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PDBsum entry 1e6y
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Oxidoreductase PDB id
1e6y

 

 

 

 

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Contents
Protein chains
568 a.a. *
432 a.a. *
247 a.a. *
Ligands
F43 ×2
TP7 ×2
COM ×2
GOL ×3
Waters ×2197
* Residue conservation analysis
PDB id:
1e6y
Name: Oxidoreductase
Title: Methyl-coenzyme m reductase from methanosarcina barkeri
Structure: Methyl-coenzyme m reductase subunit alpha. Chain: a, d. Synonym: coenzyme-b sulfoethylthiotransferase alpha, methyl-coenzyme m reductase i alpha subunit. Methyl-coenzyme m reductase i beta subunit. Chain: b, e. Synonym: methyl-coenzyme m reductase i beta subunit, coenzyme-b sulfoethylthiotransferase beta. Methyl-coenzyme m reductase subunit gamma.
Source: Methanosarcina barkeri. Organism_taxid: 2208. Cellular_location: cytoplasm. Cellular_location: cytoplasm
Biol. unit: Hetero-Hexamer (from PDB file)
Resolution:
1.60Å     R-factor:   0.160     R-free:   0.179
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    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P07962  (MCRA_METBF) -  Methyl-coenzyme M reductase subunit alpha from Methanosarcina barkeri (strain Fusaro / DSM 804)
Seq:
Struc: 		 
Seq:
Struc: 		570 a.a.
568 a.a.*
Protein chains
Pfam   ArchSchema ?
P07955  (MCRB_METBF) -  Methyl-coenzyme M reductase subunit beta from Methanosarcina barkeri (strain Fusaro / DSM 804)
Seq:
Struc: 		434 a.a.
432 a.a.
Protein chains
Pfam   ArchSchema ?
P07964  (MCRG_METBF) -  Methyl-coenzyme M reductase subunit gamma from Methanosarcina barkeri (strain Fusaro / DSM 804)
Seq:
Struc: 		248 a.a.
247 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D, E, F: E.C.2.8.4.1  - coenzyme-B sulfoethylthiotransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      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.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22121022 S.Shima, M.Krueger, T.Weinert, U.Demmer, J.Kahnt, R.K.Thauer, and U.Ermler (2012).
Structure of a methyl-coenzyme M reductase from Black Sea mats that oxidize methane anaerobically.
  Nature, 481, 98.
PDB code: 3sqg
  20944207 M.D.Miller, L.Aravind, C.Bakolitsa, C.L.Rife, D.Carlton, P.Abdubek, T.Astakhova, H.L.Axelrod, H.J.Chiu, T.Clayton, M.C.Deller, L.Duan, J.Feuerhelm, J.C.Grant, G.W.Han, L.Jaroszewski, K.K.Jin, H.E.Klock, M.W.Knuth, P.Kozbial, S.S.Krishna, A.Kumar, D.Marciano, D.McMullan, A.T.Morse, E.Nigoghossian, L.Okach, R.Reyes, H.van den Bedem, D.Weekes, Q.Xu, K.O.Hodgson, J.Wooley, M.A.Elsliger, A.M.Deacon, A.Godzik, S.A.Lesley, and I.A.Wilson (2010).
Structure of the first representative of Pfam family PF04016 (DUF364) reveals enolase and Rossmann-like folds that combine to form a unique active site with a possible role in heavy-metal chelation.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 1167-1173.
PDB code: 3l5o
19243132 R.Sarangi, M.Dey, and S.W.Ragsdale (2009).
Geometric and electronic structures of the Ni(I) and methyl-Ni(III) intermediates of methyl-coenzyme M reductase.
  Biochemistry, 48, 3146-3156.  
18442173 J.Muñoz, J.Fernández-Irigoyen, E.Santamaría, A.Parbel, J.Obeso, and F.J.Corrales (2008).
Mass spectrometric characterization of mitochondrial complex I NDUFA10 variants.
  Proteomics, 8, 1898-1908.  
18492229 P.D.Scanlan, F.Shanahan, and J.R.Marchesi (2008).
Human methanogen diversity and incidence in healthy and diseased colonic groups using mcrA gene analysis.
  BMC Microbiol, 8, 79.  
18096853 R.K.Thauer, and S.Shima (2008).
Methane as fuel for anaerobic microorganisms.
  Ann N Y Acad Sci, 1125, 158-170.  
17725644 J.Kahnt, B.Buchenau, F.Mahlert, M.Krüger, S.Shima, and R.K.Thauer (2007).
Post-translational modifications in the active site region of methyl-coenzyme M reductase from methanogenic and methanotrophic archaea.
  FEBS J, 274, 4913-4921.  
16966321 R.C.Kunz, Y.C.Horng, and S.W.Ragsdale (2006).
Spectroscopic and kinetic studies of the reaction of bromopropanesulfonate with methyl-coenzyme M reductase.
  J Biol Chem, 281, 34663-34676.  
16385054 W.F.Fricke, H.Seedorf, A.Henne, M.Krüer, H.Liesegang, R.Hedderich, G.Gottschalk, and R.K.Thauer (2006).
The genome sequence of Methanosphaera stadtmanae reveals why this human intestinal archaeon is restricted to methanol and H2 for methane formation and ATP synthesis.
  J Bacteriol, 188, 642-658.  
16148304 J.Eichler, and M.W.Adams (2005).
Posttranslational protein modification in Archaea.
  Microbiol Mol Biol Rev, 69, 393-425.  
15846525 M.Goenrich, E.C.Duin, F.Mahlert, and R.K.Thauer (2005).
Temperature dependence of methyl-coenzyme M reductase activity and of the formation of the methyl-coenzyme M reductase red2 state induced by coenzyme B.
  J Biol Inorg Chem, 10, 333-342.  
16242993 S.Shima, and R.K.Thauer (2005).
Methyl-coenzyme M reductase and the anaerobic oxidation of methane in methanotrophic Archaea.
  Curr Opin Microbiol, 8, 643-648.  
16234924 U.Ermler (2005).
On the mechanism of methyl-coenzyme M reductase.
  Dalton Trans, (), 3451-3458.  
15361623 H.J.Kim, D.W.Graham, A.A.DiSpirito, M.A.Alterman, N.Galeva, C.K.Larive, D.Asunskis, and P.M.Sherwood (2004).
Methanobactin, a copper-acquisition compound from methane-oxidizing bacteria.
  Science, 305, 1612-1615.  
12829270 S.B.Mulrooney, and R.P.Hausinger (2003).
Nickel uptake and utilization by microorganisms.
  FEMS Microbiol Rev, 27, 239-261.  
12957937 S.J.Hallam, P.R.Girguis, C.M.Preston, P.M.Richardson, and E.F.DeLong (2003).
Identification of methyl coenzyme M reductase A (mcrA) genes associated with methane-oxidizing archaea.
  Appl Environ Microbiol, 69, 5483-5491.  
12192072 B.Mamat, A.Roth, C.Grimm, U.Ermler, C.Tziatzios, D.Schubert, R.K.Thauer, and S.Shima (2002).
Crystal structures and enzymatic properties of three formyltransferases from archaea: environmental adaptation and evolutionary relationship.
  Protein Sci, 11, 2168-2178.
PDB codes: 1m5h 1m5s
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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