PDBsum entry 1xpm

Transferase

PDB id: 1xpm

Contents

Protein chains

390 a.a. *

Ligands

SO4 ×8

HMG-CAA ×4

Waters ×1083

* Residue conservation analysis

PDB id:

1xpm

Name:

Transferase

Title:

Crystal structure of staphylococcus aureus hmg-coa synthase with hmg- coa and acetoacetyl-coa and acetylated cysteine

Structure:

3-hydroxy-3-methylglutaryl coa synthase. Chain: a, b, c, d. Engineered: yes

Source:

Staphylococcus aureus subsp. Aureus. Organism_taxid: 46170. Strain: subsp. Aureus. Gene: mvas. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PQS)

Resolution:

1.60Å R-factor: 0.210 R-free: 0.226

Authors:

M.J.Theisen,I.Misra,D.Saadat,N.Campobasso,H.M.Miziorko,D.H.T.Harrison

Key ref:

M.J.Theisen et al. (2004). 3-hydroxy-3-methylglutaryl-CoA synthase intermediate complex observed in "real-time". Proc Natl Acad Sci U S A, 101, 16442-16447. PubMed id: 15498869 DOI: 10.1073/pnas.0405809101

Date:

08-Oct-04 Release date: 02-Nov-04

Protein chains

A0A0H3K1U2  (A0A0H3K1U2_STAAW) -  3-hydroxy-3-methylglutaryl CoA synthase from Staphylococcus aureus (strain MW2)

Seq: 388 a.a.

Struc: 390 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.2.3.3.10 - hydroxymethylglutaryl-CoA synthase.
• Pathway: Mevalonate Biosynthesis
• Reaction: acetoacetyl-CoA + acetyl-CoA + H2O = (3S)-3-hydroxy-3-methylglutaryl-CoA + CoA + H⁺

acetoacetyl-CoA (Bound ligand (Het Group name = HMG) matches with 93.10% similarity) + acetyl-CoA + H2O = (3S)-3-hydroxy-3-methylglutaryl-CoA + CoA + H(+)

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

reference

DOI no: 10.1073/pnas.0405809101

Proc Natl Acad Sci U S A 101:16442-16447 (2004)

PubMed id: 15498869

3-hydroxy-3-methylglutaryl-CoA synthase intermediate complex observed in "real-time".

M.J.Theisen, I.Misra, D.Saadat, N.Campobasso, H.M.Miziorko, D.H.Harrison.

ABSTRACT

The formation of carbon-carbon bonds via an acyl-enzyme intermediate plays a central role in fatty acid, polyketide, and isoprenoid biosynthesis. Uniquely among condensing enzymes, 3-hydroxy-3-methylglutaryl (HMG)-CoA synthase (HMGS) catalyzes the formation of a carbon-carbon bond by activating the methyl group of an acetylated cysteine. This reaction is essential in Gram-positive bacteria, and represents the first committed step in human cholesterol biosynthesis. Reaction kinetics, isotope exchange, and mass spectroscopy suggest surprisingly that HMGS is able to catalyze the "backwards" reaction in solution, where HMG-CoA is cleaved to form acetoacetyl-CoA (AcAc-CoA) and acetate. Here, we trap a complex of acetylated HMGS from Staphylococcus aureus and bound acetoacetyl-CoA by cryo-cooling enzyme crystals at three different times during the course of its back-reaction with its physiological product (HMG-CoA). This nonphysiological "backwards" reaction is used to understand the details of the physiological reaction with regards to individual residues involved in catalysis and substrate/product binding. The structures suggest that an active-site glutamic acid (Glu-79) acts as a general base both in the condensation between acetoacetyl-CoA and the acetylated enzyme, and the hydrolytic release of HMG-CoA from the enzyme. The ability to trap this enzyme-intermediate complex may suggest a role for protein dynamics and the interplay between protomers during the normal course of catalysis.

Selected figure(s)

Figure 3.
Fig. 3. Schematic representation of the contacts in the active site with AcAc-CoA (A) and the acetylcysteine and HMG-CoA (B). The wide dashed lines indicate close contacts that violate van der Waals distance constraints, and the narrow dashed lines indicate potential hydrogen bonds. The average distances are given in angstroms (10^-10 m) based on either 11 or 7 structures, and the numbers in parentheses are the standard deviations of the distance multiplied by 100.

Figure 4.
Fig. 4. Models of the AcAc-CoA-acetylated enzyme complex (A) and the HMG-CoA enzyme complex (B). The atoms are colored according to their CPK atom type, and the bonds are shown in either white (for protein) or gold (for the acetyl moiety and the CoA molecules). Yellow-and-red dashed bonds tie reacting atoms together.

Figures were selected by an automated process.