PDBsum entry 5u3f

Transferase

PDB id: 5u3f

Contents

Protein chains

326 a.a.

Ligands

7TS ×2

Waters ×618

PDB id:

5u3f

Name:

Transferase

Title:

Structure of mycobacterium tuberculosis ilve, a branched-chain amino acid transaminase, in complex with d-cycloserine derivative

Structure:

Branched-chain-amino-acid aminotransferase. Chain: a, b. Synonym: bcat. Engineered: yes

Source:

Mycobacterium tuberculosis (strain atcc 25618 / h37rv). Organism_taxid: 83332. Strain: atcc 25618 / h37rv. Gene: ilve, rv2210c, mtcy190.21c. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.70Å R-factor: 0.178 R-free: 0.210

Authors:

L.Favrot,T.M.Amorim Franco,J.S.Blanchard

Key ref:

T.M.Amorim Franco et al. (2017). Mechanism-Based Inhibition of the Mycobacterium tuberculosis Branched-Chain Aminotransferase by d- and l-Cycloserine. ACS Chem Biol, 12, 1235-1244. PubMed id: 28272868

Date:

02-Dec-16 Release date: 22-Mar-17

Protein chains

P9WQ75  (ILVE_MYCTU) -  Branched-chain-amino-acid aminotransferase from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

Seq: 368 a.a.

Struc: 326 a.a.

Enzyme reactions

• Enzyme class: E.C.2.6.1.42 - branched-chain-amino-acid transaminase.
• Pathway: Leucine Biosynthesis
• Reaction: L-leucine + 2-oxoglutarate = 4-methyl-2-oxopentanoate + L-glutamate
• Cofactor: Pyridoxal 5'-phosphate

Pyridoxal 5'-phosphate (Bound ligand (Het Group name = 7TS) matches with 65.22% similarity)

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

reference

ACS Chem Biol 12:1235-1244 (2017)

PubMed id: 28272868

Mechanism-Based Inhibition of the Mycobacterium tuberculosis Branched-Chain Aminotransferase by d- and l-Cycloserine.

T.M.Amorim Franco, L.Favrot, O.Vergnolle, J.S.Blanchard.

ABSTRACT

The branched-chain aminotransferase is a pyridoxal 5'-phosphate (PLP)-dependent enzyme responsible for the final step in the biosynthesis of all three branched-chain amino acids, l-leucine, l-isoleucine, and l-valine, in bacteria. We have investigated the mechanism of inactivation of the branched-chain aminotransferase from Mycobacterium tuberculosis (MtIlvE) by d- and l-cycloserine. d-Cycloserine is currently used only in the treatment of multidrug-drug-resistant tuberculosis. Our results show a time- and concentration-dependent inactivation of MtIlvE by both isomers, with l-cycloserine being a 40-fold better inhibitor of the enzyme. Minimum inhibitory concentration (MIC) studies revealed that l-cycloserine is a 10-fold better inhibitor of Mycobacterium tuberculosis growth than d-cycloserine. In addition, we have crystallized the MtIlvE-d-cycloserine inhibited enzyme, determining the structure to 1.7 Å. The structure of the covalent d-cycloserine-PMP adduct bound to MtIlvE reveals that the d-cycloserine ring is planar and aromatic, as previously observed for other enzyme systems. Mass spectrometry reveals that both the d-cycloserine- and l-cycloserine-PMP complexes have the same mass, and are likely to be the same aromatized, isoxazole product. However, the kinetics of formation of the MtIlvE d-cycloserine-PMP and MtIlvE l-cycloserine-PMP adducts are quite different. While the kinetics of the formation of the MtIlvE d-cycloserine-PMP complex can be fit to a single exponential, the formation of the MtIlvE l-cycloserine-PMP complex occurs in two steps. We propose a chemical mechanism for the inactivation of d- and l-cycloserine which suggests a stereochemically determined structural role for the differing kinetics of inactivation. These results demonstrate that the mechanism of action of d-cycloserine's activity against M. tuberculosis may be more complicated than previously thought and that d-cycloserine may compromise the in vivo activity of multiple PLP-dependent enzymes, including MtIlvE.