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Mark Levisson,
Gye Won Han,
Marc C Deller,
Qingping Xu,
Peter Biely,
Sjon Hendriks,
Lynn F Ten Eyck,
Claus Flensburg,
Pietro Roversi,
Mitchell D Miller, Daniel McMullan,
Frank von Delft,
Andreas Kreusch,
Ashley M Deacon,
John van der Oost,
Scott A Lesley,
Marc-André Elsliger,
Servé W M Kengen,
Ian A Wilson
[show abstract]
[hide abstract]
ABSTRACT: TM0077 from Thermotoga maritima is a member of the carbohydrate esterase family 7 and is active on a variety of acetylated compounds, including cephalosporin C. TM0077 esterase activity is confined to short-chain acyl esters (C2-C3), and is optimal around 100°C and pH 7.5. The positional specificity of TM0077 was investigated using 4-nitrophenyl-β-D-xylopyranoside monoacetates as substrates in a β-xylosidase-coupled assay. TM0077 hydrolyzes acetate at positions 2, 3, and 4 with equal efficiency. No activity was detected on xylan or acetylated xylan, which implies that TM0077 is an acetyl esterase and not an acetyl xylan esterase as currently annotated. Selenomethionine-substituted and native structures of TM0077 were determined at 2.1 and 2.5 Å resolution, respectively, revealing a classic α/β-hydrolase fold. TM0077 assembles into a doughnut-shaped hexamer with small tunnels on either side leading to an inner cavity, which contains the six catalytic centers. Structures of TM0077 with covalently bound phenylmethylsulfonyl fluoride and paraoxon were determined to 2.4 and 2.1 Å, respectively, and confirmed that both inhibitors bind covalently to the catalytic serine (Ser188). Upon binding of inhibitor, the catalytic serine adopts an altered conformation, as observed in other esterase and lipases, and supports a previously proposed catalytic mechanism in which Ser hydroxyl rotation prevents reversal of the reaction and allows access of a water molecule for completion of the reaction.
Proteins Structure Function and Bioinformatics 01/2012; 80(6):1545-59. · 3.39 Impact Factor
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Qingping Xu, Daniel McMullan,
Lukasz Jaroszewski,
S Sri Krishna,
Marc André Elsliger,
Andrew P Yeh,
Polat Abdubek,
Tamara Astakhova,
Herbert L Axelrod,
Dennis Carlton, [......],
Jessica Paulsen,
Ron Reyes,
Christopher L Rife,
Henry van den Bedem,
Keith O Hodgson,
John Wooley,
Ashley M Deacon,
Adam Godzik,
Scott A Lesley,
Ian A Wilson
[show abstract]
[hide abstract]
ABSTRACT: YeaZ is involved in a protein network that is essential for bacteria. The crystal structure of YeaZ from Thermotoga maritima was determined to 2.5 Å resolution. Although this protein belongs to a family of ancient actin-like ATPases, it appears that it has lost the ability to bind ATP since it lacks some key structural features that are important for interaction with ATP. A conserved surface was identified, supporting its role in the formation of protein complexes.
Acta Crystallographica Section F Structural Biology and Crystallization Communications 10/2010; 66(Pt 10):1230-6. · 0.51 Impact Factor
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Herbert L Axelrod,
Piotr Kozbial, Daniel McMullan,
S Sri Krishna,
Mitchell D Miller,
Polat Abdubek,
Claire Acosta,
Tamara Astakhova,
Dennis Carlton,
Jonathan Caruthers, [......],
Aprilfawn White,
Qingping Xu,
Chloe Zubieta,
Keith O Hodgson,
John Wooley,
Marc André Elsliger,
Ashley M Deacon,
Adam Godzik,
Scott A Lesley,
Ian A Wilson
[show abstract]
[hide abstract]
ABSTRACT: In the plant pathogen Xanthomonas campestris pv. campestris, the product of the tcmJ gene, XcTcmJ, encodes a protein belonging to the RmlC family of cupins. XcTcmJ was crystallized in a monoclinic space group (C2) in the presence of zinc acetate and the structure was determined to 1.6 Å resolution. Previously, the apo structure has been reported in the absence of any bound metal ion [Chin et al. (2006), Proteins, 65, 1046-1050]. The most significant difference between the apo structure and the structure of XcTcmJ described here is a reorganization of the binding site for zinc acetate, which was most likely acquired from the crystallization solution. This site is located in the conserved metal ion-binding domain at the putative active site of XcTcmJ. In addition, an acetate was also bound within coordination distance of the zinc. In order to accommodate this binding, rearrangement of a conserved histidine ligand is required as well as several nearby residues within and around the putative active site. These observations indicate that binding of zinc serves a functional role in this cupin protein.
