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| | ==Crystal Structure of BioH at 1.7 A== | | ==Crystal Structure of BioH at 1.7 A== |
| - | <StructureSection load='1m33' size='340' side='right' caption='[[1m33]], [[Resolution|resolution]] 1.70Å' scene=''> | + | <StructureSection load='1m33' size='340' side='right'caption='[[1m33]], [[Resolution|resolution]] 1.70Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1m33]] is a 1 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=1M33 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M33 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1m33]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M33 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M33 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3OH:3-HYDROXY-PROPANOIC+ACID'>3OH</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3OH:3-HYDROXY-PROPANOIC+ACID'>3OH</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BioH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr> | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1m33 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m33 OCA], [https://pdbe.org/1m33 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m33 RCSB], [https://www.ebi.ac.uk/pdbsum/1m33 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m33 ProSAT], [https://www.topsan.org/Proteins/MCSG/1m33 TOPSAN]</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=1m33 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m33 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1m33 RCSB], [http://www.ebi.ac.uk/pdbsum/1m33 PDBsum], [http://www.topsan.org/Proteins/MCSG/1m33 TOPSAN]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/BIOH_ECOLI BIOH_ECOLI]] The physiological role of BioH is to remove the methyl group introduced by BioC when the pimeloyl moiety is complete. It allows to synthesize pimeloyl-ACP via the fatty acid synthetic pathway through the hydrolysis of the ester bonds of pimeloyl-ACP esters. E.coli employs a methylation and demethylation strategy to allow elongation of a temporarily disguised malonate moiety to a pimelate moiety by the fatty acid synthetic enzymes. BioH shows a preference for short chain fatty acid esters (acyl chain length of up to 6 carbons) and short chain p-nitrophenyl esters. Also displays a weak thioesterase activity. Can form a complex with CoA, and may be involved in the condensation of CoA and pimelic acid into pimeloyl-CoA, a precursor in biotin biosynthesis.<ref>PMID:11904168</ref> <ref>PMID:17625941</ref> <ref>PMID:20693992</ref> <ref>PMID:12732651</ref> Catalyzes the hydrolysis of the methyl ester bond of dimethylbutyryl-S-methyl mercaptopropionate (DMB-S-MMP) to yield dimethylbutyryl mercaptopropionic acid (DMBS-MPA) during the biocatalytic conversion of simvastin acid from monacolin J acid. Can also use acyl carriers such as dimethylbutyryl-S-ethyl mercaptopropionate (DMB-S-EMP) and dimethylbutyryl-S-methyl thioglycolate (DMB-S-MTG) as the thioester substrates.<ref>PMID:11904168</ref> <ref>PMID:17625941</ref> <ref>PMID:20693992</ref> <ref>PMID:12732651</ref> | + | [https://www.uniprot.org/uniprot/BIOH_ECOLI BIOH_ECOLI] The physiological role of BioH is to remove the methyl group introduced by BioC when the pimeloyl moiety is complete. It allows to synthesize pimeloyl-ACP via the fatty acid synthetic pathway through the hydrolysis of the ester bonds of pimeloyl-ACP esters. E.coli employs a methylation and demethylation strategy to allow elongation of a temporarily disguised malonate moiety to a pimelate moiety by the fatty acid synthetic enzymes. BioH shows a preference for short chain fatty acid esters (acyl chain length of up to 6 carbons) and short chain p-nitrophenyl esters. Also displays a weak thioesterase activity. Can form a complex with CoA, and may be involved in the condensation of CoA and pimelic acid into pimeloyl-CoA, a precursor in biotin biosynthesis.<ref>PMID:11904168</ref> <ref>PMID:17625941</ref> <ref>PMID:20693992</ref> <ref>PMID:12732651</ref> Catalyzes the hydrolysis of the methyl ester bond of dimethylbutyryl-S-methyl mercaptopropionate (DMB-S-MMP) to yield dimethylbutyryl mercaptopropionic acid (DMBS-MPA) during the biocatalytic conversion of simvastin acid from monacolin J acid. Can also use acyl carriers such as dimethylbutyryl-S-ethyl mercaptopropionate (DMB-S-EMP) and dimethylbutyryl-S-methyl thioglycolate (DMB-S-MTG) as the thioester substrates.<ref>PMID:11904168</ref> <ref>PMID:17625941</ref> <ref>PMID:20693992</ref> <ref>PMID:12732651</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/m3/1m33_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/m3/1m33_consurf.spt"</scriptWhenChecked> |
| - | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
| - | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf]. | + | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1m33 ConSurf]. |
| | <div style="clear:both"></div> | | <div style="clear:both"></div> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 1m33" style="background-color:#fffaf0;"></div> |
| | == References == | | == References == |
| | <references/> | | <references/> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Escherichia coli]] | | [[Category: Escherichia coli]] |
| - | [[Category: Edwards, A]] | + | [[Category: Large Structures]] |
| - | [[Category: Joachimiak, A]] | + | [[Category: Edwards A]] |
| - | [[Category: Structural genomic]] | + | [[Category: Joachimiak A]] |
| - | [[Category: Sanishvili, R]] | + | [[Category: Sanishvili R]] |
| - | [[Category: Savchenko, A]] | + | [[Category: Savchenko A]] |
| - | [[Category: Skarina, T]] | + | [[Category: Skarina T]] |
| - | [[Category: Yakunin, A]] | + | [[Category: Yakunin A]] |
| - | [[Category: Alpha-betta-alpha sandwich]]
| + | |
| - | [[Category: Mcsg]]
| + | |
| - | [[Category: PSI, Protein structure initiative]]
| + | |
| - | [[Category: Unknown function]]
| + | |
| Structural highlights
Function
BIOH_ECOLI The physiological role of BioH is to remove the methyl group introduced by BioC when the pimeloyl moiety is complete. It allows to synthesize pimeloyl-ACP via the fatty acid synthetic pathway through the hydrolysis of the ester bonds of pimeloyl-ACP esters. E.coli employs a methylation and demethylation strategy to allow elongation of a temporarily disguised malonate moiety to a pimelate moiety by the fatty acid synthetic enzymes. BioH shows a preference for short chain fatty acid esters (acyl chain length of up to 6 carbons) and short chain p-nitrophenyl esters. Also displays a weak thioesterase activity. Can form a complex with CoA, and may be involved in the condensation of CoA and pimelic acid into pimeloyl-CoA, a precursor in biotin biosynthesis.[1] [2] [3] [4] Catalyzes the hydrolysis of the methyl ester bond of dimethylbutyryl-S-methyl mercaptopropionate (DMB-S-MMP) to yield dimethylbutyryl mercaptopropionic acid (DMBS-MPA) during the biocatalytic conversion of simvastin acid from monacolin J acid. Can also use acyl carriers such as dimethylbutyryl-S-ethyl mercaptopropionate (DMB-S-EMP) and dimethylbutyryl-S-methyl thioglycolate (DMB-S-MTG) as the thioester substrates.[5] [6] [7] [8]
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
Structural proteomics projects are generating three-dimensional structures of novel, uncharacterized proteins at an increasing rate. However, structure alone is often insufficient to deduce the specific biochemical function of a protein. Here we determined the function for a protein using a strategy that integrates structural and bioinformatics data with parallel experimental screening for enzymatic activity. BioH is involved in biotin biosynthesis in Escherichia coli and had no previously known biochemical function. The crystal structure of BioH was determined at 1.7 A resolution. An automated procedure was used to compare the structure of BioH with structural templates from a variety of different enzyme active sites. This screen identified a catalytic triad (Ser82, His235, and Asp207) with a configuration similar to that of the catalytic triad of hydrolases. Analysis of BioH with a panel of hydrolase assays revealed a carboxylesterase activity with a preference for short acyl chain substrates. The combined use of structural bioinformatics with experimental screens for detecting enzyme activity could greatly enhance the rate at which function is determined from structure.
