1m3s: Difference between revisions

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<StructureSection load='1m3s' size='340' side='right'caption='[[1m3s]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
<StructureSection load='1m3s' size='340' side='right'caption='[[1m3s]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1m3s]] is a 2 chain structure with sequence from [https://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=1M3S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M3S FirstGlance]. <br>
<table><tr><td colspan='2'>[[1m3s]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. 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 [https://proteopedia.org/fgij/fg.htm?mol=1M3S FirstGlance]. <br>
</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">YckF ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</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]] 1.95&#8491;</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=1m3s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m3s OCA], [https://pdbe.org/1m3s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m3s RCSB], [https://www.ebi.ac.uk/pdbsum/1m3s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m3s ProSAT], [https://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'>[https://proteopedia.org/fgij/fg.htm?mol=1m3s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m3s OCA], [https://pdbe.org/1m3s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m3s RCSB], [https://www.ebi.ac.uk/pdbsum/1m3s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m3s ProSAT], [https://www.topsan.org/Proteins/MCSG/1m3s TOPSAN]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/PHI_BACSU PHI_BACSU]] Catalyzes the isomerization between 3-hexulose 6-phosphate and fructose 6-phosphate. Together with HxlA, may act as a formaldehyde detoxification system.  
[https://www.uniprot.org/uniprot/PHI_BACSU 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 ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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].
</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;">
== Publication Abstract from PubMed ==
The 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<ref>PMID:15363790</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1m3s" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Vibrio subtilis ehrenberg 1835]]
[[Category: Bacillus subtilis]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Collart, F]]
[[Category: Collart F]]
[[Category: Joachimiak, A]]
[[Category: Joachimiak A]]
[[Category: Kim, D E]]
[[Category: Kim DE]]
[[Category: Structural genomic]]
[[Category: Sanishvili R]]
[[Category: Sanishvili, R]]
[[Category: Wu R]]
[[Category: Wu, R]]
[[Category: Mcsg]]
[[Category: PSI, Protein structure initiative]]
[[Category: Unknown function]]

Latest revision as of 10:39, 14 February 2024

Crystal structure of YckF from Bacillus subtilisCrystal structure of YckF from Bacillus subtilis

Structural highlights

1m3s is a 2 chain structure with sequence from Bacillus subtilis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.95Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

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.

1m3s, resolution 1.95Å

Drag the structure with the mouse to rotate

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OCA
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