1m3s: Difference between revisions
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==Crystal structure of YckF from Bacillus subtilis== | ==Crystal structure of YckF from Bacillus subtilis== | ||
<StructureSection load='1m3s' size='340' side='right' caption='[[1m3s]], [[Resolution|resolution]] 1.95Å' scene=''> | <StructureSection load='1m3s' size='340' side='right' caption='[[1m3s]], [[Resolution|resolution]] 1.95Å' scene=''> | ||
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<table><tr><td colspan='2'>[[1m3s]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M3S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M3S FirstGlance]. <br> | <table><tr><td colspan='2'>[[1m3s]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M3S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M3S FirstGlance]. <br> | ||
</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">YckF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</td></tr> | </td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">YckF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</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=1m3s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m3s OCA], [http://pdbe.org/1m3s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1m3s RCSB], [http://www.ebi.ac.uk/pdbsum/1m3s PDBsum], [http://www.topsan.org/Proteins/MCSG/1m3s 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=1m3s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m3s OCA], [http://pdbe.org/1m3s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1m3s RCSB], [http://www.ebi.ac.uk/pdbsum/1m3s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1m3s ProSAT], [http://www.topsan.org/Proteins/MCSG/1m3s TOPSAN]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
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<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/ | </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=1m3s ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
Revision as of 12:01, 12 October 2017
Crystal structure of YckF from Bacillus subtilisCrystal structure of YckF from Bacillus subtilis
Structural highlights
Function[PHI_BACSU] Catalyzes the isomerization between 3-hexulose 6-phosphate and fructose 6-phosphate. Together with HxlA, may act as a formaldehyde detoxification system. 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 PubMedThe crystal structure of the YckF protein from Bacillus subtilis was determined with MAD phasing and refined at 1.95A resolution. YckF forms a tight tetramer both in crystals and in solution. Conservation of such oligomerization in other phosphate sugar isomerases indicates that the crystallographically observed tetramer is physiologically relevant. The structure of YckF was compared to with its ortholog from Methanococcus jannaschii, MJ1247. Both of these proteins have phosphate hexulose isomerase activity, although neither of the organisms can utilize methane or methanol as source of energy and/or carbon. Extensive sequence and structural similarities with MJ1247 and with the isomerase domain of glucosamine-6-phosphate synthase from Escherichia coli allowed us to group residues contributing to substrate binding or catalysis. Few notable differences among these structures suggest possible cooperativity of the four active sites of the tetramer. Phylogenetic relationships between obligatory and facultative methylotrophs along with B. subtilis and E. coli provide clues about the possible evolution of genes as they loose their physiological importance. Crystal structure of Bacillus subtilis YckF: structural and functional evolution.,Sanishvili R, Wu R, Kim DE, Watson JD, Collart F, Joachimiak A J Struct Biol. 2004 Oct;148(1):98-109. PMID:15363790[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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