1o99: Difference between revisions

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-[[Image:1o99.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1o99", creates the "Structure Box" on the page.
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-{{STRUCTURE_1o99|  PDB=1o99  |  SCENE=  }}
-'''CRYSTAL STRUCTURE OF THE S62A MUTANT OF PHOSPHOGLYCERATE MUTASE FROM BACILLUS STEAROTHERMOPHILUS COMPLEXED WITH 2-PHOSPHOGLYCERATE'''
+==CRYSTAL STRUCTURE OF THE S62A MUTANT OF PHOSPHOGLYCERATE MUTASE FROM BACILLUS STEAROTHERMOPHILUS COMPLEXED WITH 2-PHOSPHOGLYCERATE==
+<StructureSection load='1o99' size='340' side='right'caption='[[1o99]], [[Resolution|resolution]] 2.65&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1o99]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1O99 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1O99 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.65&#8491;</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=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=1o99 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1o99 OCA], [https://pdbe.org/1o99 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1o99 RCSB], [https://www.ebi.ac.uk/pdbsum/1o99 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1o99 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/GPMI_GEOSE GPMI_GEOSE] Catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate.[HAMAP-Rule:MF_01038]
+== 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/o9/1o99_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1o99 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Phosphoglycerate mutases catalyze the isomerization of 2 and 3-phosphoglycerates, and are essential for glucose metabolism in most organisms. Here, we further characterize the 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (iPGM) from Bacillus stearothermophilus by determination of a high-resolution (1.4A) crystal structure of the wild-type enzyme and the crystal structure of its S62A mutant. The mutant structure surprisingly showed the replacement of one of the two catalytically essential manganese ions with a water molecule, offering an additional possible explanation for its lack of catalytic activity. Crystal structures invariably show substrate phosphoglycerate to be entirely buried in a deep cleft between the two iPGM domains. Flexibility analyses were therefore employed to reveal the likely route of substrate access to the catalytic site through an aperture created in the enzyme's surface during certain stages of the catalytic process. Several conserved residues lining this aperture may contribute to orientation of the substrate as it enters. Factors responsible for the retention of glycerate within the phosphoenzyme structure in the proposed mechanism are identified by molecular modeling of the glycerate complex of the phosphoenzyme. Taken together, these results allow for a better understanding of the mechanism of action of iPGMs. Many of the results are relevant to a series of evolutionarily related enzymes. These studies will facilitate the development of iPGM inhibitors which, due to the demonstrated importance of this enzyme in many bacteria, would be of great potential clinical significance.
-==Overview==
+Insights into the catalytic mechanism of cofactor-independent phosphoglycerate mutase from X-ray crystallography, simulated dynamics and molecular modeling.,Rigden DJ, Lamani E, Mello LV, Littlejohn JE, Jedrzejas MJ J Mol Biol. 2003 May 9;328(4):909-20. PMID:12729763<ref>PMID:12729763</ref>
-Phosphoglycerate mutases catalyze the isomerization of 2 and 3-phosphoglycerates, and are essential for glucose metabolism in most organisms. Here, we further characterize the 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (iPGM) from Bacillus stearothermophilus by determination of a high-resolution (1.4A) crystal structure of the wild-type enzyme and the crystal structure of its S62A mutant. The mutant structure surprisingly showed the replacement of one of the two catalytically essential manganese ions with a water molecule, offering an additional possible explanation for its lack of catalytic activity. Crystal structures invariably show substrate phosphoglycerate to be entirely buried in a deep cleft between the two iPGM domains. Flexibility analyses were therefore employed to reveal the likely route of substrate access to the catalytic site through an aperture created in the enzyme's surface during certain stages of the catalytic process. Several conserved residues lining this aperture may contribute to orientation of the substrate as it enters. Factors responsible for the retention of glycerate within the phosphoenzyme structure in the proposed mechanism are identified by molecular modeling of the glycerate complex of the phosphoenzyme. Taken together, these results allow for a better understanding of the mechanism of action of iPGMs. Many of the results are relevant to a series of evolutionarily related enzymes. These studies will facilitate the development of iPGM inhibitors which, due to the demonstrated importance of this enzyme in many bacteria, would be of great potential clinical significance.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-O99 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1O99 OCA].
+</div>
+<div class="pdbe-citations 1o99" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Insights into the catalytic mechanism of cofactor-independent phosphoglycerate mutase from X-ray crystallography, simulated dynamics and molecular modeling., Rigden DJ, Lamani E, Mello LV, Littlejohn JE, Jedrzejas MJ, J Mol Biol. 2003 May 9;328(4):909-20. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12729763 12729763]
+*[[Phosphoglycerate mutase 3D structures|Phosphoglycerate mutase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Geobacillus stearothermophilus]]
-[[Category: Phosphoglycerate mutase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Jedrzejas MJ]]
-[[Category: Jedrzejas, M J.]]
+[[Category: Lamani E]]
-[[Category: Lamani, E.]]
+[[Category: Littlejohn JE]]
-[[Category: Littlejohn, J E.]]
+[[Category: Rigden DJ]]
-[[Category: Rigden, D J.]]
-[[Category: Alpha/beta-type structure]]
-[[Category: Isomerase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 03:32:53 2008''