormidium PE was crystallized using the sitting-drop vapour-diffusion method with ammonium sulfate as a precipitant. Diffraction data were collected on the protein crystallography beamline at the Indus-2 synchrotron. The crystals diffracted to about 2.1 Å resolution at 100 K. The crystals, with an apparent hexagonal morphology, belonged to space group P1, with unit-cell parameters a = 108.3, b = 108...
Source: Acta Crystallographica Section F - July 28, 2015 Category: Biochemistry Authors: Sonani, R.R.Sharma, M.Gupta, G.D.Kumar, V.Madamwar, D. Tags: phycoerythrin crystal structure X-ray diffraction research communications Source Type: research

Cloning, expression, purification and crystallographic studies of galectin-11 from domestic sheep (Ovis aries)
Galectins are an evolutionarily conserved family of proteins that translate glycan recognition into cellular effects. Galectin-11 is a unique member of the galectin family that is only expressed in ruminants such as sheep, goat and cattle and that plays a critical role in several important biological processes, such as reproduction and parasite-mediated innate immune responses. Currently, these two areas are of major importance for the sustainability of ruminant livestock production. Despite the emerging biological significance of galectin-11, no structural information is available. It is expected that structural studies w...
Source: Acta Crystallographica Section F - July 28, 2015 Category: Biochemistry Authors: Sakthivel, D.Littler, D.Shahine, A.Troy, S.Johnson, M.Rossjohn, J.Piedrafita, D.Beddoe, T. Tags: galectin parasite glycan livestock research communications Source Type: research

The soluble Y115E–Y117E variant of human glutaminyl cyclase is a valid target for X-ray and NMR screening of inhibitors against Alzheimer disease
Recent developments in molecular pathology and genetics have allowed the identification of human glutaminyl cyclase (hQC) among the abnormal proteins involved in many neurodegenerative disorders. Difficulties in obtaining large quantities of pure protein may limit the use of crystallographic screening for drug development on this target. Site-directed mutagenesis experiments have led to the identification of some solvent-exposed residues that are absolutely critical to achieve increased solubility and to avoid precipitation of the enzyme in inclusion bodies when expressed in Escherichia coli. The designed variant Y115E&nda...
Source: Acta Crystallographica Section F - July 28, 2015 Category: Biochemistry Authors: DiPisa, F.Pozzi, C.Benvenuti, M.Andreini, M.Marconi, G.Mangani, S. Tags: glutaminyl cyclase Alzheimer disease inhibitor screening crystal structure inhibitors research communications Source Type: research

Structure of the human MLH1 N-terminus: implications for predisposition to Lynch syndrome
Mismatch repair prevents the accumulation of erroneous insertions/deletions and non-Watson–Crick base pairs in the genome. Pathogenic mutations in the MLH1 gene are associated with a predisposition to Lynch and Turcot's syndromes. Although genetic testing for these mutations is available, robust classification of variants requires strong clinical and functional support. Here, the first structure of the N-terminus of human MLH1, determined by X-ray crystallography, is described. The structure shares a high degree of similarity with previously determined prokaryotic MLH1 homologs; however, this structure affords a more...
Source: Acta Crystallographica Section F - July 28, 2015 Category: Biochemistry Authors: Wu, H.Zeng, H.Lam, R.Tempel, W.Kerr, I.D.Min, J. Tags: ATPase GHKL Lynch syndrome mismatch repair research communications Source Type: research

Crystallographic analysis of the N-terminal domain of Middle East respiratory syndrome coronavirus nucleocapsid protein
In this study, the crystallization and crystallographic analysis of MERS-CoV NP-NTD (amino acids 39–165), with a molecular weight of 14.7 kDa, are reported. MERS-CoV NP-NTD was crystallized at 293 K using PEG 3350 as a precipitant and a 94.5% complete native data set was collected from a cooled crystal at 77 K to 2.63 Å resolution with an overall Rmerge of 9.6%. The crystals were monoclinic and belonged to space group P21, with unit-cell parameters a = 35.60, b = 109.64, c = 91.99 Å, β = 101.22°. The asymmetric unit contained four MERS-CoV NP-NTD molecules. (Source: Acta Cryst...
Source: Acta Crystallographica Section F - July 28, 2015 Category: Biochemistry Authors: Wang, Y.-S.Chang, C.Hou, M.-H. Tags: Middle East respiratory syndrome coronavirus nucleocapsid protein N-terminal domain RNA binding research communications Source Type: research

Purification and crystallographic analysis of a FAD-dependent halogenase from Streptomyces sp. JCM9888
This study reports the overexpression and purification of HalY with an N-terminal hexahistidine tag, followed by crystallization experiments and X-ray crystallographic analysis. HalY was purified as a monomer in solution and crystallized to give X-ray diffraction to a resolution of 1.7 Å. The crystal belonged to the monoclinic space group P21, with unit-cell parameters a = 41.4, b = 113.4, c = 47.6 Å, α = γ = 90, β = 107.4°, and contained one monomer of HalY in the asymmetric unit, with a calculated Matthews coefficient of 2.3 Å3 Da−1 and a solvent content of 46%. The st...
Source: Acta Crystallographica Section F - July 28, 2015 Category: Biochemistry Authors: Zhao, Y.Yan, B.Yang, T.Jiang, J.Wei, H.Zhu, X. Tags: FAD-dependent halogenase regioselective halogenation adenine research communications Source Type: research

Structure of the response regulator ChrA in the haem-sensing two-component system of Corynebacterium diphtheriae
ChrA is a response regulator (RR) in the two-component system involved in regulating the degradation and transport of haem (Fe–porphyrin) in the pathogen Corynebacterium diphtheriae. Here, the crystal structure of full-length ChrA is described at a resolution of 1.8 Å. ChrA consists of an N-terminal regulatory domain, a long linker region and a C-terminal DNA-binding domain. A structural comparison of ChrA with other RRs revealed substantial differences in the relative orientation of the two domains and the conformation of the linker region. The structural flexibility of the linker could be an important featu...
Source: Acta Crystallographica Section F - July 28, 2015 Category: Biochemistry Authors: Doi, A.Nakamura, H.Shiro, Y.Sugimoto, H. Tags: transcription factor X-ray crystallography haem helix – turn phosphorylation research communications Source Type: research