6HR8 | pdb_00006hr8

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

PDB DOI: https://doi.org/10.2210/pdb6HR8/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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.243 (Depositor), 0.243 (DCC)
R-Value Work:
0.211 (Depositor), 0.216 (DCC)
R-Value Observed:
0.213 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 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

PubMed: 30702149 Search on PubMed
DOI: https://doi.org/10.1002/1873-3468.13331
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 285.79 kDa
Atom Count: 18,073
Modeled Residue Count: 2,377
Deposited Residue Count: 2,562
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HMG-CoA reductase	A	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A4V8GZY0
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HMG-CoA reductase	B, C, D, E, F	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A4V8GZY0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download:Ideal Coordinates CCD File SDF format, chain W [auth D] SDF format, chain R [auth C] SDF format, chain L [auth B] SDF format, chain G [auth A] SDF format, chain BA [auth F] SDF format, chain AA [auth E] MOL2 format, chain W [auth D] MOL2 format, chain R [auth C] MOL2 format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain BA [auth F] MOL2 format, chain AA [auth E] mmCIF format, chain W [auth D] mmCIF format, chain R [auth C] mmCIF format, chain L [auth B] mmCIF format, chain G [auth A] mmCIF format, chain BA [auth F] mmCIF format, chain AA [auth E]	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		Interactions Focus chain AA [auth E] Focus chain BA [auth F] Focus chain G [auth A] Focus chain L [auth B] Focus chain R [auth C] Focus chain W [auth D] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth F] Focus chain G [auth A] Focus chain L [auth B] Focus chain R [auth C] Focus chain W [auth D]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain X [auth D] SDF format, chain V [auth C] SDF format, chain U [auth C] SDF format, chain T [auth C] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain X [auth D] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain X [auth D] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	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		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain X [auth D] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain X [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain S [auth C] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain H [auth A] MOL2 format, chain S [auth C] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain H [auth A] mmCIF format, chain S [auth C] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain H [auth A]	H [auth A], M [auth B], N [auth B], S [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain S [auth C] Interactions & Density Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain S [auth C]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain Y [auth D] MOL2 format, chain Z [auth D] MOL2 format, chain Y [auth D] mmCIF format, chain Z [auth D] mmCIF format, chain Y [auth D]	Y [auth D], Z [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain Y [auth D] Focus chain Z [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO Query on CSO	A	L-PEPTIDE LINKING	C₃ H₇ N O₃ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.243 (Depositor), 0.243 (DCC)
R-Value Work: 0.211 (Depositor), 0.216 (DCC)
R-Value Observed: 0.213 (Depositor)

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 231.79	α = 90
b = 231.79	β = 90
c = 98.714	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-02-13

Deposition Author(s):

Funding Organization	Location	Grant Number
Max Planck Society	Germany	--

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
Version 1.3: 2024-11-20
Changes: Structure summary

6HR8 | pdb_00006hr8

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

Literature

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

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2