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2c3d

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[[Image:2c3d.gif|left|200px]]<br /><applet load="2c3d" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="2c3d, resolution 2.15&Aring;" />
 
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'''2.15 ANGSTROM CRYSTAL STRUCTURE OF 2-KETOPROPYL COENZYME M OXIDOREDUCTASE CARBOXYLASE WITH A COENZYME M DISULFIDE BOUND AT THE ACTIVE SITE'''<br />
 
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==Overview==
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==2.15 Angstrom crystal structure of 2-ketopropyl coenzyme M oxidoreductase carboxylase with a coenzyme M disulfide bound at the active site==
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The structure of the mixed, enzyme-cofactor disulfide intermediate of, ketopropyl-coenzyme M oxidoreductase/carboxylase has been determined by, X-ray diffraction methods. Ketopropyl-coenzyme M, oxidoreductase/carboxylase belongs to a family of pyridine, nucleotide-containing flavin-dependent disulfide oxidoreductases, which, couple the transfer of hydride derived from the NADPH to the reduction of, protein cysteine disulfide. Ketopropyl-coenzyme M, oxidoreductase/carboxylase, a unique member of this enzyme class, catalyzes thioether bond cleavage of the substrate, 2-ketopropyl-coenzyme, M, and carboxylation of what is thought to be an enzyme-stabilized, enolacetone intermediate. The mixed disulfide of 2-ketopropyl-coenzyme M, oxidoreductase/carboxylase was captured through crystallization of the, enzyme with the physiological products of the reaction, acetoacetate, coenzyme M, and NADP, and reduction of the crystals with dithiothreitol, just prior to data collection. Density in the active-site environment, consistent with acetone, the product of reductive decarboxylation of, acetoacetate, was revealed in this structure in addition to a well-defined, hydrophobic pocket or channel that could be involved in the access for, carbon dioxide. The analysis of this structure and that of a, coenzyme-M-bound form provides insights into the stabilization of, intermediates, substrate carboxylation, and product release.
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<StructureSection load='2c3d' size='340' side='right'caption='[[2c3d]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[2c3d]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Xanthobacter_autotrophicus_Py2 Xanthobacter autotrophicus Py2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C3D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2C3D FirstGlance]. <br>
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2C3D is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Xanthobacter_autotrophicus Xanthobacter autotrophicus] with FAD and COM as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/2-oxopropyl-CoM_reductase_(carboxylating) 2-oxopropyl-CoM reductase (carboxylating)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.8.1.5 1.8.1.5] Known structural/functional Site: <scene name='pdbsite=AC1:Fad Binding Site For Chain B'>AC1</scene>. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2C3D OCA].
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.15&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=COM:1-THIOETHANESULFONIC+ACID'>COM</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene></td></tr>
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==Reference==
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2c3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c3d OCA], [https://pdbe.org/2c3d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2c3d RCSB], [https://www.ebi.ac.uk/pdbsum/2c3d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2c3d ProSAT]</span></td></tr>
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Mechanistic implications of the structure of the mixed-disulfide intermediate of the disulfide oxidoreductase, 2-ketopropyl-coenzyme M oxidoreductase/carboxylase., Pandey AS, Nocek B, Clark DD, Ensign SA, Peters JW, Biochemistry. 2006 Jan 10;45(1):113-20. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16388586 16388586]
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</table>
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[[Category: 2-oxopropyl-CoM reductase (carboxylating)]]
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== Function ==
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[[Category: Single protein]]
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[https://www.uniprot.org/uniprot/XECC_XANP2 XECC_XANP2] Catalyzes the reductive cleavage of the thioether linkage of 2-ketopropyl-coenzyme M, and the subsequent carboxylation of the ketopropyl cleavage product, yielding the products acetoacetate and free coenzyme M.
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[[Category: Xanthobacter autotrophicus]]
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== Evolutionary Conservation ==
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[[Category: Clark, D.D.]]
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[[Image:Consurf_key_small.gif|200px|right]]
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[[Category: Ensign, S.A.]]
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Check<jmol>
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[[Category: Nocek, B.]]
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<jmolCheckbox>
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[[Category: Pandey, A.S.]]
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c3/2c3d_consurf.spt"</scriptWhenChecked>
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[[Category: Peters, J.W.]]
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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[[Category: COM]]
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<text>to colour the structure by Evolutionary Conservation</text>
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[[Category: FAD]]
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</jmolCheckbox>
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[[Category: coenzyme m]]
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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=2c3d ConSurf].
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[[Category: com disulfide]]
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<div style="clear:both"></div>
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[[Category: fad]]
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__TOC__
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[[Category: oxidoreductase]]
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</StructureSection>
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[[Category: redox-active center]]
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[[Category: Large Structures]]
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[[Category: Xanthobacter autotrophicus Py2]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Dec 18 19:07:58 2007''
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[[Category: Clark DD]]
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[[Category: Ensign SA]]
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[[Category: Nocek B]]
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[[Category: Pandey AS]]
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[[Category: Peters JW]]

Current revision

2.15 Angstrom crystal structure of 2-ketopropyl coenzyme M oxidoreductase carboxylase with a coenzyme M disulfide bound at the active site

PDB ID 2c3d

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