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 
  • R-Value Observed: 0.115 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 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 REDUCTASE
A, D
550Methanothermobacter wolfeiiMutation(s): 0 
EC: 2.8.4.1
UniProt
Find proteins for H7CHY1 (Methanothermobacter wolfeii)
Explore H7CHY1 
Go to UniProtKB:  H7CHY1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH7CHY1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
METHYL-COENZYME M REDUCTASE
B, E
443Methanothermobacter wolfeiiMutation(s): 0 
EC: 2.8.4.1
UniProt
Find proteins for A0A1C7D1E2 (Methanothermobacter wolfeii)
Explore A0A1C7D1E2 
Go to UniProtKB:  A0A1C7D1E2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1C7D1E2
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
C, F
249Methanothermobacter wolfeiiMutation(s): 0 
EC: 2.8.4.1
UniProt
Find proteins for A0A1C7D1E3 (Methanothermobacter wolfeii)
Explore A0A1C7D1E3 
Go to UniProtKB:  A0A1C7D1E3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1C7D1E3
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
F43
Query on F43

Download Ideal Coordinates CCD File 
KA [auth D],
O [auth A]
FACTOR 430
C42 H51 N6 Ni O13
XLFIRMYGVLUNOY-SXMZNAGASA-M
TP7
Query on TP7

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CA [auth D],
H [auth A]
Coenzyme B
C11 H22 N O7 P S
JBJSVEVEEGOEBZ-SCZZXKLOSA-N
COM
Query on COM

Download Ideal Coordinates CCD File 
DA [auth D],
G [auth A]
1-THIOETHANESULFONIC ACID
C2 H6 O3 S2
ZNEWHQLOPFWXOF-UHFFFAOYSA-N
ETX
Query on ETX

Download Ideal Coordinates CCD File 
BA [auth C]
BB [auth F]
CB [auth F]
DB [auth F]
LA [auth D]
BA [auth C],
BB [auth F],
CB [auth F],
DB [auth F],
LA [auth D],
MA [auth D],
NA [auth D],
P [auth A],
Q [auth A],
QA [auth E],
R [auth A],
RA [auth E],
S [auth A],
SA [auth E],
T [auth A],
TA [auth E],
UA [auth E],
V [auth B],
VA [auth E],
W [auth B],
WA [auth E],
X [auth B],
XA [auth E],
Y [auth B],
YA [auth E],
Z [auth B]
2-ETHOXYETHANOL
C4 H10 O2
ZNQVEEAIQZEUHB-UHFFFAOYSA-N
CA
Query on CA

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EA [auth D]
FA [auth D]
GA [auth D]
HA [auth D]
IA [auth D]
EA [auth D],
FA [auth D],
GA [auth D],
HA [auth D],
IA [auth D],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
OA [auth E],
U [auth B],
ZA [auth F]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
AA [auth C],
I [auth A],
JA [auth D],
N [auth A],
PA [auth E]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.140 
  • R-Value Work: 0.114 
  • R-Value Observed: 0.115 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.14α = 90
b = 150.54β = 90
c = 187.09γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

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: 2019-05-15
    Changes: Data collection, Derived calculations, Experimental preparation
  • Version 1.5: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description