Acta Crystallographica Section F Structural Biology and Crystallization Communications 10/2010; 66(Pt 10):1347-53. · 0.51 Impact Factor
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Constantina Bakolitsa,
Abhinav Kumar, Daniel McMullan,
S Sri Krishna,
Mitchell D Miller,
Dennis Carlton,
Rafael Najmanovich,
Polat Abdubek,
Tamara Astakhova,
Hsiu Ju Chiu, [......],
Dana Weekes,
Aprilfawn White,
Qingping Xu,
Keith O Hodgson,
John Wooley,
Marc André Elsliger,
Ashley M Deacon,
Adam Godzik,
Scott A Lesley,
Ian A Wilson
[show abstract]
[hide abstract]
ABSTRACT: The crystal structure of PA1994 from Pseudomonas aeruginosa, a member of the Pfam PF06475 family classified as a domain of unknown function (DUF1089), reveals a novel fold comprising a 15-stranded β-sheet wrapped around a single α-helix that assembles into a tight dimeric arrangement. The remote structural similarity to lipoprotein localization factors, in addition to the presence of an acidic pocket that is conserved in DUF1089 homologs, phospholipid-binding and sugar-binding proteins, indicate a role for PA1994 and the DUF1089 family in glycolipid metabolism. Genome-context analysis lends further support to the involvement of this family of proteins in glycolipid metabolism and indicates possible activation of DUF1089 homologs under conditions of bacterial cell-wall stress or host-pathogen interactions.
Acta Crystallographica Section F Structural Biology and Crystallization Communications 10/2010; 66(Pt 10):1211-7. · 0.51 Impact Factor
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Andrew P Yeh,
Polat Abdubek,
Tamara Astakhova,
Herbert L Axelrod,
Constantina Bakolitsa,
Xiaohui Cai,
Dennis Carlton,
Connie Chen,
Hsiu Ju Chiu,
Michelle Chiu, [......],
Dana Weekes,
Tiffany Wooten,
Qingping Xu,
Keith O Hodgson,
John Wooley,
Marc André Elsliger,
Ashley M Deacon,
Adam Godzik,
Scott A Lesley,
Ian A Wilson
[show abstract]
[hide abstract]
ABSTRACT: BT2081 from Bacteroides thetaiotaomicron (GenBank accession code NP_810994.1) is a member of a novel protein family consisting of over 160 members, most of which are found in the different classes of Bacteroidetes. Genome-context analysis lends support to the involvement of this family in carbohydrate metabolism, which plays a key role in B. thetaiotaomicron as a predominant bacterial symbiont in the human distal gut microbiome. The crystal structure of BT2081 at 2.05 Å resolution represents the first structure from this new protein family. BT2081 consists of an N-terminal domain, which adopts a β-sandwich immunoglobulin-like fold, and a larger C-terminal domain with a β-sandwich jelly-roll fold. Structural analyses reveal that both domains are similar to those found in various carbohydrate-active enzymes. The C-terminal β-jelly-roll domain contains a potential carbohydrate-binding site that is highly conserved among BT2081 homologs and is situated in the same location as the carbohydrate-binding sites that are found in structurally similar glycoside hydrolases (GHs). However, in BT2081 this site is partially occluded by surrounding loops, which results in a deep solvent-accessible pocket rather than a shallower solvent-exposed cleft.
