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Protein

Octopine dehydrogenase

Gene

odh1

Organism
Pecten maximus (King scallop) (Pilgrim's clam)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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.2 Publications

Catalytic activityi

N(2)-(D-1-carboxyethyl)-L-arginine + NAD+ + H2O = L-arginine + pyruvate + NADH.1 Publication

Enzyme regulationi

Agmatine acts as a competitive inhibitor of the condensation reaction where the L-arginine and agmatine substrates compete for the same site.1 Publication

Kineticsi

The kinetic constants are determined for the recombinant His(5)-tagged protein.2 Publications

  1. KM=0.8 mM for pyruvate for the reverse reaction of the octopine dehydrogenase activity2 Publications
  2. KM=0.5 mM for L-arginine for the reverse reaction of the octopine dehydrogenase activity2 Publications
  3. KM=0.0198 mM for NADH for the reverse reaction of the octopine dehydrogenase activity2 Publications
  4. KM=5.9 mM for ketobutyrate for the reverse reaction of the octopine dehydrogenase activity2 Publications
  5. KM=49.8 mM for ketovalerate for the reverse reaction of the octopine dehydrogenase activity2 Publications
  1. Vmax=1074 µmol/min/mg enzyme with pyruvate as substrate for the reverse reaction of the octopine dehydrogenase activity2 Publications
  2. Vmax=886 µmol/min/mg enzyme with L-arginine as substrate for the reverse reaction of the octopine dehydrogenase activity2 Publications
  3. Vmax=903 µmol/min/mg enzyme with NADH as substrate for the reverse reaction of the octopine dehydrogenase activity2 Publications
  4. Vmax=728 µmol/min/mg enzyme with ketobutyrate as substrate for the reverse reaction of the octopine dehydrogenase activity2 Publications
  5. Vmax=377 µmol/min/mg enzyme with ketovalerate as substrate for the reverse reaction of the octopine dehydrogenase activity2 Publications

pH dependencei

Optimum pH is 8.0-9.5 for the forward reaction and 6.5-7.5 for the reverse reaction.2 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei118 – 1181Pyruvate1 Publication
Binding sitei118 – 1181Substrate
Binding sitei143 – 1431Pyruvate1 Publication
Binding sitei148 – 1481NAD; via amide nitrogen and carbonyl oxygen1 Publication
Binding sitei206 – 2061L-arginine; via carbonyl oxygen1 Publication
Active sitei212 – 21211 Publication
Binding sitei212 – 2121Pyruvate1 Publication
Binding sitei324 – 3241NAD1 Publication

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi10 – 134NADH2 Publications
Nucleotide bindingi35 – 384NADH2 Publications

GO - Molecular functioni

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Ligandi

NAD, Nucleotide-binding

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-17683.
BRENDAi1.5.1.11. 4573.

Names & Taxonomyi

Protein namesi
Recommended name:
Octopine dehydrogenaseImported (EC:1.5.1.11Imported)
Short name:
OcDH1 Publication
Gene namesi
Name:odh1Imported
OrganismiPecten maximus (King scallop) (Pilgrim's clam)
Taxonomic identifieri6579 [NCBI]
Taxonomic lineageiEukaryotaMetazoaLophotrochozoaMolluscaBivalviaPteriomorphiaPectinoidaPectinoideaPectinidaePecten

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi118 – 1181Q → A: Drastically reduced enzymatic activity. 1 Publication
Mutagenesisi118 – 1181Q → D: Drastically reduced enzymatic activity. Greater effect on catalytic efficiency for pyruvate than L-arginine or NADH. 1 Publication
Mutagenesisi148 – 1481C → A or S: Reduced catalytic efficiency but no change in the activity. 3-fold decrease in affinity for pyruvate, 3-fold decrease for L-arginine and 2-fold decrease for NADH. 1 Publication
Mutagenesisi212 – 2121H → A: 2 to 10-fold decrease in specific activity. 77-fold reduction in affinity for pyruvate, 6-fold decrease for L-arginine and 3-fold decrease for NADH. 1 Publication
Mutagenesisi324 – 3241R → A: 2 to 10-fold decrease in specific activity. 119-fold reduction in affinity for pyruvate, 200-fold reduction for L-arginine and 4-fold reduction for NADH. 1 Publication
Mutagenesisi329 – 3291D → A: 2 to 10-fold decrease in specific activity. 43-fold reduction in affinity for pyruvate and 18-fold reduction for L-arginine. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 399399Octopine dehydrogenasePRO_0000414626Add
BLAST

