3igy: Difference between revisions

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 <StructureSection load='3igy' size='340' side='right'caption='[[3igy]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3igy]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Leime Leime]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IGY OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3IGY FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3igy]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Leishmania_mexicana Leishmania mexicana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IGY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IGY FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2PG:2-PHOSPHOGLYCERIC+ACID'>2PG</scene>, <scene name='pdbligand=3PG:3-PHOSPHOGLYCERIC+ACID'>3PG</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 2.003&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1ejj|1ejj]], [[1eqj|1eqj]], [[3igz|3igz]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2PG:2-PHOSPHOGLYCERIC+ACID'>2PG</scene>, <scene name='pdbligand=3PG:3-PHOSPHOGLYCERIC+ACID'>3PG</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphoglycerate_mutase Phosphoglycerate mutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.2.1 5.4.2.1] </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=3igy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3igy OCA], [https://pdbe.org/3igy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3igy RCSB], [https://www.ebi.ac.uk/pdbsum/3igy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3igy ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=3igy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3igy OCA], [http://pdbe.org/3igy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3igy RCSB], [http://www.ebi.ac.uk/pdbsum/3igy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3igy ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q86N96_LEIME Q86N96_LEIME]
 == Evolutionary Conservation ==
 [[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=3igy ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The structures of Leishmania mexicana cofactor-independent phosphoglycerate mutase (Lm iPGAM) crystallised with the substrate 3-phosphoglycerate at high and low cobalt concentrations have been solved at 2.00- and 1.90-A resolutions. Both structures are very similar and the active site contains both 3-phosphoglycerate and 2-phosphoglycerate at equal occupancies (50%). Lm iPGAM co-crystallised with the product 2-phosphoglycerate yields the same structure. Two Co(2+) are coordinated within the active site with different geometries and affinities. The cobalt at the M1 site has a distorted octahedral geometry and is present at 100% occupancy. The M2-site Co(2+) binds with distorted tetrahedral geometry, with only partial occupancy, and coordinates with Ser75, the residue involved in phosphotransfer. When the M2 site is occupied, the side chain of Ser75 adopts a position that is unfavourable for catalysis, indicating that this site may not be occupied under physiological conditions and that catalysis may occur via a one-metal mechanism. The geometry of the M2 site suggests that it is possible for Ser75 to be activated for phosphotransfer by H-bonding to nearby residues rather than by metal coordination. The 16 active-site residues of Lm iPGAM are conserved in the Mn-dependent iPGAM from Bacillus stearothermophilus (33% overall sequence identity). However, Lm iPGAM has an inserted tyrosine (Tyr210) that causes the M2 site to diminish in size, consistent with its reduced metal affinity. Tyr210 is present in trypanosomatid and plant iPGAMs, but not in the enzymes from other organisms, indicating that there are two subclasses of iPGAMs.
-Crystal structures of Leishmania mexicana phosphoglycerate mutase suggest a one-metal mechanism and a new enzyme subclass.,Nowicki MW, Kuaprasert B, McNae IW, Morgan HP, Harding MM, Michels PA, Fothergill-Gilmore LA, Walkinshaw MD J Mol Biol. 2009 Dec 4;394(3):535-43. Epub 2009 Sep 23. PMID:19781556<ref>PMID:19781556</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3igy" style="background-color:#fffaf0;"></div>
 ==See Also==
 *[[Phosphoglycerate mutase 3D structures|Phosphoglycerate mutase 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Leime]]
+[[Category: Leishmania mexicana]]
-[[Category: Phosphoglycerate mutase]]
+[[Category: Fothergill-Gilmore LA]]
-[[Category: Fothergill-Gilmore, L A]]
+[[Category: Harding MM]]
-[[Category: Harding, M M]]
+[[Category: Kuaprasert B]]
-[[Category: Kuaprasert, B]]
+[[Category: McNae IW]]
-[[Category: McNae, I W]]
+[[Category: Michels PA]]
-[[Category: Michels, P A]]
+[[Category: Morgan HP]]
-[[Category: Morgan, H P]]
+[[Category: Nowicki MW]]
-[[Category: Nowicki, M W]]
+[[Category: Walkinshaw MD]]
-[[Category: Walkinshaw, M D]]
-[[Category: Cobalt]]
-[[Category: Glycolysis]]
-[[Category: Isomerase]]
-[[Category: Mutase]]