Acta Crystallographica Section F Structural Biology and Crystallization Communications 10/2010; 66(Pt 10):1287-96. · 0.51 Impact Factor
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Qingping Xu,
Polat Abdubek,
Tamara Astakhova,
Herbert L Axelrod,
Constantina Bakolitsa,
Xiaohui Cai,
Dennis Carlton,
Connie Chen,
Hsiu Ju Chiu,
Michelle Chiu, [......],
Tiffany Wooten,
Andrew Yeh,
Jiadong Zhou,
Keith O Hodgson,
John Wooley,
Marc Andre Elsliger,
Ashley M Deacon,
Adam Godzik,
Scott A Lesley,
Ian A Wilson
[show abstract]
[hide abstract]
ABSTRACT: BT1062 from Bacteroides thetaiotaomicron is a homolog of Mfa2 (PGN0288 or PG0179), which is a component of the minor fimbriae in Porphyromonas gingivalis. The crystal structure of BT1062 revealed a conserved fold that is widely adopted by fimbrial components.
Acta Crystallographica Section F Structural Biology and Crystallization Communications 10/2010; 66(Pt 10):1281-6. · 0.51 Impact Factor
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Herbert L Axelrod,
Debanu Das,
Polat Abdubek,
Tamara Astakhova,
Constantina Bakolitsa,
Dennis Carlton,
Connie Chen,
Hsiu Ju Chiu,
Thomas Clayton,
Marc C Deller, [......],
Dana Weekes,
Tiffany Wooten,
Qingping Xu,
Keith O Hodgson,
John Wooley,
Marc André Elsliger,
Ashley M Deacon,
Adam Godzik,
Scott A Lesley,
Ian A Wilson
[show abstract]
[hide abstract]
ABSTRACT: Examination of the genomic context for members of the FmdE Pfam family (PF02663), such as the protein encoded by the fmdE gene from the methanogenic archaeon Methanobacterium thermoautotrophicum, indicates that 13 of them are co-transcribed with genes encoding subunits of molybdenum formylmethanofuran dehydrogenase (EC 1.2.99.5), an enzyme that is involved in microbial methane production. Here, the first crystal structures from PF02663 are described, representing two bacterial and one archaeal species: B8FYU2_DESHY from the anaerobic dehalogenating bacterium Desulfitobacterium hafniense DCB-2, Q2LQ23_SYNAS from the syntrophic bacterium Syntrophus aciditrophicus SB and Q9HJ63_THEAC from the thermoacidophilic archaeon Thermoplasma acidophilum. Two of these proteins, Q9HJ63_THEAC and Q2LQ23_SYNAS, contain two domains: an N-terminal thioredoxin-like α+β core domain (NTD) consisting of a five-stranded, mixed β-sheet flanked by several α-helices and a C-terminal zinc-finger domain (CTD). B8FYU2_DESHY, on the other hand, is composed solely of the NTD. The CTD of Q9HJ63_THEAC and Q2LQ23_SYNAS is best characterized as a treble-clef zinc finger. Two significant structural differences between Q9HJ63_THEAC and Q2LQ23_SYNAS involve their metal binding. First, zinc is bound to the putative active site on the NTD of Q9HJ63_THEAC, but is absent from the NTD of Q2LQ23_SYNAS. Second, whereas the structure of the CTD of Q2LQ23_SYNAS shows four Cys side chains within coordination distance of the Zn atom, the structure of Q9HJ63_THEAC is atypical for a treble-cleft zinc finger in that three Cys side chains and an Asp side chain are within coordination distance of the zinc.
