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 22, 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 22, 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 22, 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 22, 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 22, 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 22, 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 22, 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 23, 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 23, 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 23, 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 23, 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 23, 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 23, 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 126.96.36.199–4) 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 23, 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 23, 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 23, 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 23, 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 23, 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 23, 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 23, 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 22, 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 22, 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 22, 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
Structural and functional insights into the stationary-phase survival protein SurE, an important virulence factor of Brucella abortus
The stationary-phase survival protein SurE from Brucella abortus (BaSurE) is a metal-dependent phosphatase that is essential for the survival of this bacterium in the stationary phase of its life cycle. Here, BaSurE has been biochemically characterized and its crystal structure has been determined to a resolution of 1.9 Å. BaSurE was found to be a robust enzyme, showing activity over wide ranges of temperature and pH and with various phosphoester substrates. The active biomolecule is a tetramer and each monomer was found to consist of two domains: an N-terminal domain, which forms an approximate α + β fo...
Source: Acta Crystallographica Section F - April 22, 2016 Category: Biochemistry Authors: Tarique, K.F.Abdul Rehman, S.A.Devi, S.Tomar, P.Gourinath, S. Tags: stationary-phase survival protein nucleotidase Brucella abortus phagosome domain swapping Rossmann fold malachite green assay research communications Source Type: research
The periplasmic sensing domain of Vibrio fischeri chemoreceptor protein A (VfcA): cloning, purification and crystallographic analysis
Flagella-mediated motility and chemotaxis towards nutrients are important characteristics of Vibrio fischeri that play a crucial role in the development of its symbiotic relationship with its Hawaiian squid host Euprymna scolopes. The V. fischeri chemoreceptor A (VfcA) mediates chemotaxis toward amino acids. The periplasmic sensory domain of VfcA has been crystallized by the hanging-drop vapour-diffusion method using polyethylene glycol 3350 as a precipitating agent. The crystals belonged to space group P1, with unit-cell parameters a = 39.9, b = 57.0, c = 117.0 Å, α = 88.9, β = 80.5, γ =...
Source: Acta Crystallographica Section F - April 22, 2016 Category: Biochemistry Authors: Salah Ud-Din, A.I.M.Roujeinikova, A. Tags: bacterial chemotaxis receptor sensing domain methyl-accepting protein research communications Source Type: research
Crystal structure of bile salt hydrolase from Lactobacillus salivarius
Bile salt hydrolase (BSH) is a gut-bacterial enzyme that negatively influences host fat digestion and energy harvesting. The BSH enzyme activity functions as a gateway reaction in the small intestine by the deconjugation of glycine-conjugated or taurine-conjugated bile acids. Extensive gut-microbiota studies have suggested that BSH is a key mechanistic microbiome target for the development of novel non-antibiotic food additives to improve animal feed production and for the design of new measures to control obesity in humans. However, research on BSH is still in its infancy, particularly in terms of the structural basis of ...
Source: Acta Crystallographica Section F - April 22, 2016 Category: Biochemistry Authors: Xu, F.Guo, F.Hu, X.-J.Lin, J. Tags: bile salt hydrolase Lactobacillus lipid metabolism gut microbiome crystal structure research communications Source Type: research
Crystal structure of ketopantoate reductase from Thermococcus kodakarensis complexed with NADP+
Coenzyme A (CoA) plays pivotal roles in a variety of metabolic pathways in all organisms. The biosynthetic pathway of CoA is strictly regulated by feedback inhibition. In the hyperthermophilic archaeon Thermococcus kodakarensis, ketopantoate reductase (KPR), which catalyzes the NAD(P)H-dependent reduction of 2-oxopantoate, is a target of feedback inhibition by CoA. The crystal structure of KPR from T. kodakarensis (Tk-KPR) complexed with CoA and 2-oxopantoate has previously been reported. The structure provided an explanation for the competitive inhibition mechanism. Here, further biochemical analyses of Tk-KPR and the cry...
