1ef9: Difference between revisions

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OCA

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-[[Image:1ef9.jpg|left|200px]]<br /><applet load="1ef9" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1ef9, resolution 2.7&Aring;" />
-'''THE CRYSTAL STRUCTURE OF METHYLMALONYL COA DECARBOXYLASE COMPLEXED WITH 2S-CARBOXYPROPYL COA'''<br />
-==Overview==
+==THE CRYSTAL STRUCTURE OF METHYLMALONYL COA DECARBOXYLASE COMPLEXED WITH 2S-CARBOXYPROPYL COA==
-The molecular structure of methylmalonyl CoA decarboxylase (MMCD), a newly, defined member of the crotonase superfamily encoded by the Escherichia, coli genome, has been solved by X-ray crystallographic analyses to a, resolution of 1.85 A for the unliganded form and to a resolution of 2.7 A, for a complex with an inert thioether analogue of methylmalonyl CoA. Like, two other structurally characterized members of the crotonase superfamily, (crotonase and dienoyl CoA isomerase), MMCD is a hexamer (dimer of, trimers) with each polypeptide chain composed of two structural motifs., The larger N-terminal domain contains the active site while the smaller, C-terminal motif is alpha-helical and involved primarily in trimerization., Unlike the other members of the crotonase superfamily, however, the, C-terminal motif is folded back onto the N-terminal domain such that each, active site is wholly contained within a single subunit. The carboxylate, group of the thioether analogue of methylmalonyl CoA is hydrogen bonded to, the peptidic NH group of Gly 110 and the imidazole ring of His 66. From, modeling studies, it appears that Tyr 140 is positioned within the active, site to participate in the decarboxylation reaction by orienting the, carboxylate group of methylmalonyl CoA so that it is orthogonal to the, plane of the thioester carbonyl group. Surprisingly, while the active site, of MMCD contains Glu 113, which is homologous to the general acid/base Glu, 144 in the active site of crotonase, its carboxylate side chain is, hydrogen bonded to Arg 86, suggesting that it is not directly involved in, catalysis. The new constellation of putative functional groups observed in, the active site of MMCD underscores the diversity of function in this, superfamily.
+<StructureSection load='1ef9' size='340' side='right'caption='[[1ef9]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
+== Structural highlights ==
-==About this Structure==
+<table><tr><td colspan='2'>[[1ef9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EF9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EF9 FirstGlance]. <br>
-EF9 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with 2CP as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Methylmalonyl-CoA_decarboxylase Methylmalonyl-CoA decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.41 4.1.1.41] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1EF9 OCA].
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.7&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2CP:2-CARBOXYPROPYL-COENZYME+A'>2CP</scene></td></tr>
-==Reference==
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ef9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ef9 OCA], [https://pdbe.org/1ef9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ef9 RCSB], [https://www.ebi.ac.uk/pdbsum/1ef9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ef9 ProSAT]</span></td></tr>
-New reactions in the crotonase superfamily: structure of methylmalonyl CoA decarboxylase from Escherichia coli., Benning MM, Haller T, Gerlt JA, Holden HM, Biochemistry. 2000 Apr 25;39(16):4630-9. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10769118 10769118]
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SCPB_ECOLI SCPB_ECOLI] Catalyzes the decarboxylation of methylmalonyl-CoA to propionyl-CoA. Could be part of a pathway that converts succinate to propionate.<ref>PMID:10769117</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/ef/1ef9_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=1ef9 ConSurf].
+<div style="clear:both"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Escherichia coli]]
-[[Category: Methylmalonyl-CoA decarboxylase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Benning MM]]
-[[Category: Benning, M.M.]]
+[[Category: Gerlt JA]]
-[[Category: Gerlt, J.A.]]
+[[Category: Haller T]]
-[[Category: Haller, T.]]
+[[Category: Holden HM]]
-[[Category: Holden, H.M.]]
-[[Category: 2CP]]
-[[Category: 2s-carboxypropyl]]
-[[Category: methylmalonyl coa decarboxylase]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 13:57:32 2007''