1jc5: Difference between revisions

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-[[Image:1jc5.jpg|left|200px]]
- {{Structure
+==Crystal Structure of Native Methylmalonyl-CoA Epimerase==
-|PDB= 1jc5 |SIZE=350|CAPTION= <scene name='initialview01'>1jc5</scene>, resolution 2.20&Aring;
+<StructureSection load='1jc5' size='340' side='right'caption='[[1jc5]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=SO4:SULFATE ION'>SO4</scene>
+<table><tr><td colspan='2'>[[1jc5]] is a 6 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=1JC5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JC5 FirstGlance]. <br>
-|ACTIVITY= [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]
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=1jc5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jc5 OCA], [https://pdbe.org/1jc5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jc5 RCSB], [https://www.ebi.ac.uk/pdbsum/1jc5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jc5 ProSAT]</span></td></tr>
+</table>
-'''Crystal Structure of Native Methylmalonyl-CoA Epimerase'''
+== Function ==
+[https://www.uniprot.org/uniprot/Q8VQN0_PROFR Q8VQN0_PROFR]
+== Evolutionary Conservation ==
-==Overview==
+[[Image:Consurf_key_small.gif|200px|right]]
-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.
+Check<jmol>
+  <jmolCheckbox>
-==About this Structure==
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jc/1jc5_consurf.spt"</scriptWhenChecked>
-JC5 is a [[Single protein]] structure of sequence from [http://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=1JC5 OCA].
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
-==Reference==
+  </jmolCheckbox>
-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:[http://www.ncbi.nlm.nih.gov/pubmed/11470438 11470438]
+</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=1jc5 ConSurf].
-[[Category: Methylmalonyl-CoA epimerase]]
+<div style="clear:both"></div>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Propionibacterium freudenreichii subsp. shermanii]]
-[[Category: Single protein]]
+[[Category: Baker EN]]
-[[Category: Baker, E N.]]
+[[Category: Baker HM]]
-[[Category: Baker, H M.]]
+[[Category: Mc Carthy AA]]
-[[Category: Carthy, A A.Mc.]]
+[[Category: Patchett ML]]
-[[Category: Patchett, M L.]]
+[[Category: Shewry SC]]
-[[Category: Shewry, S C.]]
-[[Category: SO4]]
-[[Category: epimerisation]]
-[[Category: metal-assisted catalysis]]
-[[Category: methylmalonyl-coa]]
-[[Category: vicinal oxygen chelate superfamily]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:01:28 2008''