PDBsum entry 3f6h

Transferase

PDB id: 3f6h

Contents

Protein chains

119 a.a. *

125 a.a. *

Ligands

ILE ×2

Metals

_ZN

Waters ×185

* Residue conservation analysis

PDB id:

3f6h

Name:

Transferase

Title:

Crystal structure of the regulatory domain of licms in complexed with isoleucine - type iii

Structure:

Alpha-isopropylmalate synthase. Chain: a, b. Fragment: regulatory domain, unp residues 390-516. Synonym: citramalate synthase. Engineered: yes

Source:

Leptospira interrogans. Organism_taxid: 173. Strain: 56601. Gene: cima. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.70Å R-factor: 0.223 R-free: 0.248

Authors:

P.Zhang,J.Ma,G.Zhao,J.Ding

Key ref:

P.Zhang et al. (2009). Molecular basis of the inhibitor selectivity and insights into the feedback inhibition mechanism of citramalate synthase from Leptospira interrogans. Biochem J, 421, 133-143. PubMed id: 19351325

Date:

06-Nov-08 Release date: 21-Apr-09

Protein chain

Q8F3Q1  (Q8F3Q1_LEPIN) -  (R)-citramalate synthase CimA from Leptospira interrogans serogroup Icterohaemorrhagiae serovar Lai (strain 56601)

Seq: 516 a.a.

Struc: 119 a.a.

Protein chain

Q8F3Q1  (Q8F3Q1_LEPIN) -  (R)-citramalate synthase CimA from Leptospira interrogans serogroup Icterohaemorrhagiae serovar Lai (strain 56601)

Seq: 516 a.a.

Struc: 125 a.a.

Enzyme reactions

• Enzyme class: Chains A, B: E.C.2.3.1.182 - Transferred entry: 2.3.3.21.
• Reaction: Acetyl-CoA + pyruvate + H₂O = CoA + (2R)-2-hydroxy-2- methylbutanedioate

Acetyl-CoA + pyruvate (Bound ligand (Het Group name = ILE) matches with 50.00% similarity) + H(2)O = CoA + (2R)-2-hydroxy-2- methylbutanedioate

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

reference

Biochem J 421:133-143 (2009)

PubMed id: 19351325

Molecular basis of the inhibitor selectivity and insights into the feedback inhibition mechanism of citramalate synthase from Leptospira interrogans.

P.Zhang, J.Ma, Z.Zhang, M.Zha, H.Xu, G.Zhao, J.Ding.

ABSTRACT

LiCMS (Leptospira interrogans citramalate synthase) catalyses the first reaction of the isoleucine biosynthesis pathway in L. interrogans, the pathogen of leptospirosis. The catalytic reaction is regulated through feedback inhibition by its end product isoleucine. To understand the molecular basis of the high selectivity of the inhibitor and the mechanism of feedback inhibition, we determined the crystal structure of LiCMSC (C-terminal regulatory domain of LiCMS) in complex with isoleucine, and performed a biochemical study of the inhibition of LiCMS using mutagenesis and kinetic methods. LiCMSC forms a dimer of dimers in both the crystal structure and solution and the dimeric LiCMSC is the basic functional unit. LiCMSC consists of six beta-strands forming two anti-parallel beta-sheets and two alpha-helices and assumes a betaalphabeta three-layer sandwich structure. The inhibitor isoleucine is bound in a pocket at the dimer interface and has both hydrophobic and hydrogen-bonding interactions with several conserved residues of both subunits. The high selectivity of LiCMS for isoleucine over leucine is primarily dictated by the residues, Tyr430, Leu451, Tyr454, Ile458 and Val468, that form a hydrophobic pocket to accommodate the side chain of the inhibitor. The binding of isoleucine has inhibitory effects on the binding of both the substrate, pyruvate, and coenzyme, acetyl-CoA, in a typical pattern of K-type inhibition. The structural and biochemical data from the present study together suggest that the binding of isoleucine affects the binding of the substrate and coenzyme at the active site, possibly via conformational change of the dimer interface of the regulatory domain, leading to inhibition of the catalytic reaction.