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| | ==Crystal Structure of Se-Met Methylmalonyl-CoA Epimerase== | | ==Crystal Structure of Se-Met Methylmalonyl-CoA Epimerase== |
| - | <StructureSection load='1jc4' size='340' side='right' caption='[[1jc4]], [[Resolution|resolution]] 2.00Å' scene=''> | + | <StructureSection load='1jc4' size='340' side='right'caption='[[1jc4]], [[Resolution|resolution]] 2.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1jc4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"propionibacterium_shermanii"_van_niel_1928 "propionibacterium shermanii" van niel 1928]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JC4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JC4 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1jc4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Propionibacterium_freudenreichii_subsp._shermanii Propionibacterium freudenreichii subsp. shermanii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JC4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JC4 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1jc5|1jc5]]</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=1jc4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jc4 OCA], [https://pdbe.org/1jc4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jc4 RCSB], [https://www.ebi.ac.uk/pdbsum/1jc4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jc4 ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Methylmalonyl-CoA_epimerase Methylmalonyl-CoA epimerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.99.1 5.1.99.1] </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=1jc4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jc4 OCA], [http://pdbe.org/1jc4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1jc4 RCSB], [http://www.ebi.ac.uk/pdbsum/1jc4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1jc4 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q8VQN0_PROFR Q8VQN0_PROFR] |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | <jmolCheckbox> | | <jmolCheckbox> |
| | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jc/1jc4_consurf.spt"</scriptWhenChecked> | | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jc/1jc4_consurf.spt"</scriptWhenChecked> |
| - | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Propionibacterium shermanii van niel 1928]] | + | [[Category: Large Structures]] |
| - | [[Category: Methylmalonyl-CoA epimerase]] | + | [[Category: Propionibacterium freudenreichii subsp. shermanii]] |
| - | [[Category: Baker, E N]] | + | [[Category: Baker EN]] |
| - | [[Category: Baker, H M]] | + | [[Category: Baker HM]] |
| - | [[Category: Carthy, A A.Mc]] | + | [[Category: Mc Carthy AA]] |
| - | [[Category: Patchett, M L]] | + | [[Category: Patchett ML]] |
| - | [[Category: Shewry, S C]] | + | [[Category: Shewry SC]] |
| - | [[Category: Isomerase]]
| + | |
| - | [[Category: Methylmalonyl-coa]]
| + | |
| - | [[Category: Vicinal oxygen chelate superfamily]]
| + | |
| Structural highlights
Function
Q8VQN0_PROFR
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 PubMed
BACKGROUND: Methylmalonyl-CoA epimerase (MMCE) is an essential enzyme in the breakdown of odd-numbered fatty acids and of the amino acids valine, isoleucine, and methionine. Present in many bacteria and in animals, it catalyzes the conversion of (2R)-methylmalonyl-CoA to (2S)-methylmalonyl-CoA, the substrate for the B12-dependent enzyme, methylmalonyl-CoA mutase. Defects in this pathway can result in severe acidosis and cause damage to the central nervous system in humans. RESULTS: The crystal structure of MMCE from Propionibacterium shermanii has been determined at 2.0 A resolution. The MMCE monomer is folded into two tandem betaalphabetabetabeta modules that pack edge-to-edge to generate an 8-stranded beta sheet. Two monomers then pack back-to-back to create a tightly associated dimer. In each monomer, the beta sheet curves around to create a deep cleft, in the floor of which His12, Gln65, His91, and Glu141 provide a binding site for a divalent metal ion, as shown by the binding of Co2+. Modeling 2-methylmalonate into the active site identifies two glutamate residues as the likely essential bases for the epimerization reaction. CONCLUSIONS: The betaalphabetabetabeta modules of MMCE correspond with those found in several other proteins, including bleomycin resistance protein, glyoxalase I, and a family of extradiol dioxygenases. Differences in connectivity are consistent with the evolution of these very different proteins from a common precursor by mechanisms of gene duplication and domain swapping. The metal binding residues also align precisely, and striking structural similarities between MMCE and glyoxalase I suggest common mechanisms in their respective epimerization and isomerization reactions.
Crystal structure of methylmalonyl-coenzyme A epimerase from P. shermanii: a novel enzymatic function on an ancient metal binding scaffold.,McCarthy AA, Baker HM, Shewry SC, Patchett ML, Baker EN Structure. 2001 Jul 3;9(7):637-46. PMID:11470438[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ McCarthy AA, Baker HM, Shewry SC, Patchett ML, Baker EN. Crystal structure of methylmalonyl-coenzyme A epimerase from P. shermanii: a novel enzymatic function on an ancient metal binding scaffold. Structure. 2001 Jul 3;9(7):637-46. PMID:11470438
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