Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Hetero 6-mer - A4B2 Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 6-mer - A2BC 

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

Macromolecule Content

• Total Structure Weight: 277.25 kDa 
• Atom Count: 21958 
• Residue Count: 2474 
• Unique protein chains: 3

1HBN

METHYL-COENZYME M REDUCTASE

• DOI: 10.2210/pdb1HBN/pdb

• Classification: METHANOGENESIS
• Organism(s): Methanothermobacter thermautotrophicus
• Mutation(s): Yes 


• Deposited: 2001-04-20 Released: 2001-08-16 
• Deposition Author(s): Ermler, U., Grabarse, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.16 Å
• R-Value Free: 0.190 
• R-Value Work: 0.124 

Literature

On the Mechanism of Biological Methane Formation: Structural Evidence for Conformational Changes in Methyl-Coenzyme M Reductase Upon Substrate Binding

Grabarse, W., Mahlert, F., Duin, E.C., Goubeaud, M., Shima, S., Thauer, R.K., Lamzin, V., Ermler, U.

(2001) J Mol Biol 309: 315

• PubMed: 11491299 
• DOI: 10.1006/jmbi.2001.4647
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Methyl-coenzyme M reductase (MCR) catalyzes the final reaction of the energy conserving pathway of methanogenic archaea in which methylcoenzyme M and coenzyme B are converted to methane and the heterodisulfide CoM-S-S-CoB. It operates under strictly anaerobic conditions and contains the nickel porphinoid F430 which is present in the nickel (I) oxidation state in the active enzyme. The known crystal structures of the inactive nickel (II) enzyme in complex with coenzyme M and coenzyme B (MCR-ox1-silent) and in complex with the heterodisulfide CoM-S-S-CoB (MCR-silent) were now refined at 1.16 A and 1.8 A resolution, respectively. The atomic resolution structure of MCR-ox1-silent describes the exact geometry of the cofactor F430, of the active site residues and of the modified amino acid residues. Moreover, the observation of 18 Mg2+ and 9 Na+ ions at the protein surface of the 300 kDa enzyme specifies typical constituents of binding sites for either ion. The MCR-silent and MCR-ox1-silent structures differed in the occupancy of bound water molecules near the active site indicating that a water chain is involved in the replenishment of the active site with water molecules. The structure of the novel enzyme state MCR-red1-silent at 1.8 A resolution revealed an active site only partially occupied by coenzyme M and coenzyme B. Increased flexibility and distinct alternate conformations were observed near the active site and the substrate channel. The electron density of the MCR-red1-silent state aerobically co-crystallized with coenzyme M displayed a fully occupied coenzyme M-binding site with no alternate conformations. Therefore, the structure was very similar to the MCR-ox1-silent state. As a consequence, the binding of coenzyme M induced specific conformational changes that postulate a molecular mechanism by which the enzyme ensures that methylcoenzyme M enters the substrate channel prior to coenzyme B as required by the active-site geometry. The three different enzymatically inactive enzyme states are discussed with respect to their enzymatically active precursors and with respect to the catalytic mechanism.

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Organizational Affiliation: 

Max-Planck-Institut für Biophysik, Frankfurt, Germany.

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
METHYL-COENZYME M REDUCTASE I BETA SUBUNIT	B, E	442	Methanothermobacter thermautotrophicus	Mutation(s): 0  EC: 2.8.4.1
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: 1
Molecule	Chains	Sequence Length	Organism	Details
METHYL-COENZYME M REDUCTASE I ALPHA SUBUNIT	A, D	549	Methanothermobacter thermautotrophicus	Mutation(s): 5  EC: 2.8.4.1
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: 3
Molecule	Chains	Sequence Length	Organism	Details
METHYL-COENZYME M REDUCTASE I GAMMA SUBUNIT	C, F	248	Methanothermobacter thermautotrophicus	Mutation(s): 0  EC: 2.8.4.1
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 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
F43	A, D	FACTOR 430 C42 H51 N6 Ni O13 XLFIRMYGVLUNOY-SXMZNAGASA-M
TP7	A, D	Coenzyme B C11 H22 N O7 P S JBJSVEVEEGOEBZ-SCZZXKLOSA-N
COM	A, D	1-THIOETHANESULFONIC ACID C2 H6 O3 S2 ZNEWHQLOPFWXOF-UHFFFAOYSA-N
GOL	A, B, C, D, E	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	B, E	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	A, B, C, D, E, F	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	A, B, D	SODIUM ION Na FKNQFGJONOIPTF-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
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: 1.16 Å
• R-Value Free: 0.190 
• R-Value Work: 0.124 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.72	α = 90
b = 116.883	β = 92.02
c = 122.582	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-04-20 
• Released Date: 2001-08-16 
Deposition Author(s): Ermler, U., Grabarse, W.

Revision History 

• Version 1.0: 2001-08-16
  Type: Initial release
  
• Version 1.1: 2015-05-20
  Changes: Derived calculations, Non-polymer description, Other, Version format compliance
• Version 2.0: 2017-06-21
  Changes: Advisory, Atomic model
• Version 2.1: 2019-07-24
  Changes: Data collection, Derived calculations