Biology:D-octopine dehydrogenase
| D-octopine dehydrogenase | |||||||||
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| Identifiers | |||||||||
| EC number | 1.5.1.11 | ||||||||
| CAS number | 37256-27-2 | ||||||||
| Databases | |||||||||
| IntEnz | IntEnz view | ||||||||
| BRENDA | BRENDA entry | ||||||||
| ExPASy | NiceZyme view | ||||||||
| KEGG | KEGG entry | ||||||||
| MetaCyc | metabolic pathway | ||||||||
| PRIAM | profile | ||||||||
| PDB structures | RCSB PDB PDBe PDBsum | ||||||||
| Gene Ontology | AmiGO / QuickGO | ||||||||
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Octopine dehydrogenase (N2-(D-1-carboxyethyl)-L-arginine:NAD+ oxidoreductase, OcDH, ODH) is a dehydrogenase enzyme in the opine dehydrogenase family that helps maintain redox balance under anaerobic conditions. It is found largely in aquatic invertebrates, especially mollusks, sipunculids, and coelenterates,[1] and plays a role analogous to lactate dehydrogenase (found largely in vertebrates)[2] . In the presence of NADH, OcDH catalyzes the reductive condensation of an α-keto acid with an amino acid to form N-carboxyalkyl-amino acids (opines).[1] The purpose of this reaction is to reoxidize glycolytically formed NADH to NAD+, replenishing this important reductant used in glycolysis and allowing for the continued production of ATP in the absence of oxygen.[3][4]
- L-arginine + pyruvate + NADH + H+ [math]\displaystyle{ \rightleftharpoons }[/math] D-octopine + NAD+ + H2O
Structure
OcDH is a monomer with a molecular weight of 38kD[5] made of two functionally distinct subunits. The first, Domain I, is composed of 199 amino acids and contains a Rossmann fold.[6] Domain II is composed of 204 amino acids and is connected to the Rossmann fold of Domain I via its N-terminus.[7]
Mechanism
Isothermal titration calorimetry (ITR),[3] nuclear magnetic resonance (NMR)[8] crystallography,[6][8] and clonal studies[1][6] of OcDH and its substrates have led to the identification of the enzyme reaction mechanism. First, the Rossmann fold in Domain I of OcDH binds NADH.[6] Binding of NADH to the Rossmann fold triggers small conformational change typical in the binding of NADH to most dehydrogenases[9] resulting in an interaction between the pyrophosphate moiety of NADH with residue Arg324 on Domain II. This interaction with Arg324 generates and stabilizes the L-arginine binding site[8] and triggers partial domain closure (reduction in the distance between the two domains).[6] The binding of the guanidinium headgroup of L-arginine to the active site of the OcDH:NADH complex (located between the domains) induces a rotational movement of Domain II towards Domain I (via a helix-kink-helix structure in Domain II).[8] This conformational change forms the pyruvate binding site. Binding of pyruvate to the OcDH:NADH:L-arginine complex places the alpha-ketogroup of pyruvate in proximity with the alpha-amino group of L-arginine. The juxtaposition of these groups on the substrates results in the formation of a Schiff base which is subsequently reduced to D-octopine.[6] The priming of the pyruvate site for hydride transfer via a Schiff base through the sequential binding of NADH and L-arginine to OcDH prevents the reduction of pyruvate to lactate.[8]
Substrate specificity
Octopine dehydrogenase has at least two structural characteristics that contribute to substrate specificity. Upon binding to NADH, amino acid residues lining either side of the active site within the space between the domains of OcDH act as a “molecular ruler”, physically limiting the size of the substrates that can fit into the active site.[6] There is also a negatively charged pocket in the cleft between the two domains that acts an “electrostatic sink” that captures the positively charged side-chain of L-arginine.[6]
Evolution
Examination of OcDH reaction rates from different organisms in the presence of different substrates has demonstrated a trend of increasing specificity for substrates in animals of increasing complexity.[10] Evolutionary modification in substrate specificity is seen most drastically in the amino acid substrate. OcDH from some sea anemones has been shown to be able to use non-guanidino amino acids whereas OcDH form more complex invertebrates, such as the cuttlefish, can only use L-arginine (a guanidino amino acid).[10]
References
- ↑ 1.0 1.1 1.2 "Putative reaction mechanism of heterologously expressed octopine dehydrogenase from the great scallop, Pecten maximus (L)". FEBS Journal 274 (24): 6329–6339. 2007. doi:10.1111/j.1742-4658.2007.06151.x. PMID 18028427.
- ↑ "Gene Expression and Physiological Changes of Different Populations of the Long-Lived Bivalve Arctica islandica under Low Oxygen Conditions". PLOS ONE 7 (9): e44621. 2012. doi:10.1371/journal.pone.0044621. PMID 23028566. Bibcode: 2012PLoSO...744621P.
- ↑ 3.0 3.1 "Control of D-octopine formation in scallop adductor muscle as revealed through thermodynamic studies of octopine dehydrogenase". Journal of Experimental Biology 215 (9): 1515–1522. 2012. doi:10.1242/jeb.069344. PMID 22496288.
- ↑ "Metabolic and physiological responses in tissues of the long-lived bivalve Arctica islandica to oxygen deficiency". Comparative Biochemistry and Physiology A 158 (4): 513–519. 2011. doi:10.1016/j.cbpa.2010.12.015. PMID 21184842.
- ↑ "Octopine dehydrogenase from Pecten maximus: steady-state mechanism". Biochemistry 23 (7): 1348–53. 1984. doi:10.1021/bi00302a002. PMID 6722094.
- ↑ 6.0 6.1 6.2 6.3 6.4 6.5 6.6 6.7 "A Structural Basis for Substrate Selectivity and Stereoselectivity in Octopine Dehydrogenase from Pecten maximus". Journal of Molecular Biology 381 (1): 200–211. 2008. doi:10.1016/j.jmb.2008.06.003. PMID 18599075.
- ↑ "The geometry of domain combination in proteins". Journal of Molecular Biology 315 (4): 927–939. 2002. doi:10.1006/jmbi.2001.5288. PMID 11812158.
- ↑ 8.0 8.1 8.2 8.3 8.4 "Insights into the Mechanism of Ligand Binding to Octopine Dehydrogenase from Pecten maximus by NMR and Crystallography". PLOS ONE 5 (8): e12312. 2010. doi:10.1371/journal.pone.0012312. PMID 20808820. Bibcode: 2010PLoSO...512312S.
- ↑ "Chemical and biological evolution of nucleotide-binding protein". Nature 250 (5463): 194–199. 1974. doi:10.1038/250194a0. PMID 4368490. Bibcode: 1974Natur.250..194R.
- ↑ 10.0 10.1 "Substrate specificities of octopine dehydrogenases from marine invertebrates". Comparative Biochemistry and Physiology 73B (3): 521–528. 1982.
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