PDBsum entry: 1tj0

Oxidoreductase

PDB id: 1tj0

Contents

Protein chain

469 a.a. *

Ligands

FAD

LAC

Waters ×198

* Residue conservation analysis

PDB id:

1tj0

Name:

Oxidoreductase

Title:

Crystal structure of e. Coli puta proline dehydrogenase doma (residues 86-669) co-crystallized with l-lactate

Structure:

Bifunctional puta protein. Chain: a. Fragment: proline dehydrogenase domain (residues 86-669). Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: puta, poaa, b1014. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.10Å R-factor: 0.214 R-free: 0.259

Authors:

J.J.Tanner,M.Zhang,T.A.White,J.P.Schuermann,B.A.Baban,D.F.Be

Key ref:

M.Zhang et al. (2004). Structures of the Escherichia coli PutA proline dehydrogenase domain in complex with competitive inhibitors. Biochemistry, 43, 12539-12548. PubMed id: 15449943 DOI: 10.1021/bi048737e

Date:

02-Jun-04 Release date: 26-Oct-04

Protein chain

P09546  (PUTA_ECOLI) -  Bifunctional protein putA

Seq: 1320 a.a.

Struc: 469 a.a.

Enzyme reactions

• Enzyme class 1: E.C.1.5.1.12 - 1-pyrroline-5-carboxylate dehydrogenase.
• Reaction: (S)-1-pyrroline-5-carboxylate + NAD(P)(+) + 2 H₂O = L-glutamate + NAD(P)H

(S)-1-pyrroline-5-carboxylate (Bound ligand (Het Group name = LAC) matches with 55.56% similarity) + NAD(P)(+) (Bound ligand (Het Group name = FAD) matches with 71.19% similarity) + 2 × H(2)O = L-glutamate + NAD(P)H

• Enzyme class 2: E.C.1.5.99.8 - Proline dehydrogenase.
• Reaction: L-proline + acceptor = (S)-1-pyrroline-5-carboxylate + reduced acceptor

L-proline (Bound ligand (Het Group name = LAC) matches with 55.56% similarity) + acceptor = 2 × (S)-1-pyrroline-5-carboxylate + reduced acceptor

• Cofactor: FAD

FAD (Bound ligand (Het Group name = FAD) corresponds exactly)

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

 Gene Ontology (GO) functional annotation 

• Biological process: oxidation-reduction process (3 terms)
• Biochemical function: proline dehydrogenase activity (2 terms)

reference

DOI no: 10.1021/bi048737e

Biochemistry 43:12539-12548 (2004)

PubMed id: 15449943

Structures of the Escherichia coli PutA proline dehydrogenase domain in complex with competitive inhibitors.

M.Zhang, T.A.White, J.P.Schuermann, B.A.Baban, D.F.Becker, J.J.Tanner.

ABSTRACT

Proline dehydrogenase (PRODH) catalyzes the first step of proline catabolism, the flavin-dependent oxidation of proline to Delta(1)-pyrroline-5-carboxylate. Here we present a structure-based study of the PRODH active site of the multifunctional Escherichia coli proline utilization A (PutA) protein using X-ray crystallography, enzyme kinetic measurements, and site-directed mutagenesis. Structures of the PutA PRODH domain complexed with competitive inhibitors acetate (K(i) = 30 mM), L-lactate (K(i) = 1 mM), and L-tetrahydro-2-furoic acid (L-THFA, K(i) = 0.2 mM) have been determined to high-resolution limits of 2.1-2.0 A. The discovery of acetate as a competitive inhibitor suggests that the carboxyl is the minimum functional group recognized by the active site, and the structures show how the enzyme exploits hydrogen-bonding and nonpolar interactions to optimize affinity for the substrate. The PRODH/L-THFA complex is the first structure of PRODH with a five-membered ring proline analogue bound in the active site and thus provides new insights into substrate recognition and the catalytic mechanism. The ring of L-THFA is nearly parallel to the middle ring of the FAD isoalloxazine, with the inhibitor C5 atom 3.3 A from the FAD N5. This geometry suggests direct hydride transfer as a plausible mechanism. Mutation of conserved active site residue Leu432 to Pro caused a 5-fold decrease in k(cat) and a severe loss in thermostability. These changes are consistent with the location of Leu432 in the hydrophobic core near residues that directly contact FAD. Our results suggest that the molecular basis for increased plasma proline levels in schizophrenic subjects carrying the missense mutation L441P is due to decreased stability of human PRODH2.