4I6Y

3-hydroxy-3-methyl (HMG) Coenzyme A Reductase bound to R-Mevalonate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report


This is version 1.4 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, 4I6A, 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 intermediate is created ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3-hydroxy-3-methylglutaryl-coenzyme A reductaseA, B428Pseudomonas mevaloniiMutation(s): 0 
Gene Names: mvaA
EC: 1.1.1.88
UniProt
Find proteins for P13702 (Pseudomonas mevalonii)
Explore P13702 
Go to UniProtKB:  P13702
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13702
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MEV
Query on MEV

Download Ideal Coordinates CCD File 
C [auth A],
I [auth B]
(R)-MEVALONATE
C6 H11 O4
KJTLQQUUPVSXIM-ZCFIWIBFSA-M
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A],
L [auth B],
M [auth B],
F [auth A],
G [auth A],
H [auth A],
L [auth B],
M [auth B],
N [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
J [auth B],
K [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NO2
Query on NO2

Download Ideal Coordinates CCD File 
O [auth B]NITRITE ION
N O2
IOVCWXUNBOPUCH-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 
  • Space Group: I 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 225.806α = 90
b = 225.806β = 90
c = 225.806γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CNSrefinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-17
    Type: Initial release
  • Version 1.1: 2013-08-07
    Changes: Database references
  • Version 1.2: 2013-12-25
    Changes: Database references
  • Version 1.3: 2018-01-24
    Changes: Structure summary
  • Version 1.4: 2019-07-17
    Changes: Data collection, Derived calculations, Refinement description