1MRO

METHYL-COENZYME M REDUCTASE


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

  • DOI: 10.1126/science.278.5342.1457
  • Structures With Same Primary Citation

  • 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 thermo ...

    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.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
METHYL-COENZYME M REDUCTASEB, E442Methanothermobacter marburgensis str. MarburgMutation(s): 0 
Gene Names: mcrBMTBMA_c15520
EC: 1.8 (PDB Primary Data), 2.8.4.1 (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
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
METHYL-COENZYME M REDUCTASEA, D548Methanothermobacter marburgensis str. MarburgMutation(s): 0 
Gene Names: mcrAMTBMA_c15480
EC: 1.8 (PDB Primary Data), 2.8.4.1 (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
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
METHYL-COENZYME M REDUCTASEC, F247Methanothermobacter marburgensis str. MarburgMutation(s): 0 
Gene Names: mcrGMTBMA_c15490
EC: 1.8 (PDB Primary Data), 2.8.4.1 (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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
F43
Query on F43

Download CCD File 
A, D
FACTOR 430
C42 H51 N6 Ni O13
XLFIRMYGVLUNOY-SXMZNAGASA-M
 Ligand Interaction
TP7
Query on TP7

Download CCD File 
A
Coenzyme B
C11 H22 N O7 P S
JBJSVEVEEGOEBZ-SCZZXKLOSA-N
 Ligand Interaction
COM
Query on COM

Download CCD File 
A, D
1-THIOETHANESULFONIC ACID
C2 H6 O3 S2
ZNEWHQLOPFWXOF-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A, D
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
C, F
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  5 Unique
IDChainsTypeFormula2D DiagramParent
AGM
Query on AGM
A,DL-PEPTIDE LINKINGC7 H17 N4 O2ARG
GL3
Query on GL3
A,DL-PEPTIDE LINKINGC2 H5 N O SGLY
MGN
Query on MGN
A,DL-PEPTIDE LINKINGC6 H12 N2 O3GLN
MHS
Query on MHS
A,DL-PEPTIDE LINKINGC7 H11 N3 O2HIS
SMC
Query on SMC
A,DL-PEPTIDE LINKINGC4 H9 N O2 SCYS
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 = 81.72α = 90
b = 116.883β = 92.02
c = 122.582γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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