2cir: Difference between revisions

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-{{Seed}}
-[[Image:2cir.png|left|200px]]
-<!--
+==Structure-based functional annotation: Yeast ymr099c codes for a D- hexose-6-phosphate mutarotase. Complex with glucose-6-phosphate==
-The line below this paragraph, containing "STRUCTURE_2cir", creates the "Structure Box" on the page.
+<StructureSection load='2cir' size='340' side='right'caption='[[2cir]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2cir]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CIR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CIR FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BG6:BETA-D-GLUCOSE-6-PHOSPHATE'>BG6</scene>, <scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>
-{{STRUCTURE_2cir|  PDB=2cir  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2cir FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cir OCA], [https://pdbe.org/2cir PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2cir RCSB], [https://www.ebi.ac.uk/pdbsum/2cir PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2cir ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/YMY9_YEAST YMY9_YEAST] Catalyzes the interconversion between the alpha and beta anomers from at least three hexose 6-phosphate sugars (Glc6P, Gal6P, and Man6P).<ref>PMID:16857670</ref>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ci/2cir_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </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/main_output.php?pdb_ID=2cir ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Despite the generation of a large amount of sequence information over the last decade, more than 40% of well characterized enzymatic functions still lack associated protein sequences. Assigning protein sequences to documented biochemical functions is an interesting challenge. We illustrate here that structural genomics may be a reasonable approach in addressing these questions. We present the crystal structure of the Saccharomyces cerevisiae YMR099cp, a protein of unknown function. YMR099cp adopts the same fold as galactose mutarotase and shares the same catalytic machinery necessary for the interconversion of the alpha and beta anomers of galactose. The structure revealed the presence in the active site of a sulfate ion attached by an arginine clamp made by the side chain from two strictly conserved arginine residues. This sulfate is ideally positioned to mimic the phosphate group of hexose 6-phosphate. We have subsequently successfully demonstrated that YMR099cp is a hexose-6-phosphate mutarotase with broad substrate specificity. We solved high resolution structures of some substrate enzyme complexes, further confirming our functional hypothesis. The metabolic role of a hexose-6-phosphate mutarotase is discussed. This work illustrates that structural information has been crucial to assign YMR099cp to the orphan EC activity: hexose-phosphate mutarotase.
-===STRUCTURE-BASED FUNCTIONAL ANNOTATION: YEAST YMR099C CODES FOR A D-HEXOSE-6-PHOSPHATE MUTAROTASE. COMPLEX WITH GLUCOSE-6-PHOSPHATE===
+Structure-based functional annotation: yeast ymr099c codes for a D-hexose-6-phosphate mutarotase.,Graille M, Baltaze JP, Leulliot N, Liger D, Quevillon-Cheruel S, van Tilbeurgh H J Biol Chem. 2006 Oct 6;281(40):30175-85. Epub 2006 Jul 20. PMID:16857670<ref>PMID:16857670</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_16857670}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2cir" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 16857670 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_16857670}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-CIR is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CIR OCA].
+[[Category: Saccharomyces cerevisiae S288C]]
+[[Category: Baltaze J-P]]
-==Reference==
+[[Category: Graille M]]
-<ref group="xtra">PMID:16857670</ref><references group="xtra"/>
+[[Category: Leulliot N]]
-[[Category: Glucose-6-phosphate 1-epimerase]]
+[[Category: Liger D]]
-[[Category: Saccharomyces cerevisiae]]
+[[Category: Quevillon-Cheruel S]]
-[[Category: Baltaze, J P.]]
+[[Category: Van Tilbeurgh H]]
-[[Category: Graille, M.]]
-[[Category: Leulliot, N.]]
-[[Category: Liger, D.]]
-[[Category: Quevillon-Cheruel, S.]]
-[[Category: Tilbeurgh, H Van.]]
-[[Category: D-hexose-6-phosphate-1-mutarotase]]
-[[Category: Galactose-6-phosphate-1-epimerase]]
-[[Category: Hypothetical protein]]
-[[Category: Isomerase]]
-[[Category: Mannose-6-phosphate-1-epimerase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 22 11:37:20 2009''