Acta Crystallographica Section F Structural Biology and Crystallization Communications 10/2010; 66(Pt 10):1335-46. · 0.51 Impact Factor
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Gye Won Han,
Xiang Lei Yang, Daniel McMullan,
Yeeting E Chong,
S Sri Krishna,
Christopher L Rife,
Dana Weekes,
Scott M Brittain,
Polat Abdubek,
Eileen Ambing, [......],
Guenter Wolf,
Qingping Xu,
Keith O Hodgson,
John Wooley,
Ashley M Deacon,
Adam Godzik,
Scott A Lesley,
Marc André Elsliger,
Paul Schimmel,
Ian A Wilson
[show abstract]
[hide abstract]
ABSTRACT: A novel aminoacyl-tRNA synthetase that contains an iron-sulfur cluster in the tRNA anticodon-binding region and efficiently charges tRNA with tryptophan has been found in Thermotoga maritima. The crystal structure of TmTrpRS (tryptophanyl-tRNA synthetase; TrpRS; EC 6.1.1.2) reveals an iron-sulfur [4Fe-4S] cluster bound to the tRNA anticodon-binding (TAB) domain and an L-tryptophan ligand in the active site. None of the other T. maritima aminoacyl-tRNA synthetases (AARSs) contain this [4Fe-4S] cluster-binding motif (C-x₂₂-C-x₆-C-x₂-C). It is speculated that the iron-sulfur cluster contributes to the stability of TmTrpRS and could play a role in the recognition of the anticodon.
Acta Crystallographica Section F Structural Biology and Crystallization Communications 10/2010; 66(Pt 10):1326-34. · 0.51 Impact Factor
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Hsiu Ju Chiu,
Polat Abdubek,
Tamara Astakhova,
Herbert L Axelrod,
Dennis Carlton,
Thomas Clayton,
Debanu Das,
Marc C Deller,
Lian Duan,
Julie Feuerhelm, [......],
Henry van den Bedem,
Dana Weekes,
Qingping Xu,
Keith O Hodgson,
John Wooley,
Marc André Elsliger,
Ashley M Deacon,
Adam Godzik,
Scott A Lesley,
Ian A Wilson
[show abstract]
[hide abstract]
ABSTRACT: Chorismate mutase/prephenate dehydrogenase from Haemophilus influenzae Rd KW20 is a bifunctional enzyme that catalyzes the rearrangement of chorismate to prephenate and the NAD(P)(+)-dependent oxidative decarboxylation of prephenate to 4-hydroxyphenylpyruvate in tyrosine biosynthesis. The crystal structure of the prephenate dehydrogenase component (HinfPDH) of the TyrA protein from H. influenzae Rd KW20 in complex with the inhibitor tyrosine and cofactor NAD(+) has been determined to 2.0 Å resolution. HinfPDH is a dimeric enzyme, with each monomer consisting of an N-terminal α/β dinucleotide-binding domain and a C-terminal α-helical dimerization domain. The structure reveals key active-site residues at the domain interface, including His200, Arg297 and Ser179 that are involved in catalysis and/or ligand binding and are highly conserved in TyrA proteins from all three kingdoms of life. Tyrosine is bound directly at the catalytic site, suggesting that it is a competitive inhibitor of HinfPDH. Comparisons with its structural homologues reveal important differences around the active site, including the absence of an α-β motif in HinfPDH that is present in other TyrA proteins, such as Synechocystis sp. arogenate dehydrogenase. Residues from this motif are involved in discrimination between NADP(+) and NAD(+). The loop between β5 and β6 in the N-terminal domain is much shorter in HinfPDH and an extra helix is present at the C-terminus. Furthermore, HinfPDH adopts a more closed conformation compared with TyrA proteins that do not have tyrosine bound. This conformational change brings the substrate, cofactor and active-site residues into close proximity for catalysis. An ionic network consisting of Arg297 (a key residue for tyrosine binding), a water molecule, Asp206 (from the loop between β5 and β6) and Arg365' (from the additional C-terminal helix of the adjacent monomer) is observed that might be involved in gating the active site.