Source: Acta Crystallographica Section F - April 22, 2016 Category: Biochemistry Authors: Aikawa, Y.Nishitani, Y.Tomita, H.Atomi, H.Miki, K. Tags: coenzyme A feedback inhibition competitive inhibition hyperthermophilic archaea research communications Source Type: research
Structural analysis of a phosphonate hydroxylase with an access tunnel at the back of the active site
FrbJ is a member of the Fe2+/α-ketoglutarate-dependent dioxygenase family which hydroxylates the natural product FR-900098 of Streptomyces rubellomurinus, yielding the phosphonate antibiotic FR-33289. Here, the crystal structure of FrbJ, which shows structural homology to taurine dioxygenase (TauD), a key member of the same family, is reported. Unlike other members of the family, FrbJ has an unusual lid structure which consists of two β-strands with a long loop between them. To investigate the role of this lid motif, a molecular-dynamics simulation was performed with the FrbJ structure. The molecular-dynamics si...
Source: Acta Crystallographica Section F - April 22, 2016 Category: Biochemistry Authors: Li, C.Junaid, M.Almuqri, E.A.Hao, S.Zhang, H. Tags: FrbJ hydroxylase crystal structure access tunnel research communications Source Type: research
The Myb domain of LUX ARRHYTHMO in complex with DNA: expression, purification and crystallization
LUX ARRHYTHMO (LUX) is a Myb-domain transcription factor that plays an important role in regulating the circadian clock. Lux mutations cause severe clock defects and arrhythmia in constant light and dark. In order to examine the molecular mechanisms underlying the function of LUX, the DNA-binding Myb domain was cloned, expressed and purified. The DNA-binding activity of the Myb domain was confirmed using electrophoretic mobility shift assays (EMSAs), demonstrating that the LUX Myb domain is able to bind to DNA with nanomolar affinity. In order to investigate the specificity determinants of protein–DNA interactions, t...
Source: Acta Crystallographica Section F - April 22, 2016 Category: Biochemistry Authors: Silva, C.S.Lai, X.Nanao, M.Zubieta, C. Tags: Myb domain DNA binding protein – DNA complex LUX ARRHYTHMO Arabidopsis thaliana research communications Source Type: research
Structures of endothiapepsin–fragment complexes from crystallographic fragment screening using a novel, diverse and affordable 96-compound fragment library
Crystallographic screening of the binding of small organic compounds (termed fragments) to proteins is increasingly important for medicinal chemistry-oriented drug discovery. To enable such experiments in a widespread manner, an affordable 96-compound library has been assembled for fragment screening in both academia and industry. The library is selected from already existing protein–ligand structures and is characterized by a broad ligand diversity, including buffer ingredients, carbohydrates, nucleotides, amino acids, peptide-like fragments and various drug-like organic compounds. When applied to the model protease...
Source: Acta Crystallographica Section F - April 22, 2016 Category: Biochemistry Authors: Huschmann, F.U.Linnik, J.Sparta, K.Ühlein, M.Wang, X.Metz, A.Schiebel, J.Heine, A.Klebe, G.Weiss, M.S.Mueller, U. Tags: structural biology medicinal chemistry fragment screening X-ray crystallography protein – ligand structures research communications Source Type: research
Co-crystal structures of the protein kinase haspin with bisubstrate inhibitors
Haspin is a mitotic protein kinase that is responsible for the phosphorylation of Thr3 of histone H3, thereby creating a recognition motif for docking of the chromosomal passenger complex that is crucial for the progression of cell division. Here, two high-resolution models of haspin with previously reported inhibitors consisting of an ATP analogue and a histone H3(1–7) peptide analogue are presented. The structures of the complexes confirm the bisubstrate character of the inhibitors by revealing the signature binding modes of the moieties targeting the ATP-binding site and the protein substrate-binding site of the k...
