PDBsum entry 1vft

Isomerase

PDB id: 1vft

Contents

Protein chains

382 a.a. *

Ligands

DCS ×2

Metals

_CL

Waters ×117

* Residue conservation analysis

PDB id:

1vft

Name:

Isomerase

Title:

Crystal structure of l-cycloserine-bound form of alanine racemase from d-cycloserine-producing streptomyces lavendulae

Structure:

Alanine racemase. Chain: a, b. Engineered: yes

Source:

Streptomyces lavendulae. Organism_taxid: 1914. Gene: alr. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

2.30Å R-factor: 0.197 R-free: 0.287

Authors:

M.Noda,Y.Matoba,T.Kumagai,M.Sugiyama

Key ref:

M.Noda et al. (2004). Structural evidence that alanine racemase from a D-cycloserine-producing microorganism exhibits resistance to its own product. J Biol Chem, 279, 46153-46161. PubMed id: 15302886 DOI: 10.1074/jbc.M404605200

Date:

19-Apr-04 Release date: 14-Sep-04

Protein chains

Q65YW7  (Q65YW7_STRLA) -  Alanine racemase from Streptomyces lavendulae subsp. lavendulae

Seq: 378 a.a.

Struc: 382 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.5.1.1.1 - alanine racemase.
• Reaction: L-alanine = D-alanine
• Cofactor: Pyridoxal 5'-phosphate

Pyridoxal 5'-phosphate (Bound ligand (Het Group name = DCS) matches with 65.22% similarity)

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

reference

DOI no: 10.1074/jbc.M404605200

J Biol Chem 279:46153-46161 (2004)

PubMed id: 15302886

Structural evidence that alanine racemase from a D-cycloserine-producing microorganism exhibits resistance to its own product.

M.Noda, Y.Matoba, T.Kumagai, M.Sugiyama.

ABSTRACT

Alanine racemase (ALR), an enzyme that catalyzes the interconversion of Ala enantiomers, is essential for the synthesis of the bacterial cell wall. We have shown that it is harder to inhibit the catalytic activity of ALR from D-cycloserine (DCS)-producing Streptomyces lavendulae than that from Escherichia coli by DCS. To obtain structural evidence for the fact that Streptomyces ALR displays resistance to DCS, we determined the precise nature of the x-ray crystal structures of the cycloserine-free and cycloserine enantiomer-bound forms of Streptomyces ALR at high resolutions. Streptomyces ALR takes a dimer structure, which is formed by interactions between the N-terminal domain of one monomer with the C-terminal domain of its partner. Each of the two active sites of ALR, which is generated as a result of the formation of the dimer structure, is composed of pyridoxal 5'-phosphate (PLP), the PLP-binding residue Lys(38), and the amino acids in the immediate environment of the pyridoxal cofactor. The current model suggests that each active site of Streptomyces ALR maintains a larger space and takes a more rigid conformation than that of Bacillus stearothermophilus ALR determined previously. Furthermore, we show that Streptomyces ALR results in a slow conversion to a final form of a pyridoxal derivative arising from either isomer of cycloserine, which inhibits the catalytic activity noncompetitively. In fact, the slow conversion is confirmed by the fact that each enzyme bound cycloserine derivative, which is bound to PLP, takes an asymmetric structure.

Selected figure(s)

Figure 6.
FIG. 6. Active site around the DCS- or LCS-bound PLP derivative. DCS-bound derivatives at sites A and B are shown in a and b, respectively. The LCS-bound derivatives at sites A and B are shown in c and d, respectively. The carbon atoms of the residues from each monomer are shown in orange and cyan. The carbon atoms of the residues from the PLP derivative, designated SCP, are shown in purple.

Figure 7.
FIG. 7. Proposed mechanism of inactivation for ALR by DCS or LCS. DCS and LCS are converted to an identical final aromatic adduct through transamination, transamination, and tautomerization steps. The DCS- or LSC-bound PLP intermediate following the transamination step can be racemized to each counterpart by the same reaction as used for the true substrates.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 46153-46161) copyright 2004.

Figures were selected by an automated process.