Structurei

Secondary structure

1
399
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 86Combined sources
Helixi12 – 2110Combined sources
Beta strandi27 – 326Combined sources
Helixi38 – 469Combined sources
Beta strandi51 – 566Combined sources
Beta strandi58 – 603Combined sources
Beta strandi62 – 676Combined sources
Beta strandi70 – 745Combined sources
Helixi76 – 805Combined sources
Beta strandi84 – 885Combined sources
Helixi92 – 943Combined sources
Helixi95 – 1028Combined sources
Turni103 – 1053Combined sources
Beta strandi111 – 1144Combined sources
Helixi121 – 1299Combined sources
Helixi130 – 1345Combined sources
Beta strandi136 – 1438Combined sources
Beta strandi145 – 1528Combined sources
Turni153 – 1553Combined sources
Beta strandi156 – 1627Combined sources
Beta strandi164 – 1718Combined sources
Helixi180 – 1889Combined sources
Beta strandi190 – 1967Combined sources
Helixi200 – 2056Combined sources
Helixi211 – 22010Combined sources
Beta strandi228 – 2303Combined sources
Helixi235 – 2373Combined sources
Helixi240 – 26324Combined sources
Helixi275 – 2828Combined sources
Turni284 – 2863Combined sources
Helixi293 – 2986Combined sources
Helixi301 – 3033Combined sources
Beta strandi310 – 3134Combined sources
Beta strandi316 – 3194Combined sources
Turni325 – 3339Combined sources
Helixi334 – 34411Combined sources
Helixi349 – 36214Combined sources
Helixi377 – 3793Combined sources
Helixi383 – 3864Combined sources
Helixi391 – 3966Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3C7AX-ray2.10A1-399[»]
3C7CX-ray3.10B1-399[»]
3C7DX-ray2.50B1-399[»]
3IQDX-ray2.80B1-399[»]
ProteinModelPortaliQ9BHM6.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9BHM6.

Family & Domainsi

Sequence similaritiesi

Family and domain databases

Gene3Di1.10.1040.10. 1 hit.
3.40.50.720. 1 hit.
InterProiIPR008927. 6-PGluconate_DH_C-like.
IPR013328. 6PGD_dom_2.
IPR016040. NAD(P)-bd_dom.
IPR003421. Opine_DH.
[Graphical view]
PfamiPF02317. Octopine_DH. 1 hit.
[Graphical view]
SUPFAMiSSF48179. SSF48179. 1 hit.
SSF51735. SSF51735. 1 hit.

Sequencei

Sequence statusi: Complete.

Q9BHM6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTVKVCVCGG GNGAHTLSGL AASRDGVEVR VLTLFADEAE RWTKALGADE
60 70 80 90 100
LTVIVNEKDG TQTEVKSRPK VITKDPEIAI SGADVVILTV PAFAHEGYFQ
110 120 130 140 150
AMAPYVQDSA LIVGLPSQAG FEFQCRDILG DKAAAVSMMS FETLPWACRI
160 170 180 190 200
KEFGRKVEVL GTKSVLAASL IKGTAKTVDP LSTLQMLHGA EPVFRLAKHF
210 220 230 240 250
LEMLIMSYSF VHPAILFGRW GSWDGKPVPE APLFYQGIDQ ATADMLTACS
260 270 280 290 300
NECKDVANAI MAACPGNDLS DVKDIYQWYL EYYHEDIQDD HDLYHAITTN
310 320 330 340 350
KSYKGLVHPV KAVDGGVAPD FGNRYLTEDI PMGMIVFKGV AIAAGVAIPS
360 370 380 390
NDKLIMWAQE KIGKEYLVDG ALTGKDVATT RCPQRYGFNT LDAILTGKK
Length:399
Mass (Da):43,320
Last modified:June 1, 2001 - v1
Checksum:iDA2DB070455B4C0F
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ237916 mRNA. Translation: CAC36305.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ237916 mRNA. Translation: CAC36305.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3C7AX-ray2.10A1-399[»]
3C7CX-ray3.10B1-399[»]
3C7DX-ray2.50B1-399[»]
3IQDX-ray2.80B1-399[»]
ProteinModelPortaliQ9BHM6.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-17683.
BRENDAi1.5.1.11. 4573.

Miscellaneous databases

EvolutionaryTraceiQ9BHM6.

Family and domain databases

Gene3Di1.10.1040.10. 1 hit.
3.40.50.720. 1 hit.
InterProiIPR008927. 6-PGluconate_DH_C-like.
IPR013328. 6PGD_dom_2.
IPR016040. NAD(P)-bd_dom.
IPR003421. Opine_DH.
[Graphical view]
PfamiPF02317. Octopine_DH. 1 hit.
[Graphical view]
SUPFAMiSSF48179. SSF48179. 1 hit.
SSF51735. SSF51735. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. "Putative reaction mechanism of heterologously expressed octopine dehydrogenase from the great scallop, Pecten maximus (L)."
    Muller A., Janssen F., Grieshaber M.K.
    FEBS J. 274:6329-6339(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF CYS-148; HIS-212; ARG-324 AND ASP-329.
    Tissue: Adductor muscle1 Publication.
  2. "A structural basis for substrate selectivity and stereoselectivity in octopine dehydrogenase from Pecten maximus."
    Smits S.H., Mueller A., Schmitt L., Grieshaber M.K.
    J. Mol. Biol. 381:200-211(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) OF NATIVE PROTEIN AND IN COMPLEXES WITH L-ARGININE; NADH AND PYRUVATE, FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF GLN-118.
  3. "Insights into the mechanism of ligand binding to octopine dehydrogenase from Pecten maximus by NMR and crystallography."
    Smits S.H., Meyer T., Mueller A., van Os N., Stoldt M., Willbold D., Schmitt L., Grieshaber M.K.
    PLoS ONE 5:E12312-E12312(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.80 ANGSTROMS) IN COMPLEX WITH NADH AND AGMATINE, ENZYME REGULATION.

Entry informationi

Entry nameiOCDH_PECMA
AccessioniPrimary (citable) accession number: Q9BHM6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 14, 2011
Last sequence update: June 1, 2001
Last modified: December 9, 2015
This is version 69 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)

Miscellaneousi

Keywords - Technical termi

3D-structure

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.