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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 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) ...

    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: 

    Microbial Protein Structure Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HMG-CoA reductase427Methanothermococcus thermolithotrophicus DSM 2095Mutation(s): 0 
Gene Names: HMGR
EC: 1.1.1.34
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HMG-CoA reductase
B, C, D, E, F
427Methanothermococcus thermolithotrophicus DSM 2095Mutation(s): 0 
Gene Names: HMGR
EC: 1.1.1.34
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP
Download Ideal Coordinates CCD File 
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		 Ligand Interaction
PEG
Query on PEG
Download Ideal Coordinates CCD File 
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		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
H [auth A],
M [auth B],
N [auth B],
S [auth C]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
Y [auth D],
Z [auth D]		SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D 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

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
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