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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

Manual assertion based on experiment ini

  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)DescriptionActionsGraphical viewLength
Binding sitei118Pyruvate1 Publication1
Binding sitei118Substrate1
Binding sitei143Pyruvate1 Publication1
Binding sitei148NAD; via amide nitrogen and carbonyl oxygen1 Publication1
Binding sitei206L-arginine; via carbonyl oxygen1 Publication1
Active sitei2121 Publication1
Binding sitei212Pyruvate1 Publication1
Binding sitei324NAD1 Publication1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi10 – 13NADH2 Publications4
Nucleotide bindingi35 – 38NADH2 Publications4

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)DescriptionActionsGraphical viewLength
Mutagenesisi118Q → A: Drastically reduced enzymatic activity. 1 Publication1
Mutagenesisi118Q → D: Drastically reduced enzymatic activity. Greater effect on catalytic efficiency for pyruvate than L-arginine or NADH. 1 Publication1
Mutagenesisi148C → 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 Publication1
Mutagenesisi212H → 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 Publication1
Mutagenesisi324R → 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 Publication1
Mutagenesisi329D → A: 2 to 10-fold decrease in specific activity. 43-fold reduction in affinity for pyruvate and 18-fold reduction for L-arginine. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00004146261 – 399Octopine dehydrogenaseAdd BLAST399

Structurei

Secondary structure

1399
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi3 – 8Combined sources6
Helixi12 – 21Combined sources10
Beta strandi27 – 32Combined sources6
Helixi38 – 46Combined sources9
Beta strandi51 – 56Combined sources6
Beta strandi58 – 60Combined sources3
Beta strandi62 – 67Combined sources6
Beta strandi70 – 74Combined sources5
Helixi76 – 80Combined sources5
Beta strandi84 – 88Combined sources5
Helixi92 – 94Combined sources3
Helixi95 – 102Combined sources8
Turni103 – 105Combined sources3
Beta strandi111 – 114Combined sources4
Helixi121 – 129Combined sources9
Helixi130 – 134Combined sources5
Beta strandi136 – 143Combined sources8
Beta strandi145 – 152Combined sources8
Turni153 – 155Combined sources3
Beta strandi156 – 162Combined sources7
Beta strandi164 – 171Combined sources8
Helixi180 – 188Combined sources9
Beta strandi190 – 196Combined sources7
Helixi200 – 205Combined sources6
Helixi211 – 220Combined sources10
Beta strandi228 – 230Combined sources3
Helixi235 – 237Combined sources3
Helixi240 – 263Combined sources24
Helixi275 – 282Combined sources8
Turni284 – 286Combined sources3
Helixi293 – 298Combined sources6
Helixi301 – 303Combined sources3
Beta strandi310 – 313Combined sources4
Beta strandi316 – 319Combined sources4
Turni325 – 333Combined sources9
Helixi334 – 344Combined sources11
Helixi349 – 362Combined sources14
Helixi377 – 379Combined sources3
Helixi383 – 386Combined sources4
Helixi391 – 396Combined sources6

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3C7AX-ray2.10A1-399[»]
3C7CX-ray3.10B1-399[»]
3C7DX-ray2.50B1-399[»]
3IQDX-ray2.80B1-399[»]
ProteinModelPortaliQ9BHM6.
SMRiQ9BHM6.
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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3C7AX-ray2.10A1-399[»]
3C7CX-ray3.10B1-399[»]
3C7DX-ray2.50B1-399[»]
3IQDX-ray2.80B1-399[»]
ProteinModelPortaliQ9BHM6.
SMRiQ9BHM6.
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...

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: November 2, 2016
This is version 71 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.