OCDH_PECMA
ID OCDH_PECMA Reviewed; 399 AA.
AC Q9BHM6;
DT 14-DEC-2011, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2001, sequence version 1.
DT 03-AUG-2022, entry version 88.
DE RecName: Full=Octopine dehydrogenase {ECO:0000312|EMBL:CAC36305.1};
DE Short=OcDH {ECO:0000303|PubMed:18599075};
DE EC=1.5.1.11 {ECO:0000312|EMBL:CAC36305.1};
GN Name=odh1 {ECO:0000312|EMBL:CAC36305.1};
OS Pecten maximus (King scallop) (Pilgrim's clam).
OC Eukaryota; Metazoa; Spiralia; Lophotrochozoa; Mollusca; Bivalvia;
OC Autobranchia; Pteriomorphia; Pectinida; Pectinoidea; Pectinidae; Pecten.
OX NCBI_TaxID=6579;
RN [1] {ECO:0000305, ECO:0000312|EMBL:CAC36305.1}
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, CATALYTIC ACTIVITY,
RP BIOPHYSICOCHEMICAL PROPERTIES, AND MUTAGENESIS OF CYS-148; HIS-212; ARG-324
RP AND ASP-329.
RC TISSUE=Adductor muscle {ECO:0000269|PubMed:18028427};
RX PubMed=18028427; DOI=10.1111/j.1742-4658.2007.06151.x;
RA Muller A., Janssen F., Grieshaber M.K.;
RT "Putative reaction mechanism of heterologously expressed octopine
RT dehydrogenase from the great scallop, Pecten maximus (L).";
RL FEBS J. 274:6329-6339(2007).
RN [2] {ECO:0000305, ECO:0000312|PDB:3C7A}
RP X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) OF NATIVE PROTEIN AND IN COMPLEXES
RP WITH L-ARGININE; NADH AND PYRUVATE, FUNCTION, BIOPHYSICOCHEMICAL
RP PROPERTIES, AND MUTAGENESIS OF GLN-118.
RX PubMed=18599075; DOI=10.1016/j.jmb.2008.06.003;
RA Smits S.H., Mueller A., Schmitt L., Grieshaber M.K.;
RT "A structural basis for substrate selectivity and stereoselectivity in
RT octopine dehydrogenase from Pecten maximus.";
RL J. Mol. Biol. 381:200-211(2008).
RN [3] {ECO:0000305, ECO:0000312|PDB:3IQD}
RP X-RAY CRYSTALLOGRAPHY (2.80 ANGSTROMS) IN COMPLEX WITH NADH AND AGMATINE,
RP AND ACTIVITY REGULATION.
RX PubMed=20808820; DOI=10.1371/journal.pone.0012312;
RA Smits S.H., Meyer T., Mueller A., van Os N., Stoldt M., Willbold D.,
RA Schmitt L., Grieshaber M.K.;
RT "Insights into the mechanism of ligand binding to octopine dehydrogenase
RT from Pecten maximus by NMR and crystallography.";
RL PLoS ONE 5:E12312-E12312(2010).
CC -!- FUNCTION: Catalyzes the reverse reaction of octopine dehydrogenation.
CC Acts on L-arginine in preference to other substrates such as
CC canavanine, cysteine, L-alanine, ornithine or norvaline, owing to the
CC presence of the positively charged guanidium group.
