1MRO

METHYL-COENZYME M REDUCTASE

PDB DOI: https://doi.org/10.2210/pdb1MRO/pdb

Classification: METHANOGENESIS
Organism(s): Methanothermobacter marburgensis str. Marburg
Mutation(s): No

Deposited: 1997-10-01 Released: 1998-11-11
Deposition Author(s): Ermler, U., Grabarse, W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.16 Å
R-Value Free: 0.207
R-Value Work: 0.197
R-Value Observed: 0.197

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of methyl-coenzyme M reductase: the key enzyme of biological methane formation.

Ermler, U., Grabarse, W., Shima, S., Goubeaud, M., Thauer, R.K.

(1997) Science 278: 1457-1462

PubMed: 9367957 Search on PubMed
DOI: https://doi.org/10.1126/science.278.5342.1457
Primary Citation of Related Structures:
1MRO

PubMed Abstract:
Methyl-coenzyme M reductase (MCR), the enzyme responsible for the microbial formation of methane, is a 300-kilodalton protein organized as a hexamer in an alpha2beta2gamma2 arrangement. The crystal structure of the enzyme from Methanobacterium thermoautotrophicum, determined at 1.45 angstrom resolution for the inactive enzyme state MCRox1-silent, reveals that two molecules of the nickel porphinoid coenzyme F430 are embedded between the subunits alpha, alpha', beta, and gamma and alpha', alpha, beta', and gamma', forming two identical active sites. Each site is accessible for the substrate methyl-coenzyme M through a narrow channel locked after binding of the second substrate coenzyme B. Together with a second structurally characterized enzyme state (MCRsilent) containing the heterodisulfide of coenzymes M and B, a reaction mechanism is proposed that uses a radical intermediate and a nickel organic compound.

Organizational Affiliation

Max-Planck-Institut für Biophysik, Heinrich-Hoffmann-Strabetae 7, 60528 Frankfurt, Germany.

Macromolecule Content

Total Structure Weight: 275.39 kDa
Atom Count: 21,217
Modelled Residue Count: 2,474
Deposited Residue Count: 2,474
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
METHYL-COENZYME M REDUCTASE	A, D	548	Methanothermobacter marburgensis str. Marburg	Mutation(s): 0 EC: 1.8 (PDB Primary Data), 2.8.4.1 (UniProt)
UniProt
Find proteins for P11558 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg)) Explore P11558 Go to UniProtKB: P11558
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P11558
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
METHYL-COENZYME M REDUCTASE	B, E	442	Methanothermobacter marburgensis str. Marburg	Mutation(s): 0 EC: 1.8 (PDB Primary Data), 2.8.4.1 (UniProt)
UniProt
Find proteins for P11560 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg)) Explore P11560 Go to UniProtKB: P11560
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P11560
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
METHYL-COENZYME M REDUCTASE	C, F	247	Methanothermobacter marburgensis str. Marburg	Mutation(s): 0 EC: 1.8 (PDB Primary Data), 2.8.4.1 (UniProt)
UniProt
Find proteins for P11562 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg)) Explore P11562 Go to UniProtKB: P11562
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P11562
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
F43 Query on F43 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain O [auth D] MOL2 format, chain H [auth A] MOL2 format, chain O [auth D] mmCIF format, chain H [auth A] mmCIF format, chain O [auth D]	H [auth A], O [auth D]	FACTOR 430 C₄₂ H₅₁ N₆ Ni O₁₃ XLFIRMYGVLUNOY-SXMZNAGASA-M		Interactions Focus chain H [auth A] Focus chain O [auth D]
TP7 Query on TP7 Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A]	I [auth A], J [auth A]	Coenzyme B C₁₁ H₂₂ N O₇ P S JBJSVEVEEGOEBZ-SCZZXKLOSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A]
COM Query on COM Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain P [auth D] MOL2 format, chain K [auth A] MOL2 format, chain P [auth D] mmCIF format, chain K [auth A] mmCIF format, chain P [auth D]	K [auth A], P [auth D]	1-THIOETHANESULFONIC ACID C₂ H₆ O₃ S₂ ZNEWHQLOPFWXOF-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain P [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain Q [auth D] SDF format, chain R [auth D] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth D]	L [auth A], M [auth A], Q [auth D], R [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain M [auth A] Focus chain Q [auth D] Focus chain R [auth D]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain S [auth F] MOL2 format, chain N [auth C] MOL2 format, chain S [auth F] mmCIF format, chain N [auth C] mmCIF format, chain S [auth F]	N [auth C], S [auth F]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain N [auth C] Focus chain S [auth F]

Modified Residues 5 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
AGM Query on AGM	A, D	L-PEPTIDE LINKING	C₇ H₁₇ N₄ O₂		ARG
GL3 Query on GL3	A, D	L-PEPTIDE LINKING	C₂ H₅ N O S		GLY
MGN Query on MGN	A, D	L-PEPTIDE LINKING	C₆ H₁₂ N₂ O₃		GLN
MHS Query on MHS	A, D	L-PEPTIDE LINKING	C₇ H₁₁ N₃ O₂		HIS
SMC Query on SMC	A, D	L-PEPTIDE LINKING	C₄ H₉ N O₂ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.16 Å
R-Value Free: 0.207
R-Value Work: 0.197
R-Value Observed: 0.197
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.72	α = 90
b = 116.883	β = 92.02
c = 122.582	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 1998-11-11

Deposition Author(s):

Ermler, U.

Grabarse, W.

Revision History (Full details and data files)

Version 1.0: 1998-11-11
Type: Initial release
Version 1.1: 2008-03-24
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2015-03-04
Changes: Derived calculations
Version 1.4: 2015-05-20
Changes: Non-polymer description
Version 1.5: 2017-03-29
Changes: Non-polymer description