6HR7

HMG-CoA reductase from Methanothermococcus thermolithotrophicus apo form at 2.4 A resolution

• PDB DOI: https://doi.org/10.2210/pdb6HR7/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Methanothermococcus thermolithotrophicus DSM 2095
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2018-09-26 Released: 2019-02-13 
• Deposition Author(s): Wagner, T., Voegeli, B., Erb, T.J., Shima, S.
• Funding Organization(s): Max Planck Society

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.220 
• R-Value Work: 0.173 
• R-Value Observed: 0.175 

Literature

Crystal structure of archaeal HMG-CoA reductase: insights into structural changes of the C-terminal helix of the class-I enzyme.

Vogeli, B., Shima, S., Erb, T.J., Wagner, T.

(2019) FEBS Lett 593: 543-553

• PubMed: 30702149 
• DOI: https://doi.org/10.1002/1873-3468.13331
• Primary Citation of Related Structures:  
  6HR7, 6HR8


• PubMed Abstract: 
  

  3-hydroxy-3-methylglutaryl-CoA reductase (HMGR) catalyses the last step in mevalonate biosynthesis. HMGR is the target of statin inhibitors that regulate cholesterol concentration in human blood. Here, we report the properties and structures of HMGR from an archaeon Methanothermococcus thermolithotrophicus (mHMGR). The structures of the apoenzyme and the NADPH complex are highly similar to those of human HMGR. A notable exception is C-terminal helix (Lα10-11) that is straight in both mHMGR structures. This helix is kinked and closes the active site in the human enzyme ternary complex, pointing to a substrate-induced structural rearrangement of C-terminal in class-I HMGRs during the catalytic cycle.

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Organizational Affiliation: 

Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 94.68 kDa 
• Atom Count: 6,160 
• Modelled Residue Count: 791 
• Deposited Residue Count: 854 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HMG-CoA reductase	A, B	427	Methanothermococcus thermolithotrophicus DSM 2095	Mutation(s): 0  Gene Names: HMGR EC: 1.1.1.34
UniProt
Find proteins for A0A4V8GZY0 (Methanothermococcus thermolithotrophicus DSM 2095) Explore A0A4V8GZY0  Go to UniProtKB:  A0A4V8GZY0

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P6G	K [auth A]	HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N
DTT	E [auth A], F [auth A]	2,3-DIHYDROXY-1,4-DITHIOBUTANE C4 H10 O2 S2 VHJLVAABSRFDPM-IMJSIDKUSA-N
SO4	C [auth A], D [auth A], L [auth B], M [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	H [auth A], I [auth A], J [auth A], N [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	O [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.220 
• R-Value Work: 0.173 
• R-Value Observed: 0.175 
• Space Group: P 3₁ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.322	α = 90
b = 83.322	β = 90
c = 211.212	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-02-13 
Deposition Author(s): Wagner, T., Voegeli, B., Erb, T.J., Shima, S.

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Funding Organization	Location	Grant Number
Max Planck Society	Germany	--

Revision History  

• Version 1.0: 2019-02-13
  Type: Initial release
  
• Version 1.1: 2019-03-20
  Changes: Data collection, Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description