PDBsum entry 2zyf

Transferase

PDB id: 2zyf

Contents

Protein chain

314 a.a. *

Ligands

AKG

Metals

_MG

Waters ×142

* Residue conservation analysis

PDB id:

2zyf

Name:

Transferase

Title:

Crystal structure of homocitrate synthase from thermus thermophilus complexed with magnesuim ion and alpha-ketoglutarate

Structure:

Homocitrate synthase. Chain: a. Engineered: yes

Source:

Thermus thermophilus. Organism_taxid: 262724. Strain: hb27. Gene: hcs. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.15Å R-factor: 0.205 R-free: 0.232

Authors:

T.Okada,T.Tomita,T.Kuzuyama,M.Nishiyama

Key ref:

T.Okada et al. (2010). Mechanism of substrate recognition and insight into feedback inhibition of homocitrate synthase from Thermus thermophilus. J Biol Chem, 285, 4195-4205. PubMed id: 19996101

Date:

20-Jan-09 Release date: 22-Dec-09

Protein chain

O87198  (HOSA_THET2) -  Homocitrate synthase from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 376 a.a.

Struc: 314 a.a.

Enzyme reactions

• Enzyme class: E.C.2.3.3.14 - homocitrate synthase.
• Pathway: Oxo-acid lyases with thioester hydrolysis
• Reaction: acetyl-CoA + 2-oxoglutarate + H2O = (2R)-homocitrate + CoA + H⁺

acetyl-CoA (Bound ligand (Het Group name = AKG) corresponds exactly) + 2-oxoglutarate + H2O = (2R)-homocitrate + CoA + H(+)

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

reference

J Biol Chem 285:4195-4205 (2010)

PubMed id: 19996101

Mechanism of substrate recognition and insight into feedback inhibition of homocitrate synthase from Thermus thermophilus.

T.Okada, T.Tomita, A.P.Wulandari, T.Kuzuyama, M.Nishiyama.

ABSTRACT

Homocitrate synthase (HCS) catalyzes aldol-type condensation of acetyl coenzyme A (acetyl-CoA) and alpha-ketoglutarate (alpha-KG) to synthesize homocitrate (HC), which is the first and committed step in the lysine biosynthetic pathway through alpha-aminoadipate. As known in most enzymes catalyzing the first reactions in amino acid biosynthetic pathways, HCS is regulated via feedback inhibition by the end product, lysine. Here, we determined the crystal structures of HCS from Thermus thermophilus complexed with alpha-KG, HC, or lysine. In the HC complex, the C1-carboxyl group of HC, which is derived from acetyl-CoA, is hydrogen-bonded with His-292* from another subunit (indicated by the asterisk), indicating direct involvement of this residue in the catalytic mechanism of HCS. The crystal structure of HCS complexed with lysine showed that lysine is bound to the active site with rearrangement of amino acid residues in the substrate-binding site, which accounts for the competitive inhibition by lysine with alpha-KG. Comparison between the structures suggests that His-72, which is conserved in lysine-sensitive HCSs and binds the C5-carboxyl group of alpha-KG, serves as a switch for the conformational change. Replacement of His-72 by leucine made HCS resistant to lysine inhibition, demonstrating the regulatory role of this conserved residue.