2P8U

Crystal structure of human 3-hydroxy-3-methylglutaryl CoA synthase I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structures of human HMG-CoA synthase isoforms provide insights into inherited ketogenesis disorders and inhibitor design.

Shafqat, N.Turnbull, A.Zschocke, J.Oppermann, U.Yue, W.W.

(2010) J.Mol.Biol. 398: 497-506

  • DOI: 10.1016/j.jmb.2010.03.034
  • Primary Citation of Related Structures:  2WYA

  • PubMed Abstract: 
  • 3-Hydroxy-3-methylglutaryl coenzyme A (CoA) synthase (HMGCS) catalyzes the condensation of acetyl-CoA and acetoacetyl-CoA into 3-hydroxy-3-methylglutaryl CoA. It is ubiquitous across the phylogenetic tree and is broadly classified into three classes. ...

    3-Hydroxy-3-methylglutaryl coenzyme A (CoA) synthase (HMGCS) catalyzes the condensation of acetyl-CoA and acetoacetyl-CoA into 3-hydroxy-3-methylglutaryl CoA. It is ubiquitous across the phylogenetic tree and is broadly classified into three classes. The prokaryotic isoform is essential in Gram-positive bacteria for isoprenoid synthesis via the mevalonate pathway. The eukaryotic cytosolic isoform also participates in the mevalonate pathway but its end product is cholesterol. Mammals also contain a mitochondrial isoform; its deficiency results in an inherited disorder of ketone body formation. Here, we report high-resolution crystal structures of the human cytosolic (hHMGCS1) and mitochondrial (hHMGCS2) isoforms in binary product complexes. Our data represent the first structures solved for human HMGCS and the mitochondrial isoform, allowing for the first time structural comparison among the three isoforms. This serves as a starting point for the development of isoform-specific inhibitors that have potential cholesterol-reducing and antibiotic applications. In addition, missense mutations that cause mitochondrial HMGCS deficiency have been mapped onto the hHMGCS2 structure to rationalize the structural basis for the disease pathology.


    Organizational Affiliation

    Structural Genomics Consortium, University of Oxford, Oxford OX3 7DU, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hydroxymethylglutaryl-CoA synthase, cytoplasmic
A, B
478Homo sapiensGene Names: HMGCS1 (HMGCS)
EC: 2.3.3.10
Find proteins for Q01581 (Homo sapiens)
Go to Gene View: HMGCS1
Go to UniProtKB:  Q01581
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
COA
Query on COA

Download SDF File 
Download CCD File 
A, B
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SCY
Query on SCY
A, B
L-PEPTIDE LINKINGC5 H9 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.159 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 92.762α = 90.00
b = 92.762β = 90.00
c = 235.532γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PHASERphasing
MAR345data collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2007-04-03
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description