5N1Q

METHYL-COENZYME M REDUCTASE III FROM METHANOTHERMOCOCCUS THERMOLITHOTROPHICUS AT 1.9 A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Phylogenetic and Structural Comparisons of the Three Types of Methyl Coenzyme M Reductase from Methanococcales and Methanobacteriales.

Wagner, T.Wegner, C.E.Kahnt, J.Ermler, U.Shima, S.

(2017) J.Bacteriol. 199: --

  • DOI: 10.1128/JB.00197-17
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The phylogenetically diverse family of methanogenic archaea universally use methyl-coenzyme M reductase (MCR) for catalyzing the final methane-forming reaction step of the methanogenic energy metabolism. Some methanogens of the orders Methanobacteria ...

    The phylogenetically diverse family of methanogenic archaea universally use methyl-coenzyme M reductase (MCR) for catalyzing the final methane-forming reaction step of the methanogenic energy metabolism. Some methanogens of the orders Methanobacteriales and Methanococcales contain two isoenzymes. Comprehensive phylogenetic analyses on the basis of all three subunits grouped MCRs from Methanobacteriales, Methanococcales and Methanopyrales into three distinct types: (1) MCRs from Methanobacteriales, (2) MCRs from Methanobacteriales and Methanococcales and (3) MCRs from Methanococcales. The first and second types contain MCR isoenzyme I and II from Methanothermobacter marburgensis, respectively; therefore, they were designated as MCR type I and type II and accordingly, the third one was designated as MCR type III. For comparison with the known MCR type I and type II structures, we determined the structure of MCR type III from Methanotorris formicicus and Methanothermococcus thermolithotrophicus As predicted, the three MCR types revealed highly similar overall structures and a virtually identical active site architecture reflecting the chemically challenging mechanism of methane formation. Pronounced differences were found at the protein surface with respect to loop geometries and electrostatic properties, which also involve the entrance of the active site funnel. In addition, the C-terminal end of the γ-subunit is prolonged by an extra helix after helix γ8 in MCR type II and type III, which is, however, differently arranged in the two MCR types. MCR types I, II and III share most of the post-translational modifications which appear to fine-tune the enzymatic catalysis. Interestingly, MCR type III lacks the methyl-cysteine but possesses in subunit α of M. formicicus a 6-hydroxy-tryptophan, which has been, so far, only found in the α-amanitin toxin peptide but not in proteins.IMPORTANCE Methyl-coenzyme M reductase (MCR) represents a prime target for the mitigation of methane releases. Phylogenetic analyses of MCR suggested several distinct sequence clusters; those from Methanobacteriales and Methanococcales were subdivided into three types: MCR type I from Methanobacteriales, MCR type II from Methanobacteriales and Methanococcales and the newly designated MCR type III exclusively from Methanococcales. We determined the first X-ray structures for an MCR type III. Detailed analyses only revealed substantial differences between the three types in the peripheral region. Identified subtle modifications and electrostatic profiles suggested enhanced substrate binding for MCR type III. In addition, MCR type III from Methanotorris formicicus contains 6-hydroxy-tryptophan, a new post-translational modification that was, so far, only found in the α-amanitin toxin.


    Organizational Affiliation

    Max-Planck-Institute für terrestrische Mikrobiologie, Marburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
METHYL-COENZYME M REDUCTASE III FROM METHANOTHERMOCOCCUS THERMOLITHOTROPHICUS SUBUNIT ALPHA
A, D
553N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
METHYL-COENZYME M REDUCTASE III FROM METHANOTHERMOCOCCUS THERMOLITHOTROPHICUS SUBUNIT BETA
B, E
443N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
METHYL-COENZYME M REDUCTASE III FROM METHANOTHERMOCOCCUS THERMOLITHOTROPHICUS SUBUNIT GAMMA
C, F
261N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
COM
Query on COM

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

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Download CCD File 
B, D, F
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
F43
Query on F43

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

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Download CCD File 
A, D
Coenzyme B
7-MERCAPTOHEPTANOYLTHREONINEPHOSPHATE
C11 H22 N O7 P S
JBJSVEVEEGOEBZ-SCZZXKLOSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
E
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
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
MGN
Query on MGN
A, D
L-PEPTIDE LINKINGC6 H12 N2 O3GLN
AGM
Query on AGM
A, D
L-PEPTIDE LINKINGC7 H17 N4 O2ARG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.169 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 111.811α = 90.00
b = 77.224β = 107.01
c = 145.458γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOLREPphasing
BUSTERrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-06-14
    Type: Initial release
  • Version 1.1: 2019-05-08
    Type: Data collection, Database references