PDBsum entry 1x7d

Lyase

PDB id: 1x7d

Contents

Protein chains

340 a.a. *

Ligands

NAD ×2

ORN ×2

MPD ×6

MES

Metals

_NA ×2

Waters ×828

* Residue conservation analysis

PDB id:

1x7d

Name:

Lyase

Title:

Crystal structure analysis of ornithine cyclodeaminase complexed with NAD and ornithine to 1.6 angstroms

Structure:

Ornithine cyclodeaminase. Chain: a, b. Engineered: yes

Source:

Pseudomonas putida. Organism_taxid: 303. Gene: ornithine cyclase (deaminating). Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

1.60Å R-factor: 0.170 R-free: 0.190

Authors:

S.Alam,J.L.Goodman,S.Wang,F.J.Ruzicka,P.A.Frey,J.E.Wedekind

Key ref:

J.L.Goodman et al. (2004). Ornithine cyclodeaminase: structure, mechanism of action, and implications for the mu-crystallin family. Biochemistry, 43, 13883-13891. PubMed id: 15518536 DOI: 10.1021/bi048207i

Date:

13-Aug-04 Release date: 09-Nov-04

Protein chains

Q88H32  (OCD_PSEPK) -  Ornithine cyclodeaminase from Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)

Seq: 350 a.a.

Struc: 340 a.a.

Enzyme reactions

• Enzyme class: E.C.4.3.1.12 - ornithine cyclodeaminase.
• Pathway: Proline Biosynthesis
• Reaction: L-ornithine = L-proline + NH4⁺

L-ornithine (Bound ligand (Het Group name = ORN) corresponds exactly) = L-proline + NH4(+)

• Cofactor: NAD(+)

NAD(+) (Bound ligand (Het Group name = NAD) corresponds exactly)

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

reference

DOI no: 10.1021/bi048207i

Biochemistry 43:13883-13891 (2004)

PubMed id: 15518536

Ornithine cyclodeaminase: structure, mechanism of action, and implications for the mu-crystallin family.

J.L.Goodman, S.Wang, S.Alam, F.J.Ruzicka, P.A.Frey, J.E.Wedekind.

ABSTRACT

Ornithine cyclodeaminase catalyzes the conversion of L-ornithine to L-proline by an NAD(+)-dependent hydride transfer reaction that culminates in ammonia elimination. Phylogenetic comparisons of amino acid sequences revealed that the enzyme belongs to the mu-crystallin protein family whose three-dimensional fold has not been reported. Here we describe the crystal structure of ornithine cyclodeaminase in complex with NADH, refined to 1.80 A resolution. The enzyme consists of a homodimeric fold whose subunits comprise two functional regions: (i) a novel substrate-binding domain whose antiparallel beta-strands form a 14-stranded barrel at the oligomeric interface and (ii) a canonical Rossmann fold that interacts with a single dinucleotide positioned for re hydride transfer. The adenosyl moiety of the cofactor resides in a solvent-exposed crevice on the protein surface and makes contact with a "domain-swapped"-like coil-helix module originating from the dyad-related molecule. Diffraction data were also collected to 1.60 A resolution on crystals grown in the presence of l-ornithine. The structure revealed that the substrate carboxyl group interacts with the side chains of Arg45, Lys69, and Arg112. In addition, the ammonia leaving group hydrogen bonds to the side chain of Asp228 and the site of hydride transfer is 3.8 A from C4 of the nicotinamide. The absence of an appropriately positioned water suggested that a previously proposed mechanism that calls for hydrolytic elimination of the imino intermediate must be reconsidered. A more parsimonious description of the chemical mechanism is proposed and discussed in relation to the structure and function of mu-crystallins.