Integrating structure, bioinformatics, and enzymology to discover function: BioH, a new carboxylesterase from Escherichia coli.,Sanishvili R, Yakunin AF, Laskowski RA, Skarina T, Evdokimova E, Doherty-Kirby A, Lajoie GA, Thornton JM, Arrowsmith CH, Savchenko A, Joachimiak A, Edwards AM J Biol Chem. 2003 Jul 11;278(28):26039-45. Epub 2003 May 5. PMID:12732651[9]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Tomczyk NH, Nettleship JE, Baxter RL, Crichton HJ, Webster SP, Campopiano DJ. Purification and characterisation of the BIOH protein from the biotin biosynthetic pathway. FEBS Lett. 2002 Feb 27;513(2-3):299-304. PMID:11904168
- ↑ Xie X, Wong WW, Tang Y. Improving simvastatin bioconversion in Escherichia coli by deletion of bioH. Metab Eng. 2007 Jul;9(4):379-86. Epub 2007 Jun 5. PMID:17625941 doi:http://dx.doi.org/10.1016/j.ymben.2007.05.006
- ↑ Lin S, Hanson RE, Cronan JE. Biotin synthesis begins by hijacking the fatty acid synthetic pathway. Nat Chem Biol. 2010 Sep;6(9):682-8. doi: 10.1038/nchembio.420. Epub 2010 Aug 8. PMID:20693992 doi:http://dx.doi.org/10.1038/nchembio.420
- ↑ Sanishvili R, Yakunin AF, Laskowski RA, Skarina T, Evdokimova E, Doherty-Kirby A, Lajoie GA, Thornton JM, Arrowsmith CH, Savchenko A, Joachimiak A, Edwards AM. Integrating structure, bioinformatics, and enzymology to discover function: BioH, a new carboxylesterase from Escherichia coli. J Biol Chem. 2003 Jul 11;278(28):26039-45. Epub 2003 May 5. PMID:12732651 doi:10.1074/jbc.M303867200
- ↑ Tomczyk NH, Nettleship JE, Baxter RL, Crichton HJ, Webster SP, Campopiano DJ. Purification and characterisation of the BIOH protein from the biotin biosynthetic pathway. FEBS Lett. 2002 Feb 27;513(2-3):299-304. PMID:11904168
- ↑ Xie X, Wong WW, Tang Y. Improving simvastatin bioconversion in Escherichia coli by deletion of bioH. Metab Eng. 2007 Jul;9(4):379-86. Epub 2007 Jun 5. PMID:17625941 doi:http://dx.doi.org/10.1016/j.ymben.2007.05.006
- ↑ Lin S, Hanson RE, Cronan JE. Biotin synthesis begins by hijacking the fatty acid synthetic pathway. Nat Chem Biol. 2010 Sep;6(9):682-8. doi: 10.1038/nchembio.420. Epub 2010 Aug 8. PMID:20693992 doi:http://dx.doi.org/10.1038/nchembio.420
- ↑ Sanishvili R, Yakunin AF, Laskowski RA, Skarina T, Evdokimova E, Doherty-Kirby A, Lajoie GA, Thornton JM, Arrowsmith CH, Savchenko A, Joachimiak A, Edwards AM. Integrating structure, bioinformatics, and enzymology to discover function: BioH, a new carboxylesterase from Escherichia coli. J Biol Chem. 2003 Jul 11;278(28):26039-45. Epub 2003 May 5. PMID:12732651 doi:10.1074/jbc.M303867200
- ↑ Sanishvili R, Yakunin AF, Laskowski RA, Skarina T, Evdokimova E, Doherty-Kirby A, Lajoie GA, Thornton JM, Arrowsmith CH, Savchenko A, Joachimiak A, Edwards AM. Integrating structure, bioinformatics, and enzymology to discover function: BioH, a new carboxylesterase from Escherichia coli. J Biol Chem. 2003 Jul 11;278(28):26039-45. Epub 2003 May 5. PMID:12732651 doi:10.1074/jbc.M303867200
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