5A8W | pdb_00005a8w

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), 0.167 (DCC) 
  • R-Value Observed: 
    0.167 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


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 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.

Macromolecule Content 

  • Total Structure Weight: 561.29 kDa 
  • Atom Count: 42,336 
  • Modeled Residue Count: 5,013 
  • Deposited Residue Count: 5,048 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  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
Find similar proteins by:|  3D Structure
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:|  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
Expand
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]
AA [auth G],
BA [auth H],
CA [auth I],
HA [auth J],
IA [auth K],
JA [auth L],
O [auth A],
T [auth D],
U [auth E],
V [auth E],
W [auth F]
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), 0.167 (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

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Ligand Structure Quality Assessment 


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