Acta Crystallographica Section F Structural Biology and Crystallization Communications 10/2010; 66(Pt 10):1317-25. · 0.51 Impact Factor
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Constantina Bakolitsa,
Qingping Xu,
Christopher L Rife,
Polat Abdubek,
Tamara Astakhova,
Herbert L Axelrod,
Dennis Carlton,
Connie Chen,
Hsiu Ju Chiu,
Thomas Clayton, [......],
Christine B Trame,
Henry van den Bedem,
Dana Weekes,
Keith O Hodgson,
John Wooley,
Marc André Elsliger,
Ashley M Deacon,
Adam Godzik,
Scott A Lesley,
Ian A Wilson
[show abstract]
[hide abstract]
ABSTRACT: The crystal structure of the Bacteroides thetaiotaomicron protein BT_3984 was determined to a resolution of 1.7 Å and was the first structure to be determined from the extensive SusD family of polysaccharide-binding proteins. SusD is an essential component of the sus operon that defines the paradigm for glycan utilization in dominant members of the human gut microbiota. Structural analysis of BT_3984 revealed an N-terminal region containing several tetratricopeptide repeats (TPRs), while the signature C-terminal region is less structured and contains extensive loop regions. Sequence and structure analysis of BT_3984 suggests the presence of binding interfaces for other proteins from the polysaccharide-utilization complex.
Acta Crystallographica Section F Structural Biology and Crystallization Communications 10/2010; 66(Pt 10):1274-80. · 0.51 Impact Factor
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Debanu Das,
Robert D Finn,
Dennis Carlton,
Mitchell D Miller,
Polat Abdubek,
Tamara Astakhova,
Herbert L Axelrod,
Constantina Bakolitsa,
Connie Chen,
Hsiu Ju Chiu, [......],
Dana Weekes,
Tiffany Wooten,
Qingping Xu,
Keith O Hodgson,
John Wooley,
Marc André Elsliger,
Ashley M Deacon,
Adam Godzik,
Scott A Lesley,
Ian A Wilson
[show abstract]
[hide abstract]
ABSTRACT: Proteins that contain the DUF2874 domain constitute a new Pfam family PF11396. Members of this family have predominantly been identified in microbes found in the human gut and oral cavity. The crystal structure of one member of this family, BVU2987 from Bacteroides vulgatus, has been determined, revealing a β-lactamase inhibitor protein-like structure with a tandem repeat of domains. Sequence analysis and structural comparisons reveal that BVU2987 and other DUF2874 proteins are related to β-lactamase inhibitor protein, PepSY and SmpA_OmlA proteins and hence are likely to function as inhibitory proteins.
Acta Crystallographica Section F Structural Biology and Crystallization Communications 10/2010; 66(Pt 10):1265-73. · 0.51 Impact Factor
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Debanu Das,
Piotr Kozbial,
Gye Won Han,
Dennis Carlton,
Lukasz Jaroszewski,
Polat Abdubek,
Tamara Astakhova,
Herbert L Axelrod,
Constantina Bakolitsa,
Connie Chen, [......],
Henry van den Bedem,
Dana Weekes,
Tiffany Wooten,
Qingping Xu,
Keith O Hodgson,
John Wooley,
Ashley M Deacon,
Adam Godzik,
Scott A Lesley,
Ian A Wilson
[show abstract]
[hide abstract]
ABSTRACT: KPN03535 (gi|152972051) is a putative lipoprotein of unknown function that is secreted by Klebsiella pneumoniae MGH 78578. The crystal structure reveals that despite a lack of any detectable sequence similarity to known structures, it is a novel variant of the OB-fold and structurally similar to the bacterial Cpx-pathway protein NlpE, single-stranded DNA-binding (SSB) proteins and toxins. K. pneumoniae MGH 78578 forms part of the normal human skin, mouth and gut flora and is an opportunistic pathogen that is linked to about 8% of all hospital-acquired infections in the USA. This structure provides the foundation for further investigations into this divergent member of the OB-fold family.
