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1vh9

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Revision as of 12:22, 25 December 2014

Crystal structure of a putative thioesterase

Structural highlights

1vh9 is a 2 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Gene:	YBDB, B0597, C0684 (Escherichia coli)
Resources:	FirstGlance, OCA, RCSB, PDBsum

Function

[YBDB_ECOLI] Required for optimal enterobactin synthesis. Acts as a proofreading enzyme that prevents EntB misacylation by hydrolyzing the thioester bound existing between EntB and wrongly charged molecules. Displays esterase activity toward a wide range of substrates, including acyl-CoAs and aryl-CoAs.^[1] ^[2] ^[3] ^[4]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The targets of the Structural GenomiX (SGX) bacterial genomics project were proteins conserved in multiple prokaryotic organisms with no obvious sequence homolog in the Protein Data Bank of known structures. The outcome of this work was 80 structures, covering 60 unique sequences and 49 different genes. Experimental phase determination from proteins incorporating Se-Met was carried out for 45 structures with most of the remainder solved by molecular replacement using members of the experimentally phased set as search models. An automated tool was developed to deposit these structures in the Protein Data Bank, along with the associated X-ray diffraction data (including refined experimental phases) and experimentally confirmed sequences. BLAST comparisons of the SGX structures with structures that had appeared in the Protein Data Bank over the intervening 3.5 years since the SGX target list had been compiled identified homologs for 49 of the 60 unique sequences represented by the SGX structures. This result indicates that, for bacterial structures that are relatively easy to express, purify, and crystallize, the structural coverage of gene space is proceeding rapidly. More distant sequence-structure relationships between the SGX and PDB structures were investigated using PDB-BLAST and Combinatorial Extension (CE). Only one structure, SufD, has a truly unique topology compared to all folds in the PDB.

Structural analysis of a set of proteins resulting from a bacterial genomics project.,Badger J, Sauder JM, Adams JM, Antonysamy S, Bain K, Bergseid MG, Buchanan SG, Buchanan MD, Batiyenko Y, Christopher JA, Emtage S, Eroshkina A, Feil I, Furlong EB, Gajiwala KS, Gao X, He D, Hendle J, Huber A, Hoda K, Kearins P, Kissinger C, Laubert B, Lewis HA, Lin J, Loomis K, Lorimer D, Louie G, Maletic M, Marsh CD, Miller I, Molinari J, Muller-Dieckmann HJ, Newman JM, Noland BW, Pagarigan B, Park F, Peat TS, Post KW, Radojicic S, Ramos A, Romero R, Rutter ME, Sanderson WE, Schwinn KD, Tresser J, Winhoven J, Wright TA, Wu L, Xu J, Harris TJ Proteins. 2005 Sep 1;60(4):787-96. PMID:16021622^[5]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Kuznetsova E, Proudfoot M, Sanders SA, Reinking J, Savchenko A, Arrowsmith CH, Edwards AM, Yakunin AF. Enzyme genomics: Application of general enzymatic screens to discover new enzymes. FEMS Microbiol Rev. 2005 Apr;29(2):263-79. PMID:15808744 doi:S0168-6445(05)00004-5
↑ Leduc D, Battesti A, Bouveret E. The hotdog thioesterase EntH (YbdB) plays a role in vivo in optimal enterobactin biosynthesis by interacting with the ArCP domain of EntB. J Bacteriol. 2007 Oct;189(19):7112-26. Epub 2007 Aug 3. PMID:17675380 doi:http://dx.doi.org/10.1128/JB.00755-07
↑ Chen D, Wu R, Bryan TL, Dunaway-Mariano D. In vitro kinetic analysis of substrate specificity in enterobactin biosynthetic lower pathway enzymes provides insight into the biochemical function of the hot dog-fold thioesterase EntH. Biochemistry. 2009 Jan 27;48(3):511-3. PMID:19119850 doi:http://dx.doi.org/10.1021/bi802207t
↑ Guo ZF, Sun Y, Zheng S, Guo Z. Preferential hydrolysis of aberrant intermediates by the type II thioesterase in Escherichia coli nonribosomal enterobactin synthesis: substrate specificities and mutagenic studies on the active-site residues. Biochemistry. 2009 Mar 3;48(8):1712-22. doi: 10.1021/bi802165x. PMID:19193103 doi:http://dx.doi.org/10.1021/bi802165x
↑ Badger J, Sauder JM, Adams JM, Antonysamy S, Bain K, Bergseid MG, Buchanan SG, Buchanan MD, Batiyenko Y, Christopher JA, Emtage S, Eroshkina A, Feil I, Furlong EB, Gajiwala KS, Gao X, He D, Hendle J, Huber A, Hoda K, Kearins P, Kissinger C, Laubert B, Lewis HA, Lin J, Loomis K, Lorimer D, Louie G, Maletic M, Marsh CD, Miller I, Molinari J, Muller-Dieckmann HJ, Newman JM, Noland BW, Pagarigan B, Park F, Peat TS, Post KW, Radojicic S, Ramos A, Romero R, Rutter ME, Sanderson WE, Schwinn KD, Tresser J, Winhoven J, Wright TA, Wu L, Xu J, Harris TJ. Structural analysis of a set of proteins resulting from a bacterial genomics project. Proteins. 2005 Sep 1;60(4):787-96. PMID:16021622 doi:http://dx.doi.org/10.1002/prot.20541

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1vh9"

Categories: Escherichia coli | GenomiX, Structural | Structural genomic | Unknown function

@@ Line 3: / Line 3: @@
 == Structural highlights ==
 <table><tr><td colspan='2'>[[1vh9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VH9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1VH9 FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">YBDB, B0597, C0684 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
+</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">YBDB, B0597, C0684 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1vh9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vh9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1vh9 RCSB], [http://www.ebi.ac.uk/pdbsum/1vh9 PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1vh9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vh9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1vh9 RCSB], [http://www.ebi.ac.uk/pdbsum/1vh9 PDBsum]</span></td></tr>
-<table>
+</table>
+== Function ==
+[[http://www.uniprot.org/uniprot/YBDB_ECOLI YBDB_ECOLI]] Required for optimal enterobactin synthesis. Acts as a proofreading enzyme that prevents EntB misacylation by hydrolyzing the thioester bound existing between EntB and wrongly charged molecules. Displays esterase activity toward a wide range of substrates, including acyl-CoAs and aryl-CoAs.<ref>PMID:15808744</ref> <ref>PMID:17675380</ref> <ref>PMID:19119850</ref> <ref>PMID:19193103</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 29: / Line 31: @@
 </StructureSection>
 [[Category: Escherichia coli]]
-[[Category: GenomiX, Structural.]]
+[[Category: GenomiX, Structural]]
 [[Category: Structural genomic]]
 [[Category: Unknown function]]

1vh9

From Proteopedia

Revision as of 12:22, 25 December 2014

Crystal structure of a putative thioesterase

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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