CC {ECO:0000269|PubMed:18028427, ECO:0000269|PubMed:18599075}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-octopine + H2O + NAD(+) = H(+) + L-arginine + NADH +
CC pyruvate; Xref=Rhea:RHEA:16285, ChEBI:CHEBI:15361, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:32682, ChEBI:CHEBI:57520,
CC ChEBI:CHEBI:57540, ChEBI:CHEBI:57945; EC=1.5.1.11;
CC Evidence={ECO:0000269|PubMed:18028427};
CC -!- ACTIVITY REGULATION: Agmatine acts as a competitive inhibitor of the
CC condensation reaction where the L-arginine and agmatine substrates
CC compete for the same site. {ECO:0000269|PubMed:20808820}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.8 mM for pyruvate for the reverse reaction of the octopine
CC dehydrogenase activity {ECO:0000269|PubMed:18028427,
CC ECO:0000269|PubMed:18599075};
CC KM=0.5 mM for L-arginine for the reverse reaction of the octopine
CC dehydrogenase activity {ECO:0000269|PubMed:18028427,
CC ECO:0000269|PubMed:18599075};
CC KM=0.0198 mM for NADH for the reverse reaction of the octopine
CC dehydrogenase activity {ECO:0000269|PubMed:18028427,
CC ECO:0000269|PubMed:18599075};
CC KM=5.9 mM for ketobutyrate for the reverse reaction of the octopine
CC dehydrogenase activity {ECO:0000269|PubMed:18028427,
CC ECO:0000269|PubMed:18599075};
CC KM=49.8 mM for ketovalerate for the reverse reaction of the octopine
CC dehydrogenase activity {ECO:0000269|PubMed:18028427,
CC ECO:0000269|PubMed:18599075};
CC Vmax=1074 umol/min/mg enzyme with pyruvate as substrate for the
CC reverse reaction of the octopine dehydrogenase activity
CC {ECO:0000269|PubMed:18028427, ECO:0000269|PubMed:18599075};
CC Vmax=886 umol/min/mg enzyme with L-arginine as substrate for the
CC reverse reaction of the octopine dehydrogenase activity
CC {ECO:0000269|PubMed:18028427, ECO:0000269|PubMed:18599075};
CC Vmax=903 umol/min/mg enzyme with NADH as substrate for the reverse
CC reaction of the octopine dehydrogenase activity
CC {ECO:0000269|PubMed:18028427, ECO:0000269|PubMed:18599075};
CC Vmax=728 umol/min/mg enzyme with ketobutyrate as substrate for the
CC reverse reaction of the octopine dehydrogenase activity
CC {ECO:0000269|PubMed:18028427, ECO:0000269|PubMed:18599075};
CC Vmax=377 umol/min/mg enzyme with ketovalerate as substrate for the
CC reverse reaction of the octopine dehydrogenase activity
CC {ECO:0000269|PubMed:18028427, ECO:0000269|PubMed:18599075};
CC Note=The kinetic constants are determined for the recombinant His(5)-
CC tagged protein. {ECO:0000269|PubMed:18028427,
CC ECO:0000269|PubMed:18599075};
CC pH dependence:
CC Optimum pH is 8.0-9.5 for the forward reaction and 6.5-7.5 for the
CC reverse reaction. {ECO:0000269|PubMed:18028427,
CC ECO:0000269|PubMed:18599075};
CC -!- SIMILARITY: Belongs to the lysopine/nopaline/octopine/opine/vitopine
CC dehydrogenases family. {ECO:0000255}.
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DR EMBL; AJ237916; CAC36305.1; -; mRNA.
DR PDB; 3C7A; X-ray; 2.10 A; A=1-399.
DR PDB; 3C7C; X-ray; 3.10 A; B=1-399.
DR PDB; 3C7D; X-ray; 2.50 A; B=1-399.
DR PDB; 3IQD; X-ray; 2.80 A; B=1-399.
DR PDBsum; 3C7A; -.
DR PDBsum; 3C7C; -.
DR PDBsum; 3C7D; -.
DR PDBsum; 3IQD; -.
DR AlphaFoldDB; Q9BHM6; -.
DR SMR; Q9BHM6; -.
DR KEGG; ag:CAC36305; -.
DR BioCyc; MetaCyc:MON-17683; -.
DR BRENDA; 1.5.1.11; 4573.
DR EvolutionaryTrace; Q9BHM6; -.
DR GO; GO:0047830; F:D-octopine dehydrogenase activity; IEA:UniProtKB-EC.
DR GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
DR Gene3D; 1.10.1040.10; -; 1.
DR InterPro; IPR008927; 6-PGluconate_DH-like_C_sf.
DR InterPro; IPR013328; 6PGD_dom2.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR InterPro; IPR003421; Opine_DH.