Source: Acta Crystallographica Section F - April 22, 2016 Category: Biochemistry Authors: Lavogina, D.Kestav, K.Chaikuad, A.Heroven, C.Knapp, S.Uri, A. Tags: protein kinase haspin histone inhibitor bisubstrate linker research communications Source Type: research
Response to Errors in Crystal structure of HINT from Helicobacter pylori
A response is published to a Letter to the Editor by Maize [(2016), Acta Cryst. F72, 336-337]. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - March 24, 2016 Category: Biochemistry Authors: Tarique, K.F.Devi, S.Abdul Rehman, S.A.Gourinath, S. Tags: HINT PKCI letters to the editor Source Type: research
Errors in Crystal structure of HINT from Helicobacter pylori
Inaccuracies in the article, Crystal structure of HINT from Helicobacter pylori by Tarique et al. [(2016) Acta Cryst. F72, 42–48] are presented, and a brief history of HINT nomenclature is discussed. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - March 24, 2016 Category: Biochemistry Authors: Maize, K.M. Tags: HINT PKCI letters to the editor Source Type: research
Crystal structure of CotA laccase complexed with 2,2-azinobis-(3-ethylbenzothiazoline-6-sulfonate) at a novel binding site
The CotA laccase from Bacillus subtilis is an abundant component of the spore outer coat and has been characterized as a typical laccase. The crystal structure of CotA complexed with 2,2-azinobis-(3-ethylbenzothiazoline-6-sulfonate) (ABTS) in a hole motif has been solved. The novel binding site was about 26 Å away from the T1 binding pocket. Comparison with known structures of other laccases revealed that the hole is a specific feature of CotA. The key residues Arg476 and Ser360 were directly bound to ABTS. Site-directed mutagenesis studies revealed that the residues Arg146, Arg429 and Arg476, which are located at ...
Source: Acta Crystallographica Section F - March 24, 2016 Category: Biochemistry Authors: Liu, Z.Xie, T.Zhong, Q.Wang, G. Tags: 2,2-azinobis-(3-ethylbenzothiazoline-6-sulfonate) laccase mutagenesis substrate binding protein engineering research communications Source Type: research
Crystal structure of a tankyrase 1–telomere repeat factor 1 complex
Telomere repeat factor 1 (TRF1) is a subunit of shelterin (also known as the telosome) and plays a critical role in inhibiting telomere elongation by telomerase. Tankyrase 1 (TNKS1) is a poly(ADP-ribose) polymerase that regulates the activity of TRF1 through poly(ADP-ribosyl)ation (PARylation). PARylation of TRF1 by TNKS1 leads to the release of TRF1 from telomeres and allows telomerase to access telomeres. The interaction between TRF1 and TNKS1 is thus important for telomere stability and the mitotic cell cycle. Here, the crystal structure of a complex between the N-terminal acidic domain of TRF1 (residues 1–55) and...
Source: Acta Crystallographica Section F - March 24, 2016 Category: Biochemistry Authors: Li, B.Qiao, R.Wang, Z.Zhou, W.Li, X.Xu, W.Rao, Z. Tags: TNKS tankyrase telomere TRF1 telomere repeat factor 1 PARylation complex structure research communications Source Type: research
Applications of thin-film sandwich crystallization platforms
Examples are shown of protein crystallization in, and data collection from, solutions sandwiched between thin polymer films using vapour-diffusion and batch methods. The crystallization platform is optimal for both visualization and in situ data collection, with the need for traditional harvesting being eliminated. In wells constructed from the thinnest plastic and with a minimum of aqueous liquid, flash-cooling to 100 K is possible without significant ice formation and without any degradation in crystal quality. The approach is simple; it utilizes low-cost consumables but yields high-quality data with minimal sample int...
Source: Acta Crystallographica Section F - March 24, 2016 Category: Biochemistry Authors: Axford, D.Aller, P.Sanchez-Weatherby, J.Sandy, J. Tags: protein crystallization devices in situ X-ray analysis crystal visual inspection diffraction data collection research communications Source Type: research
A novel microseeding method for the crystallization of membrane proteins in lipidic cubic phase
Random microseed matrix screening (rMMS), in which seed crystals are added to random crystallization screens, is an important breakthrough in soluble protein crystallization that increases the number of crystallization hits that are available for optimization. This greatly increases the number of soluble protein structures generated every year by typical structural biology laboratories. Inspired by this success, rMMS has been adapted to the crystallization of membrane proteins, making LCP seed stock by scaling up LCP crystallization conditions without changing the physical and chemical parameters that are critical for crys...
