Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 92.57 kDa 
• Atom Count: 6697 
• Modelled Residue Count: 751 
• Deposited Residue Count: 856 
• Unique protein chains: 1

4I6Y

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

• PDB DOI: 10.2210/pdb4I6Y/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pseudomonas mevalonii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-11-30 Released: 2013-07-17 
• Deposition Author(s): Steussy, C.N., Stauffacher, C.V., Schmidt, T., Burgner II, J.W., Rodwell, V.W., Wrensford, L.V., Critchelow, C.J., Min, J.

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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 

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

• PubMed: 23802607 
• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-hydroxy-3-methylglutaryl-coenzyme A reductase	A, B	428	Pseudomonas mevalonii	Mutation(s): 0  Gene Names: mvaA EC: 1.1.1.88
UniProt
Find proteins for P13702 (Pseudomonas mevalonii) Explore P13702  Go to UniProtKB:  P13702

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MEV	C [auth A], I [auth B]	(R)-MEVALONATE C6 H11 O4 KJTLQQUUPVSXIM-ZCFIWIBFSA-M
SO4	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
GOL	D [auth A], E [auth A], J [auth B], K [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NO2	O [auth B]	NITRITE ION N O2 IOVCWXUNBOPUCH-UHFFFAOYSA-M

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 = 225.806	α = 90
b = 225.806	β = 90
c = 225.806	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CNS	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-11-30 
• Released Date: 2013-07-17 
Deposition Author(s): Steussy, C.N., Stauffacher, C.V., Schmidt, T., Burgner II, J.W., Rodwell, V.W., Wrensford, L.V., Critchelow, C.J., Min, J.

Revision History  

• 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