PDBsum entry 1e6v

Oxidoreductase

PDB id: 1e6v

Contents

Protein chains

545 a.a. *

436 a.a. *

248 a.a. *

Ligands

F43 ×2

TP7 ×2

COM ×2

* Residue conservation analysis

PDB id:

1e6v

Name:

Oxidoreductase

Title:

Methyl-coenzyme m reductase from methanopyrus kandleri

Structure:

Methyl-coenzyme m reductase i alpha subunit. Chain: a, d. Methyl-coenzyme m reductase i beta subunit. Chain: b, e. Methyl-coenzyme m reductase i gamma subunit. Chain: c, f

Source:

Methanopyrus kandleri. Organism_taxid: 2320. Cellular_location: cytoplasma. Cellular_location: cytoplasma

Biol. unit:

Hetero-Hexamer (from PDB file)

Resolution:

2.70Å R-factor: 0.239 R-free: 0.278

Authors:

W.Grabarse,U.Ermler

Key ref:

W.Grabarse et al. (2000). Comparison of three methyl-coenzyme M reductases from phylogenetically distant organisms: unusual amino acid modification, conservation and adaptation. J Mol Biol, 303, 329-344. PubMed id: 11023796 DOI: 10.1006/jmbi.2000.4136

Date:

23-Aug-00 Release date: 18-Oct-00

Protein chains

Q49605  (MCRA_METKA) -  Methyl-coenzyme M reductase I subunit alpha from Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938)

Seq: 553 a.a.

Struc: 545 a.a.*

Protein chains

Q49601  (Q49601_9EURY) -  Methyl-coenzyme M reductase subunit beta from Methanopyrus kandleri

Seq: 444 a.a.

Struc: 436 a.a.*

Protein chains

Q49604  (Q49604_9EURY) -  Methyl-coenzyme M reductase subunit gamma from Methanopyrus kandleri

Seq: 258 a.a.

Struc: 248 a.a.

* PDB and UniProt seqs differ at 6 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, B, C, D, E, F: E.C.2.8.4.1 - coenzyme-B sulfoethylthiotransferase.
• Pathway: Methane Biosynthesis
• Reaction: coenzyme B + methyl-coenzyme M = methane + coenzyme M-coenzyme B heterodisulfide

coenzyme B (Bound ligand (Het Group name = TP7) corresponds exactly) + methyl-coenzyme M (Bound ligand (Het Group name = COM) matches with 87.50% similarity) = methane + coenzyme M-coenzyme B heterodisulfide

• Cofactor: Coenzyme F430

Coenzyme F430 (Bound ligand (Het Group name = F43) matches with 96.83% similarity)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1006/jmbi.2000.4136

J Mol Biol 303:329-344 (2000)

PubMed id: 11023796

Comparison of three methyl-coenzyme M reductases from phylogenetically distant organisms: unusual amino acid modification, conservation and adaptation.

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

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.

Selected figure(s)

Figure 2.
Figure 2. Active sites of MCR from Methanosarcina barkeri and Methanopyrus kandleri. (a) 2F[o] -F[c] Electron density map at 1.6 Å resolution of the active site of MCR from M. barkeri. Residual electron density between the sulfur atoms of the coenzymes M and B was observed that can be explained by the presence of small amounts of CoM-SS-CoB (red model) in the same conformation as observed in the structure of MCR from M. thermoautotrophicum in the MCR-silent state. (b) 2F[o] -F[c] Electron density map at 3.2 Å effective resolution of the active site of MCR from M. kandleri. Coenzyme M is the axial nickel ligand. To obtain an undisturbed acive-site view, the electron density of residue Phea439 was clipped off. The Figure was prepared using the program O [Jones et al 1991].

Figure 6.
Figure 6. Chemical environment of the methylated arginine in methyl-coenzyme M reductase from M. barkeri. The additional methyl group (arrow) of the 5-methylarginine a285 is surrounded by hydrophobic residues (shown in green). A water molecule bridges between the substrate coenzyme B and the guanidyl group of the methylarginine which forms an intersubunit salt bridge with Glub183 and a hydrogen bond with Asna494. The Figure was prepared using the program SETOR [Evans 1993].

The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 303, 329-344) copyright 2000.

Figures were selected by an automated process.