5A8W

METHYL-COENZYME M REDUCTASE II FROM METHANOTHERMOBACTER WOLFEII AT 1. 8 A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.201 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.165 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.167 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted F43Click on this verticalbar to view detailsBest fitted TP7Click on this verticalbar to view details

This is version 1.4 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: https://doi.org/10.1002/anie.201603882
  • Primary Citation of Related Structures:  
    5A0Y, 5A8K, 5A8R, 5A8W

  • 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, 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
METHYL-COENZYME M II REDUCTASE
A, D, G, J
554Methanothermobacter wolfeiiMutation(s): 0 
EC: 2.8.4.1
UniProt
Find proteins for H7CHY2 (Methanothermobacter wolfeii)
Explore H7CHY2 
Go to UniProtKB:  H7CHY2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH7CHY2
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
METHYL-COENZYME M REDUCTASE II
B, E, H, K
443Methanothermobacter wolfeiiMutation(s): 0 
EC: 2.8.4.1
UniProt
Find proteins for A0A1C7D1E4 (Methanothermobacter wolfeii)
Explore A0A1C7D1E4 
Go to UniProtKB:  A0A1C7D1E4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1C7D1E4
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
METHYL-COENZYME M REDUCTASE II
C, F, I, L
265Methanothermobacter wolfeiiMutation(s): 0 
EC: 2.8.4.1
UniProt
Find proteins for A0A1C7D1E5 (Methanothermobacter wolfeii)
Explore A0A1C7D1E5 
Go to UniProtKB:  A0A1C7D1E5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1C7D1E5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
F43
Query on F43

Download Ideal Coordinates CCD File 
EA [auth J],
Q [auth D],
S [auth D],
Z [auth G]
FACTOR 430
C42 H51 N6 Ni O13
XLFIRMYGVLUNOY-SXMZNAGASA-M
TP7
Query on TP7

Download Ideal Coordinates CCD File 
DA [auth J],
GA [auth J],
N [auth A],
P [auth D]
Coenzyme B
C11 H22 N O7 P S
JBJSVEVEEGOEBZ-SCZZXKLOSA-N
COM
Query on COM

Download Ideal Coordinates CCD File 
FA [auth J],
M [auth A],
R [auth D],
Y [auth G]
1-THIOETHANESULFONIC ACID
C2 H6 O3 S2
ZNEWHQLOPFWXOF-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
AA [auth G]
BA [auth H]
CA [auth I]
HA [auth J]
IA [auth K]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
X [auth F]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  5 Unique
IDChains TypeFormula2D DiagramParent
AGM
Query on AGM
A, D, G, J
L-PEPTIDE LINKINGC7 H17 N4 O2ARG
GL3
Query on GL3
A, D, G, J
L-PEPTIDE LINKINGC2 H5 N O SGLY
MGN
Query on MGN
A, D, G, J
L-PEPTIDE LINKINGC6 H12 N2 O3GLN
MHS
Query on MHS
A, D, G, J
L-PEPTIDE LINKINGC7 H11 N3 O2HIS
SMC
Query on SMC
A, D, G, J
L-PEPTIDE LINKINGC4 H9 N O2 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.201 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.165 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.167 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.391α = 89.2
b = 102.185β = 93.97
c = 118.739γ = 90.98
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted F43Click on this verticalbar to view detailsBest fitted TP7Click on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-03
    Type: Initial release
  • Version 1.1: 2016-08-10
    Changes: Database references
  • Version 1.2: 2016-09-28
    Changes: Database references
  • Version 1.3: 2017-03-29
    Changes: Non-polymer description
  • Version 1.4: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description