3c7c

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Current revision (09:33, 21 February 2024) (edit) (undo)
 
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<StructureSection load='3c7c' size='340' side='right'caption='[[3c7c]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
<StructureSection load='3c7c' size='340' side='right'caption='[[3c7c]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3c7c]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/King_scallop King scallop]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C7C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3C7C FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3c7c]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pecten_maximus Pecten maximus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C7C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3C7C FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ARG:ARGININE'>ARG</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
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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]] 3.1&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3c7a|3c7a]], [[3c7d|3c7d]]</div></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=ARG:ARGININE'>ARG</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">odh1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6579 King scallop])</td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/D-octopine_dehydrogenase D-octopine dehydrogenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.1.11 1.5.1.11] </span></td></tr>
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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=3c7c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c7c OCA], [https://pdbe.org/3c7c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3c7c RCSB], [https://www.ebi.ac.uk/pdbsum/3c7c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3c7c ProSAT]</span></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=3c7c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c7c OCA], [https://pdbe.org/3c7c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3c7c RCSB], [https://www.ebi.ac.uk/pdbsum/3c7c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3c7c ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[https://www.uniprot.org/uniprot/OCDH_PECMA OCDH_PECMA]] Catalyzes the reverse reaction of octopine dehydrogenation. Acts on L-arginine in preference to other substrates such as canavanine, cysteine, L-alanine, ornithine or norvaline, owing to the presence of the positively charged guanidium group.<ref>PMID:18028427</ref> <ref>PMID:18599075</ref>
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[https://www.uniprot.org/uniprot/OCDH_PECMA OCDH_PECMA] Catalyzes the reverse reaction of octopine dehydrogenation. Acts on L-arginine in preference to other substrates such as canavanine, cysteine, L-alanine, ornithine or norvaline, owing to the presence of the positively charged guanidium group.<ref>PMID:18028427</ref> <ref>PMID:18599075</ref>
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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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=3c7c ConSurf].
</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=3c7c ConSurf].
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== Publication Abstract from PubMed ==
 
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Octopine dehydrogenase [N(2)-(D-1-carboxyethyl)-L-arginine:NAD(+) oxidoreductase] (OcDH) from the adductor muscle of the great scallop Pecten maximus catalyzes the reductive condensation of l-arginine and pyruvate to octopine during escape swimming. This enzyme, which is a prototype of opine dehydrogenases (OpDHs), oxidizes glycolytically born NADH to NAD(+), thus sustaining anaerobic ATP provision during short periods of strenuous muscular activity. In contrast to some other OpDHs, OcDH uses only l-arginine as the amino acid substrate. Here, we report the crystal structures of OcDH in complex with NADH and the binary complexes NADH/l-arginine and NADH/pyruvate, providing detailed information about the principles of substrate recognition, ligand binding and the reaction mechanism. OcDH binds its substrates through a combination of electrostatic forces and size selection, which guarantees that OcDH catalysis proceeds with substrate selectivity and stereoselectivity, giving rise to a second chiral center and exploiting a "molecular ruler" mechanism.
 
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A structural basis for substrate selectivity and stereoselectivity in octopine dehydrogenase from Pecten maximus.,Smits SH, Mueller A, Schmitt L, Grieshaber MK J Mol Biol. 2008 Aug 1;381(1):200-11. Epub 2008 Jun 7. PMID:18599075<ref>PMID:18599075</ref>
 
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 
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</div>
 
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<div class="pdbe-citations 3c7c" style="background-color:#fffaf0;"></div>
 
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: D-octopine dehydrogenase]]
 
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[[Category: King scallop]]
 
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Grieshaber, M K]]
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[[Category: Pecten maximus]]
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[[Category: Mueller, A]]
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[[Category: Grieshaber MK]]
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[[Category: Schmitt, L]]
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[[Category: Mueller A]]
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[[Category: Smits, S H.J]]
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[[Category: Schmitt L]]
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[[Category: Oxidoreductase]]
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[[Category: Smits SHJ]]

Current revision

A structural basis for substrate and stereo selectivity in octopine dehydrogenase (ODH-NADH-L-Arginine)

PDB ID 3c7c

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