Acta Crystallographica Section F Structural Biology and Crystallization Communications 10/2010; 66(Pt 10):1254-60. · 0.51 Impact Factor
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Abhinav Kumar,
Andrei Lomize,
Kevin K Jin,
Dennis Carlton,
Mitchell D Miller,
Lukasz Jaroszewski,
Polat Abdubek,
Tamara Astakhova,
Herbert L Axelrod,
Hsiu Ju Chiu, [......],
Henry van den Bedem,
Dana Weekes,
Qingping Xu,
Keith O Hodgson,
John Wooley,
Marc André Elsliger,
Ashley M Deacon,
Adam Godzik,
Scott A Lesley,
Ian A Wilson
[show abstract]
[hide abstract]
ABSTRACT: The crystal structures of the proteins encoded by the YP_749275.1 and YP_001095227.1 genes from Shewanella frigidimarina and S. loihica, respectively, have been determined at 1.8 and 2.25 Å resolution, respectively. These proteins are members of a novel family of bacterial proteins that adopt the α/β SpoIIAA-like fold found in STAS and CRAL-TRIO domains. Despite sharing 54% sequence identity, these two proteins adopt distinct conformations arising from different dispositions of their α2 and α3 helices. In the `open' conformation (YP_001095227.1), these helices are 15 Å apart, leading to the creation of a deep nonpolar cavity. In the `closed' structure (YP_749275.1), the helices partially unfold and rearrange, occluding the cavity and decreasing the solvent-exposed hydrophobic surface. These two complementary structures are reminiscent of the conformational switch in CRAL-TRIO carriers of hydrophobic compounds. It is suggested that both proteins may associate with the lipid bilayer in their `open' monomeric state by inserting their amphiphilic helices, α2 and α3, into the lipid bilayer. These bacterial proteins may function as carriers of nonpolar substances or as interfacially activated enzymes.
Acta Crystallographica Section F Structural Biology and Crystallization Communications 10/2010; 66(Pt 10):1245-53. · 0.51 Impact Factor
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Gye Won Han,
Marc André Elsliger,
Todd O Yeates,
Qingping Xu,
Alexey G Murzin,
S Sri Krishna,
Lukasz Jaroszewski,
Polat Abdubek,
Tamara Astakhova,
Herbert L Axelrod, [......],
Henry J Tien,
Christine B Trame,
Henry van den Bedem,
Dana Weekes,
Keith O Hodgson,
John Wooley,
Ashley M Deacon,
Adam Godzik,
Scott A Lesley,
Ian A Wilson
[show abstract]
[hide abstract]
ABSTRACT: The crystal structure of a putative NTPase, YP_001813558.1 from Exiguobacterium sibiricum 255-15 (PF09934, DUF2166) was determined to 1.78 Å resolution. YP_001813558.1 and its homologs (dimeric dUTPases, MazG proteins and HisE-encoded phosphoribosyl ATP pyrophosphohydrolases) form a superfamily of all-α-helical NTP pyrophosphatases. In dimeric dUTPase-like proteins, a central four-helix bundle forms the active site. However, in YP_001813558.1, an unexpected intertwined swapping of two of the helices that compose the conserved helix bundle results in a `linked dimer' that has not previously been observed for this family. Interestingly, despite this novel mode of dimerization, the metal-binding site for divalent cations, such as magnesium, that are essential for NTPase activity is still conserved. Furthermore, the active-site residues that are involved in sugar binding of the NTPs are also conserved when compared with other α-helical NTPases, but those that recognize the nucleotide bases are not conserved, suggesting a different substrate specificity.
Acta Crystallographica Section F Structural Biology and Crystallization Communications 10/2010; 66(Pt 10):1237-44. · 0.51 Impact Factor
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Gye Won Han,
Constantina Bakolitsa,
Mitchell D Miller,
Abhinav Kumar,
Dennis Carlton,
Rafael J Najmanovich,
Polat Abdubek,
Tamara Astakhova,
Herbert L Axelrod,
Connie Chen, [......],
Henry van den Bedem,
Dana Weekes,
Qingping Xu,
Keith O Hodgson,
John Wooley,
Marc André Elsliger,
Ashley M Deacon,
Adam Godzik,
Scott A Lesley,
Ian A Wilson
[show abstract]
[hide abstract]
ABSTRACT: The crystal structures of SPO0140 and Sbal_2486 were determined using the semiautomated high-throughput pipeline of the Joint Center for Structural Genomics (JCSG) as part of the NIGMS Protein Structure Initiative (PSI). The structures revealed a conserved core with domain duplication and a superficial similarity of the C-terminal domain to pleckstrin homology-like folds. The conservation of the domain interface indicates a potential binding site that is likely to involve a nucleotide-based ligand, with genome-context and gene-fusion analyses additionally supporting a role for this family in signal transduction, possibly during oxidative stress.
