A structural basis for substrate and stereo selectivity in octopine dehydrogenase (ODH-NADH-L-Arginine)

Experimental Data Snapshot

  • Resolution: 3.10 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

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A structural basis for substrate selectivity and stereoselectivity in octopine dehydrogenase from Pecten maximus.

Smits, S.H.Mueller, A.Schmitt, L.Grieshaber, M.K.

(2008) J Mol Biol 381: 200-211

  • DOI: https://doi.org/10.1016/j.jmb.2008.06.003
  • Primary Citation of Related Structures:  
    3C7A, 3C7C, 3C7D

  • PubMed Abstract: 

    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.

  • Organizational Affiliation

    Institute of Biochemistry, Heinrich Heine University, Universitaetsstrasse 1, 40225 Duesseldorf, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Octopine dehydrogenaseA [auth B]404Pecten maximusMutation(s): 0 
Gene Names: odh1
Find proteins for Q9BHM6 (Pecten maximus)
Explore Q9BHM6 
Go to UniProtKB:  Q9BHM6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BHM6
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAD

Download Ideal Coordinates CCD File 
C21 H27 N7 O14 P2
Query on ARG

Download Ideal Coordinates CCD File 
C6 H15 N4 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 3.10 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95α = 90
b = 95β = 90
c = 120.2γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
Integratedata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-07-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations