Biological Assembly 1  

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: 276.76 kDa 
• Atom Count: 22,747 
• Modelled Residue Count: 2,477 
• Deposited Residue Count: 2,484 
• Unique protein chains: 3

 5A0Y

METHYL-COENZYME M REDUCTASE FROM METHANOTHERMOBACTER MARBURGENSIS AT 1.1 A RESOLUTION

• PDB DOI: 10.2210/pdb5A0Y/pdb

• Classification: TRANSFERASE
• Organism(s): Methanothermobacter marburgensis
• Mutation(s): No 


• Deposited: 2015-04-24 Released: 2016-05-11 
• Deposition Author(s): Wagner, T., Ermler, U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 0.129 
• R-Value Work: 0.111 
• R-Value Observed: 0.112 

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

• PubMed: 27467699 
• DOI: 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.

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Organizational Affiliation: 

CREST, Japan Science and Technology Agency (JST), Saitama, 332-0012, Japan. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
METHYL-COENZYME M REDUCTASE I SUBUNIT ALPHA	A, D	550	Methanothermobacter marburgensis	Mutation(s): 0  EC: 2.8.4.1
UniProt
Find proteins for P11558 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg)) Explore P11558  Go to UniProtKB:  P11558

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
METHYL-COENZYME M REDUCTASE I SUBUNIT BETA	B, E	443	Methanothermobacter marburgensis	Mutation(s): 0  EC: 2.8.4.1
UniProt
Find proteins for P11560 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg)) Explore P11560  Go to UniProtKB:  P11560

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
METHYL-COENZYME M REDUCTASE I SUBUNIT GAMMA	C, F	249	Methanothermobacter marburgensis	Mutation(s): 0  EC: 2.8.4.1
UniProt
Find proteins for P11562 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg)) Explore P11562  Go to UniProtKB:  P11562

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
F43	I [auth A], V [auth D]	FACTOR 430 C42 H51 N6 Ni O13 XLFIRMYGVLUNOY-SXMZNAGASA-M
TP7	K [auth A], X [auth D]	Coenzyme B C11 H22 N O7 P S JBJSVEVEEGOEBZ-SCZZXKLOSA-N
COM	J [auth A], W [auth D]	1-THIOETHANESULFONIC ACID C2 H6 O3 S2 ZNEWHQLOPFWXOF-UHFFFAOYSA-N
K	L [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	AA [auth D], P [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	BA [auth D], CA [auth E], DA [auth E], EA [auth E], FA [auth F], G [auth A], GA [auth F], H [auth A], M [auth A], N [auth A], Q [auth B], R [auth B], S [auth C], T [auth C], U [auth D], Y [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	O [auth A], Z [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  6 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
AGM	A, D	L-PEPTIDE LINKING	C7 H17 N4 O2		ARG
DYA	A, D	L-PEPTIDE LINKING	C4 H5 N O4		ASP
GL3	A, D	L-PEPTIDE LINKING	C2 H5 N O S		GLY
MGN	A, D	L-PEPTIDE LINKING	C6 H12 N2 O3		GLN
MHS	A, D	L-PEPTIDE LINKING	C7 H11 N3 O2		HIS
SMC	A, D	L-PEPTIDE LINKING	C4 H9 N O2 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 0.129 
• R-Value Work: 0.111 
• R-Value Observed: 0.112 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.227	α = 90
b = 118.3	β = 91.9
c = 122.56	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-05-11 
Deposition Author(s): Wagner, T., Ermler, U.

Revision History  

• Version 1.0: 2016-05-11
  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 2.0: 2019-04-24
  Changes: Data collection, Derived calculations, Polymer sequence