Acta Crystallographica Section F Structural Biology and Crystallization Communications 10/2010; 66(Pt 10):1218-25. · 0.51 Impact Factor
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Constantina Bakolitsa,
Abhinav Kumar,
Dennis Carlton,
Mitchell D Miller,
S Sri Krishna,
Polat Abdubek,
Tamara Astakhova,
Herbert L Axelrod,
Hsiu Ju Chiu,
Thomas Clayton, [......],
Christina V Trout,
Henry van den Bedem,
Dana Weekes,
Qingping Xu,
Keith O Hodgson,
John Wooley,
Ashley M Deacon,
Adam Godzik,
Scott A Lesley,
Ian A Wilson
[show abstract]
[hide abstract]
ABSTRACT: The structure of LP2179, a member of the PF08866 (DUF1831) family, suggests a novel α+β fold comprising two β-sheets packed against a single helix. A remote structural similarity to two other uncharacterized protein families specific to the Bacillus genus (PF08868 and PF08968), as well as to prokaryotic S-adenosylmethionine decarboxylases, is consistent with a role in amino-acid metabolism. Genomic neighborhood analysis of LP2179 supports this functional assignment, which might also then be extended to PF08868 and PF08968.
Acta Crystallographica Section F Structural Biology and Crystallization Communications 10/2010; 66(Pt 10):1205-10. · 0.51 Impact Factor
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Constantina Bakolitsa,
Alex Bateman,
Kevin K Jin, Daniel McMullan,
S Sri Krishna,
Mitchell D Miller,
Polat Abdubek,
Claire Acosta,
Tamara Astakhova,
Herbert L Axelrod, [......],
Dana Weekes,
Aprilfawn White,
Qingping Xu,
Keith O Hodgson,
John Wooley,
Marc André Elsliger,
Ashley M Deacon,
Adam Godzik,
Scott Lesley,
Ian A Wilson
[show abstract]
[hide abstract]
ABSTRACT: The crystal structure of Jann_2411 from Jannaschia sp. strain CCS1, a member of the Pfam PF07336 family classified as a domain of unknown function (DUF1470), was solved to a resolution of 1.45 Å by multiple-wavelength anomalous dispersion (MAD). This protein is the first structural representative of the DUF1470 Pfam family. Structural analysis revealed a two-domain organization, with the N-terminal domain presenting a new fold called the ABATE domain that may bind an as yet unknown ligand. The C-terminal domain forms a treble-clef zinc finger that is likely to be involved in DNA binding. Analysis of the Jann_2411 protein and the broader ABATE-domain family suggests a role as stress-induced transcriptional regulators.
Acta Crystallographica Section F Structural Biology and Crystallization Communications 10/2010; 66(Pt 10):1198-204. · 0.51 Impact Factor
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Constantina Bakolitsa,
Abhinav Kumar,
Kevin K Jin, Daniel McMullan,
S Sri Krishna,
Mitchell D Miller,
Polat Abdubek,
Claire Acosta,
Tamara Astakhova,
Herbert L Axelrod, [......],
Dana Weekes,
Aprilfawn White,
Qingping Xu,
Keith O Hodgson,
John Wooley,
Marc Andre Elsliger,
Ashley M Deacon,
Adam Godzik,
Scott A Lesley,
Ian A Wilson
[show abstract]
[hide abstract]
ABSTRACT: The crystal structures of BB2672 and SPO0826 were determined to resolutions of 1.7 and 2.1 Å by single-wavelength anomalous dispersion and multiple-wavelength anomalous dispersion, respectively, using the semi-automated high-throughput pipeline of the Joint Center for Structural Genomics (JCSG) as part of the NIGMS Protein Structure Initiative (PSI). These proteins are the first structural representatives of the PF06684 (DUF1185) Pfam family. Structural analysis revealed that both structures adopt a variant of the Bacillus chorismate mutase fold (BCM). The biological unit of both proteins is a hexamer and analysis of homologs indicates that the oligomer interface residues are highly conserved. The conformation of the critical regions for oligomerization appears to be dependent on pH or salt concentration, suggesting that this protein might be subject to environmental regulation. Structural similarities to BCM and genome-context analysis suggest a function in amino-acid synthesis.
