PDBsum entry 3c7c

Oxidoreductase

PDB id: 3c7c

Contents

Protein chain

403 a.a. *

Ligands

NAD

ARG

* Residue conservation analysis

PDB id:

3c7c

Name:

Oxidoreductase

Title:

A structural basis for substrate and stereo selectivity in octopine dehydrogenase (odh-nadh-l-arginine)

Structure:

Octopine dehydrogenase. Chain: b. Engineered: yes

Source:

Pecten maximus. King scallop. Organism_taxid: 6579. Gene: odh1. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

3.10Å R-factor: 0.197 R-free: 0.241

Authors:

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

Key ref:

S.H.Smits et al. (2008). A structural basis for substrate selectivity and stereoselectivity in octopine dehydrogenase from Pecten maximus. J Mol Biol, 381, 200-211. PubMed id: 18599075 DOI: 10.1016/j.jmb.2008.06.003

Date:

07-Feb-08 Release date: 22-Jul-08

Protein chain

Q9BHM6  (OCDH_PECMA) -  Octopine dehydrogenase from Pecten maximus

Seq: 399 a.a.

Struc: 403 a.a.

Enzyme reactions

• Enzyme class: E.C.1.5.1.11 - D-octopine dehydrogenase.
• Reaction: D-octopine + NAD⁺ + H2O = L-arginine + pyruvate + NADH + H⁺

D-octopine + NAD(+) + H2O (Bound ligand (Het Group name = NAD) corresponds exactly) = L-arginine + pyruvate (Bound ligand (Het Group name = ARG) corresponds exactly) + NADH + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/j.jmb.2008.06.003

J Mol Biol 381:200-211 (2008)

PubMed id: 18599075

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

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

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.

Selected figure(s)

Figure 2.
Fig. 2. Stereoview of the arginine binding pocket. The arginine binding pocket is located in domain II, directly at the N-terminal helix–kink–helix motif of domain II. The side chain of arginine is coordinated by Trp278, backbone interactions with Tyr208 (domain II) and those with Glu142 (domain I). The C^α of l-arginine is bound by His212 of the Asp–His dyad. NADH is bound in a canonical fashion (Table 2) to the Rossmann fold, while interactions of the amide side chain of the nicotine amide ring with the backbone atoms of Cys148 (domain I) ensure the syn conformation.

Figure 4.
Fig. 4. The role of Arg324 in substrate-dependent domain closure. (a) Superpositions of the OcDH–NADH (green) and OcDH–NADH/l-arginine (blue) complexes highlight the inward rotation of domain II. The rmsd is 0.75° over 404 C^α atoms. (b) Superpositions of the OcDH–NADH (green), OcDH–NADH/l-arginine (blue) and OcDH–NADH/pyruvate (yellow) complexes. The interactions between NADH and Arg324 are highlighted, and the corresponding distances are shown. The final 2F[o] − F[c] electron density map for NADH of the binary OcDH–NADH structure contoured at 1σ is shown as a blue mesh.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 381, 200-211) copyright 2008.

Figures were selected by the author.