DR Pfam; PF02317; Octopine_DH; 1.
DR SUPFAM; SSF48179; SSF48179; 1.
DR SUPFAM; SSF51735; SSF51735; 1.
PE 1: Evidence at protein level;
KW 3D-structure; NAD; Nucleotide-binding; Oxidoreductase.
FT CHAIN 1..399
FT /note="Octopine dehydrogenase"
FT /id="PRO_0000414626"
FT ACT_SITE 212
FT /evidence="ECO:0000269|PubMed:18599075"
FT BINDING 10..13
FT /ligand="NADH"
FT /ligand_id="ChEBI:CHEBI:57945"
FT /evidence="ECO:0000269|PubMed:18599075,
FT ECO:0000269|PubMed:20808820"
FT BINDING 35..38
FT /ligand="NADH"
FT /ligand_id="ChEBI:CHEBI:57945"
FT /evidence="ECO:0000269|PubMed:18599075,
FT ECO:0000269|PubMed:20808820"
FT BINDING 118
FT /ligand="pyruvate"
FT /ligand_id="ChEBI:CHEBI:15361"
FT /evidence="ECO:0000269|PubMed:18599075"
FT BINDING 118
FT /ligand="substrate"
FT BINDING 143
FT /ligand="pyruvate"
FT /ligand_id="ChEBI:CHEBI:15361"
FT /evidence="ECO:0000269|PubMed:18599075"
FT BINDING 148
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:20808820"
FT BINDING 206
FT /ligand="L-arginine"
FT /ligand_id="ChEBI:CHEBI:32682"
FT /evidence="ECO:0000269|PubMed:18599075"
FT BINDING 212
FT /ligand="pyruvate"
FT /ligand_id="ChEBI:CHEBI:15361"
FT /evidence="ECO:0000269|PubMed:18599075"
FT BINDING 324
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:20808820"
FT MUTAGEN 118
FT /note="Q->A: Drastically reduced enzymatic activity."
FT /evidence="ECO:0000269|PubMed:18599075"
FT MUTAGEN 118
FT /note="Q->D: Drastically reduced enzymatic activity.
FT Greater effect on catalytic efficiency for pyruvate than L-
FT arginine or NADH."
FT /evidence="ECO:0000269|PubMed:18599075"
FT MUTAGEN 148
FT /note="C->A,S: Reduced catalytic efficiency but no change
FT in the activity. 3-fold decrease in affinity for pyruvate,
FT 3-fold decrease for L-arginine and 2-fold decrease for
FT NADH."
FT /evidence="ECO:0000269|PubMed:18028427"
FT MUTAGEN 212
FT /note="H->A: 2 to 10-fold decrease in specific activity.
FT 77-fold reduction in affinity for pyruvate, 6-fold decrease
FT for L-arginine and 3-fold decrease for NADH."
FT /evidence="ECO:0000269|PubMed:18028427"
FT MUTAGEN 324
FT /note="R->A: 2 to 10-fold decrease in specific activity.
FT 119-fold reduction in affinity for pyruvate, 200-fold
FT reduction for L-arginine and 4-fold reduction for NADH."
FT /evidence="ECO:0000269|PubMed:18028427"
FT MUTAGEN 329
FT /note="D->A: 2 to 10-fold decrease in specific activity.
FT 43-fold reduction in affinity for pyruvate and 18-fold
FT reduction for L-arginine."
