PDBsum entry 3mp5

Lyase

PDB id: 3mp5

Contents

Protein chain

(+ 0 more) 296 a.a. *

Ligands

HMG

Metals

_MG ×2

Waters ×344

* Residue conservation analysis

PDB id:

3mp5

Name:

Lyase

Title:

Crystal structure of human lyase r41m in complex with hmg-coa

Structure:

Hydroxymethylglutaryl-coa lyase. Chain: a, b, c, d, e, f. Synonym: hmg-coa lyase, hl, 3-hydroxy-3-methylglutarate-coa lyase. Engineered: yes. Mutation: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: hmgcl. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.25Å R-factor: 0.221 R-free: 0.271

Authors:

Z.Fu,J.A.Runquist,C.Montgomery,H.M.Miziorko,J.-J.P.Kim

Key ref:

Z.Fu et al. (2010). Functional insights into human HMG-CoA lyase from structures of Acyl-CoA-containing ternary complexes. J Biol Chem, 285, 26341-26349. PubMed id: 20558737

Date:

24-Apr-10 Release date: 16-Jun-10

Protein chains

P35914  (HMGCL_HUMAN) -  Hydroxymethylglutaryl-CoA lyase, mitochondrial from Homo sapiens

Seq: 325 a.a.

Struc: 296 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.4.1.3.4 - hydroxymethylglutaryl-CoA lyase.
• Pathway: Mevalonate Biosynthesis
• Reaction: (3S)-3-hydroxy-3-methylglutaryl-CoA = acetoacetate + acetyl-CoA

(3S)-3-hydroxy-3-methylglutaryl-CoA = acetoacetate + acetyl-CoA (Bound ligand (Het Group name = HMG) matches with 87.93% similarity)

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

Added reference

J Biol Chem 285:26341-26349 (2010)

PubMed id: 20558737

Functional insights into human HMG-CoA lyase from structures of Acyl-CoA-containing ternary complexes.

Z.Fu, J.A.Runquist, C.Montgomery, H.M.Miziorko, J.J.Kim.

ABSTRACT

HMG-CoA lyase (HMGCL) is crucial to ketogenesis and inherited human mutations are potentially lethal. Detailed understanding of HMGCL reaction mechanism and the molecular basis for correlating human mutations with enzyme deficiency have been limited by the lack of structural information for enzyme liganded to an acyl-CoA substrate or inhibitor. Crystal structures of ternary complexes of wild-type HMGCL with the competitive inhibitor 3-hydroxyglutaryl-CoA (HG-CoA) and of the catalytically deficient HMGCL R41M mutant with substrate HMG-CoA have been determined to 2.4 A and 2.2 A,respectively. Comparison of these beta/alpha barrel structures with those of unliganded HMGCL and R41M reveals substantial differences for Mg++ coordination and positioning of the flexible loop containing the conserved HMGCL signature sequence. In the ternary substrate-Mg++-R41M complex, loop residue C266 (implicated in active site function by mechanistic and mutagenesis observations) is more closely juxtaposed to the catalytic site than in the case of unliganded enzyme or the wild-type enzyme-Mg++-HG-CoA inhibitor complex. In both ternary complexes, the S-stereoisomer of substrate or inhibitor is specifically bound, in accord with the observed Mg++ liganding of both C3 hydroxyl and C5 carboxyl oxygens. In addition to H233 and H235 imidazoles, other Mg++ ligands are D42 carboxyl oxygen and an ordered water molecule. This water, positioned between D42 and the C3 hydroxyl of bound substrate/inhibitor, may function as a proton shuttle. The observed interaction of R41 with acyl-CoA C1 carbonyl oxygen explains the effects of R41 mutation on reaction product enolization and accounts for why human R41 mutations cause drastic enzyme deficiency.