Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 6-mer - A2B2C2 Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Hetero 6-mer - A4B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 273.16 kDa 
• Atom Count: 21340 
• Modelled Residue Count: 2495 
• Deposited Residue Count: 2498 
• Unique protein chains: 3

1E6Y

Methyl-coenzyme M reductase from Methanosarcina barkeri

• PDB DOI: 10.2210/pdb1E6Y/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Methanosarcina barkeri
• Mutation(s): No 


• Deposited: 2000-08-23 Released: 2000-10-18 
• Deposition Author(s): Grabarse, W., Ermler, U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.179 
• R-Value Work: 0.160 
• R-Value Observed: 0.160 

Literature

Comparison of Three Methyl-Coenzyme M Reductases from Phylogenetically Distant Organisms: Unusual Amino Acid Modification, Conservation and Adaptation

Grabarse, W., Mahlert, F., Shima, S., Thauer, R.K., Ermler, U.

(2000) J Mol Biol 303: 329

• PubMed: 11023796 
• DOI: 10.1006/jmbi.2000.4136
• Primary Citation of Related Structures:  
  1E6V, 1E6Y


• PubMed Abstract: 
  

The nickel enzyme methyl-coenzyme M reductase (MCR) catalyzes the terminal step of methane formation in the energy metabolism of all methanogenic archaea. In this reaction methyl-coenzyme M and coenzyme B are converted to methane and the heterodisulfide of coenzyme M and coenzyme B. The crystal structures of methyl-coenzyme M reductase from Methanosarcina barkeri (growth temperature optimum, 37 degrees C) and Methanopyrus kandleri (growth temperature optimum, 98 degrees C) were determined and compared with the known structure of MCR from Methanobacterium thermoautotrophicum (growth temperature optimum, 65 degrees C). The active sites of MCR from M. barkeri and M. kandleri were almost identical to that of M. thermoautotrophicum and predominantly occupied by coenzyme M and coenzyme B. The electron density at 1.6 A resolution of the M. barkeri enzyme revealed that four of the five modified amino acid residues of MCR from M. thermoautotrophicum, namely a thiopeptide, an S-methylcysteine, a 1-N-methylhistidine and a 5-methylarginine were also present. Analysis of the environment of the unusual amino acid residues near the active site indicates that some of the modifications may be required for the enzyme to be catalytically effective. In M. thermoautotrophicum and M. kandleri high temperature adaptation is coupled with increasing intracellular concentrations of lyotropic salts. This was reflected in a higher fraction of glutamate residues at the protein surface of the thermophilic enzymes adapted to high intracellular salt concentrations.

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Organizational Affiliation: 

Max-Planck-Institut für Biophysik, Heinrich-Hoffmann-Strasse 7, 60528 Frankfurt, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
METHYL-COENZYME M REDUCTASE SUBUNIT ALPHA	A, D	569	Methanosarcina barkeri	Mutation(s): 0  EC: 2.8.4.1
UniProt
Find proteins for P07962 (Methanosarcina barkeri (strain Fusaro / DSM 804)) Explore P07962  Go to UniProtKB:  P07962

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
METHYL-COENZYME M REDUCTASE I BETA SUBUNIT	B, E	433	Methanosarcina barkeri	Mutation(s): 0  EC: 2.8.4.1
UniProt
Find proteins for P07955 (Methanosarcina barkeri (strain Fusaro / DSM 804)) Explore P07955  Go to UniProtKB:  P07955

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
METHYL-COENZYME M REDUCTASE SUBUNIT GAMMA	C, F	247	Methanosarcina barkeri	Mutation(s): 0  EC: 2.8.4.1
UniProt
Find proteins for P07964 (Methanosarcina barkeri (strain Fusaro / DSM 804)) Explore P07964  Go to UniProtKB:  P07964

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
F43	G [auth A], L [auth D]	FACTOR 430 C42 H51 N6 Ni O13 XLFIRMYGVLUNOY-SXMZNAGASA-M
TP7	H [auth A], M [auth D]	Coenzyme B C11 H22 N O7 P S JBJSVEVEEGOEBZ-SCZZXKLOSA-N
COM	I [auth A], N [auth D]	1-THIOETHANESULFONIC ACID C2 H6 O3 S2 ZNEWHQLOPFWXOF-UHFFFAOYSA-N
GOL	J [auth A], K [auth A], O [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  5 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
AGM	A, D	L-PEPTIDE LINKING	C7 H17 N4 O2		ARG
GL3	A, D	L-PEPTIDE LINKING	C2 H5 N O S		GLY
MHS	A, D	L-PEPTIDE LINKING	C7 H11 N3 O2		HIS
SMC	A, D	L-PEPTIDE LINKING	C4 H9 N O2 S		CYS
OCS	C, F	L-PEPTIDE LINKING	C3 H7 N O5 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.179 
• R-Value Work: 0.160 
• R-Value Observed: 0.160 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.678	α = 90
b = 153.099	β = 90
c = 153.288	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-08-23 
• Released Date: 2000-10-18 
Deposition Author(s): Grabarse, W., Ermler, U.

Revision History  

• Version 1.0: 2000-10-18
  Type: Initial release
  
• Version 1.1: 2011-11-16
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Source and taxonomy, Structure summary, Version format compliance
• Version 1.2: 2015-05-20
  Changes: Non-polymer description
• Version 1.3: 2017-03-29
  Changes: Advisory, Non-polymer description
• Version 1.4: 2018-10-17
  Changes: Data collection, Derived calculations
• Version 1.5: 2019-07-10
  Changes: Data collection, Derived calculations
• Version 1.6: 2019-07-24
  Changes: Data collection
• Version 1.7: 2022-05-04
  Changes: Database references, Derived calculations, Other