1X9E

Crystal structure of HMG-CoA synthase from Enterococcus faecalis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.235 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

X-ray Crystal Structures of HMG-CoA Synthase from Enterococcus faecalis and a Complex with Its Second Substrate/Inhibitor Acetoacetyl-CoA

Steussy, C.N.Vartia, A.A.Burgner II, J.W.Sutherlin, A.Rodwell, V.W.Stauffacher, C.V.

(2005) Biochemistry 44: 14256-14267

  • DOI: https://doi.org/10.1021/bi051487x
  • Primary Citation of Related Structures:  
    1X9E, 1YSL

  • PubMed Abstract: 

    Biosynthesis of the isoprenoid precursor, isopentenyl diphosphate, is a critical function in all independently living organisms. There are two major pathways for this synthesis, the non-mevalonate pathway found in most eubacteria and the mevalonate pathway found in animal cells and a number of pathogenic bacteria. An early step in this pathway is the condensation of acetyl-CoA and acetoacetyl-CoA into HMG-CoA, catalyzed by the enzyme HMG-CoA synthase. To explore the possibility of a small molecule inhibitor of the enzyme functioning as a non-cell wall antibiotic, the structure of HMG-CoA synthase from Enterococcus faecalis (MVAS) was determined by selenomethionine MAD phasing to 2.4 A and the enzyme complexed with its second substrate, acetoacetyl-CoA, to 1.9 A. These structures show that HMG-CoA synthase from Enterococcus is a member of the family of thiolase fold enzymes and, while similar to the recently published HMG-CoA synthase structures from Staphylococcus aureus, exhibit significant differences in the structure of the C-terminal domain. The acetoacetyl-CoA binary structure demonstrates reduced coenzyme A and acetoacetate covalently bound to the active site cysteine through a thioester bond. This is consistent with the kinetics of the reaction that have shown acetoacetyl-CoA to be a potent inhibitor of the overall reaction, and provides a starting point in the search for a small molecule inhibitor.


  • Organizational Affiliation

    Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HMG-CoA synthase
A, B
383Enterococcus faecalisMutation(s): 0 
Gene Names: MVAS
EC: 4.1.3.5 (PDB Primary Data), 2.3.3.10 (UniProt)
UniProt
Find proteins for Q9FD71 (Enterococcus faecalis)
Explore Q9FD71 
Go to UniProtKB:  Q9FD71
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9FD71
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.235 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.368α = 90
b = 109.82β = 90
c = 141.54γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-11-01
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations, Refinement description