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==YfiT from Bacillus subtilis is a probable metal-dependent hydrolase with an unusual four-helix bundle topology== | ==YfiT from Bacillus subtilis is a probable metal-dependent hydrolase with an unusual four-helix bundle topology== | ||
<StructureSection load='1rxq' size='340' side='right' caption='[[1rxq]], [[Resolution|resolution]] 1.70Å' scene=''> | <StructureSection load='1rxq' size='340' side='right' caption='[[1rxq]], [[Resolution|resolution]] 1.70Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1rxq]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/" | <table><tr><td colspan='2'>[[1rxq]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RXQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RXQ FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLU:GLUTAMIC+ACID'>GLU</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ALA:ALANINE'>ALA</scene>, <scene name='pdbligand=GLU:GLUTAMIC+ACID'>GLU</scene>, <scene name='pdbligand=GLY:GLYCINE'>GLY</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=SER:SERINE'>SER</scene>, <scene name='pdbligand=THR:THREONINE'>THR</scene></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='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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">yfiT ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 " | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">yfiT ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</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=1rxq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rxq OCA], [http://pdbe.org/1rxq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1rxq RCSB], [http://www.ebi.ac.uk/pdbsum/1rxq PDBsum], [http://www.topsan.org/Proteins/MCSG/1rxq 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=1rxq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rxq OCA], [http://pdbe.org/1rxq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1rxq RCSB], [http://www.ebi.ac.uk/pdbsum/1rxq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1rxq ProSAT], [http://www.topsan.org/Proteins/MCSG/1rxq TOPSAN]</span></td></tr> | ||
</table> | </table> | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
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Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rx/1rxq_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rx/1rxq_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
| Line 31: | Line 32: | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Vibrio subtilis ehrenberg 1835]] | ||
[[Category: Anderson, W F]] | [[Category: Anderson, W F]] | ||
[[Category: Structural genomic]] | [[Category: Structural genomic]] | ||
Revision as of 09:34, 8 March 2018
YfiT from Bacillus subtilis is a probable metal-dependent hydrolase with an unusual four-helix bundle topologyYfiT from Bacillus subtilis is a probable metal-dependent hydrolase with an unusual four-helix bundle topology
Structural highlights
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 PubMedYfiT, a 19-kDa polypeptide from Bacillus subtilis, belongs to a small sequence family with members predominantly from Gram positive bacteria. We have determined the crystal structure of YfiT in complex with Ni(2+) to a resolution of 1.7 A. YfiT exists as a dimer and binds Ni(2+) in a 1:1 stoichiometry. The protein has an unusual four-helix bundle topology and coordinates Ni(2+) in an octahedral geometry with three conserved histidines and three waters. Although there is no similarity in their overall structures, the coordination geometry of the metal and the residues that constitute the putative active site in YfiT are similar to those of metalloproteases such as thermolysin. Our structural analyses suggest that YfiT might function as a metal-dependent hydrolase. YfiT from Bacillus subtilis is a probable metal-dependent hydrolase with an unusual four-helix bundle topology.,Rajan SS, Yang X, Shuvalova L, Collart F, Anderson WF Biochemistry. 2004 Dec 14;43(49):15472-9. PMID:15581359[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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