1E6Y

Methyl-coenzyme M reductase from Methanosarcina barkeri


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.160 

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Ligand Structure Quality Assessment 


This is version 1.7 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:  
    1E6V, 1E6Y

  • 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 heterodisulfide of coenzyme M and coenzyme B ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
METHYL-COENZYME M REDUCTASE SUBUNIT ALPHAA, D569Methanosarcina barkeriMutation(s): 0 
EC: 2.8.4.1
UniProt
Find proteins for P07962 (Methanosarcina barkeri (strain Fusaro / DSM 804))
Explore P07962 
Go to UniProtKB:  P07962
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07962
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
METHYL-COENZYME M REDUCTASE I BETA SUBUNITB, E433Methanosarcina barkeriMutation(s): 0 
EC: 2.8.4.1
UniProt
Find proteins for P07955 (Methanosarcina barkeri (strain Fusaro / DSM 804))
Explore P07955 
Go to UniProtKB:  P07955
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07955
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
METHYL-COENZYME M REDUCTASE SUBUNIT GAMMAC, F247Methanosarcina barkeriMutation(s): 0 
EC: 2.8.4.1
UniProt
Find proteins for P07964 (Methanosarcina barkeri (strain Fusaro / DSM 804))
Explore P07964 
Go to UniProtKB:  P07964
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07964
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  5 Unique
IDChainsTypeFormula2D DiagramParent
AGM
Query on AGM
A, D L-PEPTIDE LINKINGC7 H17 N4 O2ARG
GL3
Query on GL3
A, D L-PEPTIDE LINKINGC2 H5 N O SGLY
MHS
Query on MHS
A, D L-PEPTIDE LINKINGC7 H11 N3 O2HIS
SMC
Query on SMC
A, D L-PEPTIDE LINKINGC4 H9 N O2 SCYS
OCS
Query on OCS
C, F L-PEPTIDE LINKINGC3 H7 N O5 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.160 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.678α = 90
b = 153.099β = 90
c = 153.288γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-10-18
    Type: Initial release
  • Version 1.1: 2011-11-16
    Changes: 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
    Changes: Non-polymer description
  • Version 1.3: 2017-03-29
    Changes: Advisory, Non-polymer description
  • Version 1.4: 2018-10-17
    Changes: Data collection, Derived calculations
  • Version 1.5: 2019-07-10
    Changes: Data collection, Derived calculations
  • Version 1.6: 2019-07-24
    Changes: Data collection
  • Version 1.7: 2022-05-04
    Changes: Database references, Derived calculations, Other