3SQG

Crystal structure of a methyl-coenzyme M reductase purified from Black Sea mats


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Structure of a methyl-coenzyme M reductase from Black Sea mats that oxidize methane anaerobically.

Shima, S.Krueger, M.Weinert, T.Demmer, U.Kahnt, J.Thauer, R.K.Ermler, U.

(2011) Nature 481: 98-101

  • DOI: 10.1038/nature10663

  • PubMed Abstract: 
  • The anaerobic oxidation of methane (AOM) with sulphate, an area currently generating great interest in microbiology, is accomplished by consortia of methanotrophic archaea (ANME) and sulphate-reducing bacteria. The enzyme activating methane in methan ...

    The anaerobic oxidation of methane (AOM) with sulphate, an area currently generating great interest in microbiology, is accomplished by consortia of methanotrophic archaea (ANME) and sulphate-reducing bacteria. The enzyme activating methane in methanotrophic archaea has tentatively been identified as a homologue of methyl-coenzyme M reductase (MCR) that catalyses the methane-forming step in methanogenic archaea. Here we report an X-ray structure of the 280 kDa heterohexameric ANME-1 MCR complex. It was crystallized uniquely from a protein ensemble purified from consortia of microorganisms collected with a submersible from a Black Sea mat catalysing AOM with sulphate. Crystals grown from the heterogeneous sample diffract to 2.1 Å resolution and consist of a single ANME-1 MCR population, demonstrating the strong selective power of crystallization. The structure revealed ANME-1 MCR in complex with coenzyme M and coenzyme B, indicating the same substrates for MCR from methanotrophic and methanogenic archaea. Differences between the highly similar structures of ANME-1 MCR and methanogenic MCR include a F(430) modification, a cysteine-rich patch and an altered post-translational amino acid modification pattern, which may tune the enzymes for their functions in different biological contexts.


    Organizational Affiliation

    Max Planck Institute for Terrestrial Microbiology, Karl-Frisch-Strasse 10, D-35043 Marburg, Germany. shima@mpi-marburg.mpg.de




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Methyl coenzyme M reductase, alpha subunit
A, D, G
579uncultured archaeonMutation(s): 0 
Gene Names: mcrA
EC: 2.8.4.1
Find proteins for D1JBK4 (uncultured archaeon)
Go to UniProtKB:  D1JBK4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Methyl-coenzyme M reductase, beta subunit
B, E, H
433uncultured archaeonMutation(s): 0 
Gene Names: mcrB
EC: 2.8.4.1
Find proteins for D1JBK2 (uncultured archaeon)
Go to UniProtKB:  D1JBK2
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Methyl-coenzyme M reductase, gamma subunit
C, F, I
279uncultured archaeonMutation(s): 0 
Gene Names: mcrG
EC: 2.8.4.1
Find proteins for D1JBK3 (uncultured archaeon)
Go to UniProtKB:  D1JBK3
Small Molecules
Ligands 10 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
COM
Query on COM

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A, D, G
1-THIOETHANESULFONIC ACID
C2 H6 O3 S2
ZNEWHQLOPFWXOF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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A, B, C, D, H, I
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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C, E
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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A, G
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
TP7
Query on TP7

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A, G
Coenzyme B
7-MERCAPTOHEPTANOYLTHREONINEPHOSPHATE
C11 H22 N O7 P S
JBJSVEVEEGOEBZ-SCZZXKLOSA-N
 Ligand Interaction
P6G
Query on P6G

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B
HEXAETHYLENE GLYCOL
POLYETHYLENE GLYCOL PEG400
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

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A, D, G
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
M43
Query on M43

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A, D, G
(17[2]S)-17[2]-methylthio-coenzyme F43
C43 H53 N6 Ni O13 S
UOYNURPVGLQPFO-AEEVBHTRSA-M
 Ligand Interaction
1PE
Query on 1PE

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A, D, E, F, G, H
PENTAETHYLENE GLYCOL
PEG400
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
0AF
Query on 0AF
A, D, G
L-PEPTIDE LINKINGC11 H12 N2 O3TRP
GL3
Query on GL3
A, D, G
L-PEPTIDE LINKINGC2 H5 N O SGLY
MHO
Query on MHO
A, D, G
L-PEPTIDE LINKINGC5 H11 N O3 SMET
MHS
Query on MHS
A, D, G
L-PEPTIDE LINKINGC7 H11 N3 O2HIS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.161 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 128.860α = 90.00
b = 412.490β = 90.00
c = 165.510γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-11-30
    Type: Initial release
  • Version 1.1: 2011-12-28
    Type: Database references
  • Version 1.2: 2012-01-04
    Type: Database references
  • Version 1.3: 2015-05-20
    Type: Non-polymer description
  • Version 1.4: 2015-05-27
    Type: Other
  • Version 1.5: 2017-11-08
    Type: Refinement description