Acta Crystallographica Section F Structural Biology and Crystallization Communications 10/2010; 66(Pt 10):1182-9. · 0.51 Impact Factor
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Mitchell D Miller,
L Aravind,
Constantina Bakolitsa,
Christopher L Rife,
Dennis Carlton,
Polat Abdubek,
Tamara Astakhova,
Herbert L Axelrod,
Hsiu Ju Chiu,
Thomas Clayton, [......],
Henry van den Bedem,
Dana Weekes,
Qingping Xu,
Keith O Hodgson,
John Wooley,
Marc André Elsliger,
Ashley M Deacon,
Adam Godzik,
Scott A Lesley,
Ian A Wilson
[show abstract]
[hide abstract]
ABSTRACT: The crystal structure of Dhaf4260 from Desulfitobacterium hafniense DCB-2 was determined by single-wavelength anomalous diffraction (SAD) to a resolution of 2.01 Å using the semi-automated high-throughput pipeline of the Joint Center for Structural Genomics (JCSG) as part of the NIGMS Protein Structure Initiative (PSI). This protein structure is the first representative of the PF04016 (DUF364) Pfam family and reveals a novel combination of two well known domains (an enolase N-terminal-like fold followed by a Rossmann-like domain). Structural and bioinformatic analyses reveal partial similarities to Rossmann-like methyltransferases, with residues from the enolase-like fold combining to form a unique active site that is likely to be involved in the condensation or hydrolysis of molecules implicated in the synthesis of flavins, pterins or other siderophores. The genome context of Dhaf4260 and homologs additionally supports a role in heavy-metal chelation.
Acta Crystallographica Section F Structural Biology and Crystallization Communications 10/2010; 66(Pt 10):1167-73. · 0.51 Impact Factor
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S Sri Krishna,
L Aravind,
Constantina Bakolitsa,
Jonathan Caruthers,
Dennis Carlton,
Mitchell D Miller,
Polat Abdubek,
Tamara Astakhova,
Herbert L Axelrod,
Hsiu Ju Chiu, [......],
Henry van den Bedem,
Dana Weekes,
Qingping Xu,
Keith O Hodgson,
John Wooley,
Marc André Elsliger,
Ashley M Deacon,
Adam Godzik,
Scott A Lesley,
Ian A Wilson
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ABSTRACT: SSO2064 is the first structural representative of PF01796 (DUF35), a large prokaryotic family with a wide phylogenetic distribution. The structure reveals a novel two-domain architecture comprising an N-terminal, rubredoxin-like, zinc ribbon and a C-terminal, oligonucleotide/oligosaccharide-binding (OB) fold domain. Additional N-terminal helical segments may be involved in protein-protein interactions. Domain architectures, genomic context analysis and functional evidence from certain bacterial representatives of this family suggest that these proteins form a novel fatty-acid-binding component that is involved in the biosynthesis of lipids and polyketide antibiotics and that they possibly function as acyl-CoA-binding proteins. This structure has led to a re-evaluation of the DUF35 family, which has now been split into two entries in the latest Pfam release (v.24.0).
Acta Crystallographica Section F Structural Biology and Crystallization Communications 10/2010; 66(Pt 10):1160-6. · 0.51 Impact Factor
