5A8K

METHYL-COENZYME M REDUCTASE FROM METHANOTHERMOBACTER WOLFEII AT 1.4 A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.140 
  • R-Value Work: 0.114 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Didehydroaspartate Modification in Methyl-Coenzyme M Reductase Catalyzing Methane Formation.

Wagner, T.Kahnt, J.Ermler, U.Shima, S.

(2016) Angew.Chem.Int.Ed.Engl. 55: 10630

  • DOI: 10.1002/anie.201603882
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • All methanogenic and methanotrophic archaea known to date contain methyl-coenzyme M reductase (MCR) that catalyzes the reversible reduction of methyl-coenzyme M to methane. This enzyme contains the nickel porphinoid F430 as a prosthetic group and, hi ...

    All methanogenic and methanotrophic archaea known to date contain methyl-coenzyme M reductase (MCR) that catalyzes the reversible reduction of methyl-coenzyme M to methane. This enzyme contains the nickel porphinoid F430 as a prosthetic group and, highly conserved, a thioglycine and four methylated amino acid residues near the active site. We describe herein the presence of a novel post-translationally modified amino acid, didehydroaspartate, adjacent to the thioglycine as revealed by mass spectrometry and high-resolution X-ray crystallography. Upon chemical reduction, the didehydroaspartate residue was converted into aspartate. Didehydroaspartate was found in MCR I and II from Methanothermobacter marburgensis and in MCR of phylogenetically distantly related Methanosarcina barkeri but not in MCR I and II of Methanothermobacter wolfeii, which indicates that didehydroaspartate is dispensable but might have a role in fine-tuning the active site to increase the catalytic efficiency.


    Organizational Affiliation

    Max-Planck-Institut für terrestrische Mikrobiologie, Karl-von-Frisch-Strasse 10, 35043, Marburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
METHYL-COENZYME M REDUCTASE
A, D
550Methanothermobacter wolfeiiMutation(s): 0 
Gene Names: mcrA
Find proteins for H7CHY1 (Methanothermobacter wolfeii)
Go to UniProtKB:  H7CHY1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
METHYL-COENZYME M REDUCTASE
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
C, F
249N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, C, D, E
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
CA
Query on CA

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Download CCD File 
A, B, D, E, F
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-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

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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 
F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
ETX
Query on ETX

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Download CCD File 
A, B, C, D, E, F
2-ETHOXYETHANOL
C4 H10 O2
ZNQVEEAIQZEUHB-UHFFFAOYSA-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
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: 1.41 Å
  • R-Value Free: 0.140 
  • R-Value Work: 0.114 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 84.140α = 90.00
b = 150.540β = 90.00
c = 187.090γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-07-16 
  • Released Date: 2016-08-03 
  • Deposition Author(s): Wagner, T., Ermler, U.

Revision History 

  • Version 1.0: 2016-08-03
    Type: Initial release
  • Version 1.1: 2016-08-10
    Type: Database references
  • Version 1.2: 2016-09-28
    Type: Database references
  • Version 1.3: 2017-03-29
    Type: Non-polymer description