FT /evidence="ECO:0000269|PubMed:18028427"
FT STRAND 3..8
FT /evidence="ECO:0007829|PDB:3C7A"
FT HELIX 12..21
FT /evidence="ECO:0007829|PDB:3C7A"
FT STRAND 27..32
FT /evidence="ECO:0007829|PDB:3C7A"
FT HELIX 38..46
FT /evidence="ECO:0007829|PDB:3C7A"
FT STRAND 51..56
FT /evidence="ECO:0007829|PDB:3C7A"
FT STRAND 58..60
FT /evidence="ECO:0007829|PDB:3C7A"
FT STRAND 62..67
FT /evidence="ECO:0007829|PDB:3C7A"
FT STRAND 70..74
FT /evidence="ECO:0007829|PDB:3C7A"
FT HELIX 76..80
FT /evidence="ECO:0007829|PDB:3C7A"
FT STRAND 84..88
FT /evidence="ECO:0007829|PDB:3C7A"
FT HELIX 92..94
FT /evidence="ECO:0007829|PDB:3C7A"
FT HELIX 95..102
FT /evidence="ECO:0007829|PDB:3C7A"
FT TURN 103..105
FT /evidence="ECO:0007829|PDB:3C7A"
FT STRAND 111..114
FT /evidence="ECO:0007829|PDB:3C7A"
FT HELIX 121..129
FT /evidence="ECO:0007829|PDB:3C7A"
FT HELIX 130..134
FT /evidence="ECO:0007829|PDB:3C7A"
FT STRAND 136..143
FT /evidence="ECO:0007829|PDB:3C7A"
FT STRAND 145..152
FT /evidence="ECO:0007829|PDB:3C7A"
FT TURN 153..155
FT /evidence="ECO:0007829|PDB:3C7A"
FT STRAND 156..162
FT /evidence="ECO:0007829|PDB:3C7A"
FT STRAND 164..171
FT /evidence="ECO:0007829|PDB:3C7A"
FT HELIX 180..188
FT /evidence="ECO:0007829|PDB:3C7A"
FT STRAND 190..196
FT /evidence="ECO:0007829|PDB:3C7A"
FT HELIX 200..205
FT /evidence="ECO:0007829|PDB:3C7A"
FT HELIX 211..220
FT /evidence="ECO:0007829|PDB:3C7A"
FT STRAND 228..230
FT /evidence="ECO:0007829|PDB:3C7A"
FT HELIX 235..237
FT /evidence="ECO:0007829|PDB:3C7A"
FT HELIX 240..263
FT /evidence="ECO:0007829|PDB:3C7A"
FT HELIX 275..282
FT /evidence="ECO:0007829|PDB:3C7A"
FT TURN 284..286
FT /evidence="ECO:0007829|PDB:3C7A"
FT HELIX 293..298
FT /evidence="ECO:0007829|PDB:3C7A"
FT HELIX 301..303
FT /evidence="ECO:0007829|PDB:3C7A"
FT STRAND 310..313
FT /evidence="ECO:0007829|PDB:3C7A"
FT STRAND 316..319
FT /evidence="ECO:0007829|PDB:3C7A"
FT TURN 325..333
FT /evidence="ECO:0007829|PDB:3C7A"
FT HELIX 334..344
FT /evidence="ECO:0007829|PDB:3C7A"
FT HELIX 349..362
FT /evidence="ECO:0007829|PDB:3C7A"
FT HELIX 377..379
FT /evidence="ECO:0007829|PDB:3C7A"
FT HELIX 383..386
FT /evidence="ECO:0007829|PDB:3C7A"
FT HELIX 391..396
FT /evidence="ECO:0007829|PDB:3C7A"
SQ SEQUENCE 399 AA; 43320 MW; DA2DB070455B4C0F CRC64;
MTVKVCVCGG GNGAHTLSGL AASRDGVEVR VLTLFADEAE RWTKALGADE LTVIVNEKDG
TQTEVKSRPK VITKDPEIAI SGADVVILTV PAFAHEGYFQ AMAPYVQDSA LIVGLPSQAG
FEFQCRDILG DKAAAVSMMS FETLPWACRI KEFGRKVEVL GTKSVLAASL IKGTAKTVDP
LSTLQMLHGA EPVFRLAKHF LEMLIMSYSF VHPAILFGRW GSWDGKPVPE APLFYQGIDQ
ATADMLTACS NECKDVANAI MAACPGNDLS DVKDIYQWYL EYYHEDIQDD HDLYHAITTN
KSYKGLVHPV KAVDGGVAPD FGNRYLTEDI PMGMIVFKGV AIAAGVAIPS NDKLIMWAQE
KIGKEYLVDG ALTGKDVATT RCPQRYGFNT LDAILTGKK