Source: Acta Crystallographica Section F - March 24, 2016 Category: Biochemistry Authors: Kolek, S.A.Bräuning, B.Shaw Stewart, P.D. Tags: membrane-protein crystallization microseeding lipidic cubic phase microseed matrix screening research communications Source Type: research
Crystal structure of histone-like protein from Streptococcus mutans refined to 1.9 Å resolution
Nucleoid-associated proteins (NAPs) in prokaryotes play an important architectural role in DNA bending, supercoiling and DNA compaction. In addition to architectural roles, some NAPs also play regulatory roles in DNA replication and repair, and act as global transcriptional regulators in many bacteria. Bacteria encode multiple NAPs and some of them are even essential for survival. Streptococcus mutans, a dental pathogen, encodes one such essential NAP called histone-like protein (HLP). Here, the three-dimensional structure of S. mutans HLP has been determined to 1.9 Å resolution. The HLP structure is a dimer and sh...
Source: Acta Crystallographica Section F - March 17, 2016 Category: Biochemistry Authors: O'Neil, P.Lovell, S.Mehzabeen, N.Battaile, K.Biswas, I. Tags: Streptococcus mutans HLP nucleoid-associated protein histone-like protein research communications Source Type: research
Crystal structures of Leishmania mexicana arginase complexed with α,α-disubstituted boronic amino-acid inhibitors
Leishmania arginase is a potential drug target for the treatment of leishmaniasis because this binuclear manganese metalloenzyme initiates de novo polyamine biosynthesis by catalyzing the hydrolysis of l-arginine to generate l-ornithine and urea. The product l-ornithine subsequently undergoes decarboxylation to yield putrescine, which in turn is utilized for spermidine biosynthesis. Polyamines such as spermidine are essential for the growth and survival of the parasite, so inhibition of enzymes in the polyamine-biosynthetic pathway comprises an effective strategy for treating parasitic infections. To this end, two X-ray cr...
Source: Acta Crystallographica Section F - March 16, 2016 Category: Biochemistry Authors: Hai, Y.Christianson, D.W. Tags: Leishmania mexicana arginase α , -disubstituted boronic amino-acid inhibitors research communications Source Type: research
Purification, crystallization and X-ray diffraction analysis of the DNA-binding domain of human heat-shock factor 2
Cells respond to various proteotoxic stimuli and maintain protein homeostasis through a conserved mechanism called the heat-shock response, which is characterized by the enhanced synthesis of heat-shock proteins. This response is mediated by heat-shock factors (HSFs). Four genes encoding HSF1–HSF4 exist in the genome of mammals. In this protein family, HSF1 is the orthologue of the single HSF in lower eukaryotic organisms and is the major regulator of the heat-shock response, while HSF2, which shows low sequence homology to HSF1, serves as a developmental regulator. Increasing evidence has revealed biochemical proper...
Source: Acta Crystallographica Section F - March 16, 2016 Category: Biochemistry Authors: Feng, H.Liu, W.Wang, D.-C. Tags: heat-shock factor DNA-binding domain transcription HSF2 research communications Source Type: research
Crystal structure of a putative exo-β-1,3-galactanase from Bifidobacterium bifidum S17
Given the current interest in second-generation biofuels, carbohydrate-active enzymes have become the most important tool to overcome the structural recalcitrance of the plant cell wall. While some glycoside hydrolase families have been exhaustively described, others remain poorly characterized, especially with regard to structural information. The family 43 glycoside hydrolases are a diverse group of inverting enzymes; the available structure information on these enzymes is mainly from xylosidases and arabinofuranosidase. Currently, only one structure of an exo-β-1,3-galactanase is available. Here, the production, cr...
