4I6A

3-hydroxy-3-methylglutaryl (HMG) Coenzyme A reductase from Pseudomonas mevalonii complexed with HMG-CoA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A Novel Role for Coenzyme A during Hydride Transfer in 3-Hydroxy-3-methylglutaryl-coenzyme A Reductase.

Steussy, C.N.Critchelow, C.J.Schmidt, T.Min, J.K.Wrensford, L.V.Burgner, J.W.Rodwell, V.W.Stauffacher, C.V.

(2013) Biochemistry 52: 5195-5205

  • DOI: 10.1021/bi400335g
  • Primary Citation of Related Structures:  4I4B, 4I56, 4I64, 4I6W, 4I6Y

  • PubMed Abstract: 
  • In this study, we take advantage of the ability of HMG-CoA reductase (HMGR) from Pseudomonas mevalonii to remain active while in its crystallized form to study the changing interactions between the ligands and protein as the first reaction intermedia ...

    In this study, we take advantage of the ability of HMG-CoA reductase (HMGR) from Pseudomonas mevalonii to remain active while in its crystallized form to study the changing interactions between the ligands and protein as the first reaction intermediate is created. HMG-CoA reductase catalyzes one of the few double oxidation-reduction reactions in intermediary metabolism that take place in a single active site. Our laboratory has undertaken an exploration of this reaction space using structures of HMG-CoA reductase complexed with various substrate, nucleotide, product, and inhibitor combinations. With a focus in this publication on the first hydride transfer, our structures follow this reduction reaction as the enzyme converts the HMG-CoA thioester from a flat sp(2)-like geometry to a pyramidal thiohemiacetal configuration consistent with a transition to an sp(3) orbital. This change in the geometry propagates through the coenzyme A (CoA) ligand whose first amide bond is rotated 180° where it anchors a web of hydrogen bonds that weave together the nucleotide, the reaction intermediate, the enzyme, and the catalytic residues. This creates a stable intermediate structure prepared for nucleotide exchange and the second reduction reaction within the HMG-CoA reductase active site. Identification of this reaction intermediate provides a template for the development of an inhibitor that would act as an antibiotic effective against the HMG-CoA reductase of methicillin-resistant Staphylococcus aureus.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3-hydroxy-3-methylglutaryl-coenzyme A reductase
A, B
428Pseudomonas mevaloniiGene Names: mvaA
EC: 1.1.1.88
Find proteins for P13702 (Pseudomonas mevalonii)
Go to UniProtKB:  P13702
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HMG
Query on HMG

Download SDF File 
Download CCD File 
A
3-HYDROXY-3-METHYLGLUTARYL-COENZYME A
(S)-HMG-COA
C27 H39 N7 O20 P3 S
CABVTRNMFUVUDM-VRHQGPGLSA-I
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.178 
  • Space Group: I 41 3 2
Unit Cell:
Length (Å)Angle (°)
a = 225.771α = 90.00
b = 225.771β = 90.00
c = 225.771γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
ADSCdata collection
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-17
    Type: Initial release
  • Version 1.1: 2013-08-07
    Type: Database references
  • Version 1.2: 2013-12-25
    Type: Database references