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

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.232 

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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 dehydrogenase404Pecten 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 EDO

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A]
C2 H6 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.232 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.816α = 90
b = 99.816β = 90
c = 126.513γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata 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: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references, Derived calculations