1E6Y

Methyl-coenzyme M reductase from Methanosarcina barkeri

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.6 of the entry. See complete history. 

Literature

Comparison of Three Methyl-Coenzyme M Reductases from Phylogenetically Distant Organisms: Unusual Amino Acid Modification, Conservation and Adaptation

Grabarse, W., Mahlert, F., Shima, S., Thauer, R.K., Ermler, U.

(2000) J.Mol.Biol. 303: 329

  • DOI: 10.1006/jmbi.2000.4136
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • The nickel enzyme methyl-coenzyme M reductase (MCR) catalyzes the terminal step of methane formation in the energy metabolism of all methanogenic archaea. In this reaction methyl-coenzyme M and coenzyme B are converted to methane and the heterodisulf ...

    The nickel enzyme methyl-coenzyme M reductase (MCR) catalyzes the terminal step of methane formation in the energy metabolism of all methanogenic archaea. In this reaction methyl-coenzyme M and coenzyme B are converted to methane and the heterodisulfide of coenzyme M and coenzyme B. The crystal structures of methyl-coenzyme M reductase from Methanosarcina barkeri (growth temperature optimum, 37 degrees C) and Methanopyrus kandleri (growth temperature optimum, 98 degrees C) were determined and compared with the known structure of MCR from Methanobacterium thermoautotrophicum (growth temperature optimum, 65 degrees C). The active sites of MCR from M. barkeri and M. kandleri were almost identical to that of M. thermoautotrophicum and predominantly occupied by coenzyme M and coenzyme B. The electron density at 1.6 A resolution of the M. barkeri enzyme revealed that four of the five modified amino acid residues of MCR from M. thermoautotrophicum, namely a thiopeptide, an S-methylcysteine, a 1-N-methylhistidine and a 5-methylarginine were also present. Analysis of the environment of the unusual amino acid residues near the active site indicates that some of the modifications may be required for the enzyme to be catalytically effective. In M. thermoautotrophicum and M. kandleri high temperature adaptation is coupled with increasing intracellular concentrations of lyotropic salts. This was reflected in a higher fraction of glutamate residues at the protein surface of the thermophilic enzymes adapted to high intracellular salt concentrations.

    Organizational Affiliation: 

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
METHYL-COENZYME M REDUCTASE SUBUNIT ALPHA
A, D
569Methanosarcina barkeri (strain Fusaro / DSM 804)Mutation(s): 0 
Gene Names: mcrA
EC: 2.8.4.1
Find proteins for P07962 (Methanosarcina barkeri (strain Fusaro / DSM 804))
Go to UniProtKB:  P07962
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
METHYL-COENZYME M REDUCTASE I BETA SUBUNIT
B, E
433Methanosarcina barkeri (strain Fusaro / DSM 804)Mutation(s): 0 
Gene Names: mcrB
EC: 2.8.4.1
Find proteins for P07955 (Methanosarcina barkeri (strain Fusaro / DSM 804))
Go to UniProtKB:  P07955
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
METHYL-COENZYME M REDUCTASE SUBUNIT GAMMA
C, F
247Methanosarcina barkeri (strain Fusaro / DSM 804)Mutation(s): 0 
Gene Names: mcrG
EC: 2.8.4.1
Find proteins for P07964 (Methanosarcina barkeri (strain Fusaro / DSM 804))
Go to UniProtKB:  P07964
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
COM
Query on COM
Download SDF File 
Download CCD File 
A, D
1-THIOETHANESULFONIC ACID
C2 H6 O3 S2
ZNEWHQLOPFWXOF-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL
Download SDF File 
Download CCD File 
A, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
F43
Query on F43
Download SDF File 
Download CCD File 
A, D
FACTOR 430
C42 H51 N6 Ni O13
XLFIRMYGVLUNOY-SXMZNAGASA-M
 Ligand Interaction
TP7
Query on TP7
Download SDF File 
Download CCD File 
A, D
Coenzyme B
7-MERCAPTOHEPTANOYLTHREONINEPHOSPHATE
C11 H22 N O7 P S
JBJSVEVEEGOEBZ-SCZZXKLOSA-N
 Ligand Interaction
Modified Residues  5 Unique
IDChainsTypeFormula2D DiagramParent
GL3
Query on GL3
A, D
L-PEPTIDE LINKINGC2 H5 N O SGLY
SMC
Query on SMC
A, D
L-PEPTIDE LINKINGC4 H9 N O2 SCYS
MHS
Query on MHS
A, D
L-PEPTIDE LINKINGC7 H11 N3 O2HIS
AGM
Query on AGM
A, D
L-PEPTIDE LINKINGC7 H17 N4 O2ARG
OCS
Query on OCS
C, F
L-PEPTIDE LINKINGC3 H7 N O5 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.160 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 113.678α = 90.00
b = 153.099β = 90.00
c = 153.288γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-10-18
    Type: Initial release
  • Version 1.1: 2011-11-16
    Type: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Source and taxonomy, Structure summary, Version format compliance
  • Version 1.2: 2015-05-20
    Type: Non-polymer description
  • Version 1.3: 2017-03-29
    Type: Advisory, Non-polymer description
  • Version 1.4: 2018-10-17
    Type: Data collection, Derived calculations
  • Version 1.5: 2019-07-10
    Type: Data collection, Derived calculations
  • Version 1.6: 2019-07-24
    Type: Data collection