Source: Acta Crystallographica Section F - March 16, 2016 Category: Biochemistry Authors: Godoy, A.S.de Lima, M.Z.T.Camilo, C.M.Polikarpov, I. Tags: galactanase Bifidobacterium GH43 family 43 hydrolase research communications Source Type: research
Isolation, crystallization and crystal structure determination of bovine kidney Na+,K+-ATPase
Na+,K+-ATPase is responsible for the transport of Na+ and K+ across the plasma membrane in animal cells, thereby sustaining vital electrochemical gradients that energize channels and secondary transporters. The crystal structure of Na+,K+-ATPase has previously been elucidated using the enzyme from native sources such as porcine kidney and shark rectal gland. Here, the isolation, crystallization and first structure determination of bovine kidney Na+,K+-ATPase in a high-affinity E2–BeF3−–ouabain complex with bound magnesium are described. Crystals belonging to the orthorhombic space group C2221 with one mol...
Source: Acta Crystallographica Section F - March 16, 2016 Category: Biochemistry Authors: Gregersen, J.L.Mattle, D.Fedosova, N.U.Nissen, P.Reinhard, L. Tags: P-type ATPase native source isolation cardiotonic steroids Na ,K -ATPase ouabain research communications Source Type: research
Binding of Gd3+ to the neuronal signalling protein calexcitin identifies an exchangeable Ca2+-binding site
Calexcitin was first identified in the marine snail Hermissenda crassicornis as a neuronal-specific protein that becomes upregulated and phosphorylated in associative learning. Calexcitin possesses four EF-hand motifs, but only the first three (EF-1 to EF-3) are involved in binding metal ions. Past work has indicated that under physiological conditions EF-1 and EF-2 bind Mg2+ and Ca2+, while EF-3 is likely to bind only Ca2+. The fourth EF-hand is nonfunctional owing to a lack of key metal-binding residues. The aim of this study was to use a crystallographic approach to determine which of the three metal-binding sites of ca...
Source: Acta Crystallographica Section F - March 16, 2016 Category: Biochemistry Authors: Chataigner, L.Guo, J.Erskine, P.T.Coker, A.R.Wood, S.P.Gombos, Z.Cooper, J.B. Tags: neuronal calcium signalling EF-hand protein structure heavy-atom complex co-crystallization research communications Source Type: research
Crystal structure of the substrate-recognition domain of the Shigella E3 ligase IpaH9.8
Infectious diseases caused by bacteria have significant impacts on global public health. During infection, pathogenic bacteria deliver a variety of virulence factors, called effectors, into host cells. The Shigella effector IpaH9.8 functions as an ubiquitin ligase, ubiquitinating the NF-κB essential modulator (NEMO)/IKK-γ to inhibit host inflammatory responses. IpaH9.8 contains leucine-rich repeats (LRRs) involved in substrate recognition and an E3 ligase domain. To elucidate the structural basis of the function of IpaH9.8, the crystal structure of the LRR domain of Shigella IpaH9.8 was determined and this stru...
Source: Acta Crystallographica Section F - March 16, 2016 Category: Biochemistry Authors: Takagi, K.Kim, M.Sasakawa, C.Mizushima, T. Tags: Shigella flexneri effector leucine-rich repeats IpaH9.8 E3 ligase research communications Source Type: research
Cloning, expression, purification and crystallization of Schizosaccharomyces pombe Set7, a putative histone methyltransferase
Dysfunction of histone-modifying enzymes affects chromatin regulation and is involved in carcinogenesis, tumour progression and other diseases. Histone methyltransferases are a family of key histone-modifying enzymes, but their structures, functions and mechanisms are incompletely understood, thus constraining drug-design efforts. Here, preliminary steps towards structure–function studies of Schizosaccharomyces pombe Set7, a putative histone methyltransferase and the first yeast full-length SET-domain-containing protein to be studied using X-ray crystallography, are reported. The methods from cloning to X-ray diffrac...
