|
|
| (One intermediate revision not shown.) |
| Line 1: |
Line 1: |
| | | | |
| | ==A structural basis for substrate and stereo selectivity in octopine dehydrogenase (ODH-NADH-Pyruvate)== | | ==A structural basis for substrate and stereo selectivity in octopine dehydrogenase (ODH-NADH-Pyruvate)== |
| - | <StructureSection load='3c7d' size='340' side='right' caption='[[3c7d]], [[Resolution|resolution]] 2.50Å' scene=''> | + | <StructureSection load='3c7d' size='340' side='right'caption='[[3c7d]], [[Resolution|resolution]] 2.50Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3c7d]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/King_scallop King scallop]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C7D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3C7D FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3c7d]] 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=3C7D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3C7D FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</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]] 2.5Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3c7a|3c7a]], [[3c7c|3c7c]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">odh1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6579 King scallop])</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=3c7d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c7d OCA], [https://pdbe.org/3c7d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3c7d RCSB], [https://www.ebi.ac.uk/pdbsum/3c7d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3c7d 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/D-octopine_dehydrogenase D-octopine dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.1.11 1.5.1.11] </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=3c7d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c7d OCA], [http://pdbe.org/3c7d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3c7d RCSB], [http://www.ebi.ac.uk/pdbsum/3c7d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3c7d ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://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> | + | [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]] |
| Line 35: |
Line 33: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: D-octopine dehydrogenase]] | + | [[Category: Large Structures]] |
| - | [[Category: King scallop]] | + | [[Category: Pecten maximus]] |
| - | [[Category: Grieshaber, M K]] | + | [[Category: Grieshaber MK]] |
| - | [[Category: Mueller, A]] | + | [[Category: Mueller A]] |
| - | [[Category: Schmitt, L]] | + | [[Category: Schmitt L]] |
| - | [[Category: Smits, S H.J]] | + | [[Category: Smits SHJ]] |
| - | [[Category: Oxidoreductase]]
| + | |
| Structural highlights
Function
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.[1] [2]
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
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.
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[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Muller A, Janssen F, Grieshaber MK. Putative reaction mechanism of heterologously expressed octopine dehydrogenase from the great scallop, Pecten maximus (L). FEBS J. 2007 Dec;274(24):6329-39. Epub 2007 Nov 19. PMID:18028427 doi:EJB6151
- ↑ Smits SH, Mueller A, Schmitt L, Grieshaber MK. A structural basis for substrate selectivity and stereoselectivity in octopine dehydrogenase from Pecten maximus. J Mol Biol. 2008 Aug 1;381(1):200-11. Epub 2008 Jun 7. PMID:18599075 doi:10.1016/j.jmb.2008.06.003
- ↑ Smits SH, Mueller A, Schmitt L, Grieshaber MK. A structural basis for substrate selectivity and stereoselectivity in octopine dehydrogenase from Pecten maximus. J Mol Biol. 2008 Aug 1;381(1):200-11. Epub 2008 Jun 7. PMID:18599075 doi:10.1016/j.jmb.2008.06.003
|
