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 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 

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:  
    5A0Y, 5A8K, 5A8W, 5A8R

  • 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 ...

    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

    CREST, Japan Science and Technology Agency (JST), Saitama, 332-0012, Japan. shima@mpi-marburg.mpg.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
METHYL-COENZYME M II REDUCTASEA, D, G, J554Methanothermobacter wolfeiiMutation(s): 0 
Gene Names: mrtA
EC: 2.8.4.1
UniProt
Find proteins for H7CHY2 (Methanothermobacter wolfeii)
Explore H7CHY2 
Go to UniProtKB:  H7CHY2
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
METHYL-COENZYME M REDUCTASE IIB, E, H, K443Methanothermobacter wolfeiiMutation(s): 0 
Gene Names: mrtBMWSIV6_1524
EC: 2.8.4.1
UniProt
Find proteins for A0A1C7D1E4 (Methanothermobacter wolfeii)
Explore A0A1C7D1E4 
Go to UniProtKB:  A0A1C7D1E4
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
METHYL-COENZYME M REDUCTASE IIC, F, I, L265Methanothermobacter wolfeiiMutation(s): 0 
Gene Names: mrtGMWSIV6_1522
EC: 2.8.4.1
UniProt
Find proteins for A0A1C7D1E5 (Methanothermobacter wolfeii)
Explore A0A1C7D1E5 
Go to UniProtKB:  A0A1C7D1E5
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / 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
 Ligand Interaction
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
 Ligand Interaction
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
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
AA [auth G] , BA [auth H] , CA [auth I] , HA [auth J] , IA [auth K] , JA [auth L] , O [auth A] , T [auth D] , 
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
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
X [auth F]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  5 Unique
IDChainsTypeFormula2D DiagramParent
AGM
Query on AGM
A, D, G, JL-PEPTIDE LINKINGC7 H17 N4 O2ARG
GL3
Query on GL3
A, D, G, JL-PEPTIDE LINKINGC2 H5 N O SGLY
MGN
Query on MGN
A, D, G, JL-PEPTIDE LINKINGC6 H12 N2 O3GLN
MHS
Query on MHS
A, D, G, JL-PEPTIDE LINKINGC7 H11 N3 O2HIS
SMC
Query on SMC
A, D, G, JL-PEPTIDE LINKINGC4 H9 N O2 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 
  • 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



Entry History 

Deposition Data

  • Deposited Date: 2015-07-17 
  • Released Date: 2016-08-03 
  • Deposition Author(s): Wagner, T., Ermler, U.

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