Source: Acta Crystallographica Section F - March 16, 2016 Category: Biochemistry Authors: Mevius, D.E.H.F.Shen, Y.Morishita, M.di Luccio, E. Tags: histone modifications histone methyltransferase Schizosaccharomyces pombe Set7 X-ray crystallography research communications Source Type: research
Applications of the second virial coefficient: protein crystallization and solubility. Corrigendum
A number of citations in the article by Wilson & DeLucas [(2014). Acta Cryst. F70, 543–554] are corrected. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - February 19, 2016 Category: Biochemistry Authors: Wilson, W.W.DeLucas, L.J. Tags: second virial coefficient crystallization solubility corrigendum addenda and errata Source Type: research
Re-refinement of 4g4a: room-temperature X-ray diffraction study of cisplatin and its binding to His15 of HEWL after 14 months chemical exposure in the presence of DMSO
A re-refinement of 4g4a, the room-temperature X-ray diffraction study of cisplatin and its binding to His15 of HEWL after 14 months chemical exposure in the presence of DMSO is published as an addendum to Tanley et al. [(2012), Acta Cryst. F68, 1300–1306]. This example illustrates the benefits of sharing raw diffraction images, as well as structure factors and molecular coordinates, as the diffraction resolution of the study is now much improved at 1.70 Å. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - February 19, 2016 Category: Biochemistry Authors: Tanley, S.W.M.Schreurs, A.M.M.Kroon-Batenburg, L.M.J.Helliwell, J.R. Tags: improved diffraction resolution raw diffraction images. re-refinement cisplatin histidine addendum addenda and errata Source Type: research
Re-refinement of 4xan: hen egg-white lysozyme with carboplatin in sodium bromide solution
A re-refinement of 4xan, hen egg-white lysozyme (HEWL) with carboplatin crystallized in NaBr solution, has been made and is published here as an addendum to Tanley et al. [(2014), Acta Cryst. F70, 1135–1142]. This follows a previous re-refinement and PDB deposition (4yem) by Shabalin et al. [(2015), Acta Cryst. D71, 1965–1979]. The critical evaluation of the original PDB deposition (4xan), and the subsequent critical examination of the re-refined structure (4yem), has led to an improved model (PDB code 5hmj). (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - February 19, 2016 Category: Biochemistry Authors: Tanley, S.W.M.Schreurs, A.M.M.Kroon-Batenburg, L.M.J.Helliwell, J.R. Tags: 4xan re-refinement raw diffraction data paired model refinement electron density assessment resolution limit assessment addendum addenda and errata Source Type: research
Crystal structure of recombinant tyrosinase-binding protein MtaL at 1.35 Å resolution
In this study, the crystal structure of recombinant MtaL is reported at 1.35 Å resolution. Comparison of its structure with that of the truncated and cleaved MtaL present in the complex with tyrosinase directly isolated from mushroom shows that the general β-trefoil fold is conserved. However, differences are detected in the loop regions, particularly in the β2–β3 loop, which is intact and not cleaved in the recombinant MtaL. Furthermore, the N-terminal tail is rotated inwards, covering the tyrosinase-binding interface. Thus, MtaL must undergo conformational changes in order to bind mature mush...
Source: Acta Crystallographica Section F - February 19, 2016 Category: Biochemistry Authors: Lai, X.Soler-Lopez, M.Ismaya, W.T.Wichers, H.J.Dijkstra, B.W. Tags: tyrosinase lectin tyrosinase-binding protein MtaL carbohydrate binding research communications Source Type: research
Crystallization and X-ray diffraction analysis of the CH domain of the cotton kinesin GhKCH2
GhKCH2 belongs to a group of plant-specific kinesins (KCHs) containing an actin-binding calponin homology (CH) domain in the N-terminus. Previous studies revealed that the GhKCH2 CH domain (GhKCH2-CH) had a higher affinity for F-actin (Kd = 0.42 ± 0.02 µM) than most other CH-domain-containing proteins. To understand the underlying mechanism, prokaryotically expressed GhKCH2-CH (amino acids 30–166) was purified and crystallized. Crystals were grown by the sitting-drop vapour-diffusion method using 0.1 M Tris–HCl pH 7.0, 20%(w/v) PEG 8000 as a precipitant. The crystals diffracted to a resolution ...
Source: Acta Crystallographica Section F - February 19, 2016 Category: Biochemistry Authors: Qin, X.Chen, Z.Li, P.Liu, G. Tags: plant-specific kinesin CH domain cotton kinesin GhKCH2 research communications Source Type: research