6HR8

HMG-CoA reductase from Methanothermococcus thermolithotrophicus in complex with NADPH at 2.9 A resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


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

  • 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.

    • Organizational Affiliation: 

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HMG-CoA reductase427Methanothermococcus thermolithotrophicus DSM 2095Mutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4V8GZY0
Sequence Annotations
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HMG-CoA reductase
B, C, D, E, F
427Methanothermococcus thermolithotrophicus DSM 2095Mutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4V8GZY0
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP
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AA [auth E]
BA [auth F]
G [auth A]
L [auth B]
R [auth C]
AA [auth E],
BA [auth F],
G [auth A],
L [auth B],
R [auth C],
W [auth D]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
PEG
Query on PEG
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I [auth A]
J [auth A]
K [auth A]
O [auth B]
P [auth B]
I [auth A],
J [auth A],
K [auth A],
O [auth B],
P [auth B],
Q [auth B],
T [auth C],
U [auth C],
V [auth C],
X [auth D]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4
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H [auth A],
M [auth B],
N [auth B],
S [auth C]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
NA
Query on NA
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Y [auth D],
Z [auth D]		SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 231.79α = 90
b = 231.79β = 90
c = 98.714γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--

Revision History  (Full details and data files)

  • 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