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PDBsum entry 1mro

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protein ligands metals Protein-protein interface(s) links
Methanogenesis PDB id
1mro
Jmol
Contents
Protein chains
548 a.a. *
442 a.a. *
247 a.a. *
Ligands
F43 ×2
TP7 ×2
COM ×2
GOL ×4
Metals
_NA ×2
_ZN
Waters ×1713
* Residue conservation analysis
PDB id:
1mro
Name: Methanogenesis
Title: Methyl-coenzyme m reductase
Structure: Methyl-coenzyme m reductase. Chain: a, d. Other_details: mcr-ox-silent state, enzyme-substrate comple methyl-coenzyme m reductase. Chain: b, e. Other_details: mcr-ox-silent state, enzyme-substrate comple methyl-coenzyme m reductase. Chain: c, f. Other_details: mcr-ox-silent state, enzyme-substrate comple
Source: Methanothermobacter marburgensis str. Organism_taxid: 79929. Strain: marburg. Cellular_location: cytoplasm. Cellular_location: cytoplasm
Biol. unit: Hexamer (from PDB file)
Resolution:
1.16Å     R-factor:   0.197     R-free:   0.207
Authors: U.Ermler,W.Grabarse
Key ref:
U.Ermler et al. (1997). Crystal structure of methyl-coenzyme M reductase: the key enzyme of biological methane formation. Science, 278, 1457-1462. PubMed id: 9367957 DOI: 10.1126/science.278.5342.1457
Date:
01-Oct-97     Release date:   11-Nov-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P11558  (MCRA_METTM) -  Methyl-coenzyme M reductase I subunit alpha
Seq:
Struc:
 
Seq:
Struc:
550 a.a.
548 a.a.*
Protein chains
Pfam   ArchSchema ?
P11560  (MCRB_METTM) -  Methyl-coenzyme M reductase I subunit beta
Seq:
Struc:
443 a.a.
442 a.a.
Protein chains
Pfam   ArchSchema ?
P11562  (MCRG_METTM) -  Methyl-coenzyme M reductase I subunit gamma
Seq:
Struc:
249 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: Methyl-CoM + CoB = CoM-S-S-CoB + methane
Methyl-CoM
+ CoB
=
CoM-S-S-CoB
Bound ligand (Het Group name = TP7)
matches with 75.00% similarity
+ methane
      Cofactor: Coenzyme F430
Coenzyme F430
Bound ligand (Het Group name = F43) matches with 89.23% similarity
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     methanogenesis   1 term 
  Biochemical function     transferase activity     3 terms  

 

 
    reference    
 
 
DOI no: 10.1126/science.278.5342.1457 Science 278:1457-1462 (1997)
PubMed id: 9367957  
 
 
Crystal structure of methyl-coenzyme M reductase: the key enzyme of biological methane formation.
U.Ermler, W.Grabarse, S.Shima, M.Goubeaud, R.K.Thauer.
 
  ABSTRACT  
 
Methyl-coenzyme M reductase (MCR), the enzyme responsible for the microbial formation of methane, is a 300-kilodalton protein organized as a hexamer in an alpha2beta2gamma2 arrangement. The crystal structure of the enzyme from Methanobacterium thermoautotrophicum, determined at 1.45 angstrom resolution for the inactive enzyme state MCRox1-silent, reveals that two molecules of the nickel porphinoid coenzyme F430 are embedded between the subunits alpha, alpha', beta, and gamma and alpha', alpha, beta', and gamma', forming two identical active sites. Each site is accessible for the substrate methyl-coenzyme M through a narrow channel locked after binding of the second substrate coenzyme B. Together with a second structurally characterized enzyme state (MCRsilent) containing the heterodisulfide of coenzymes M and B, a reaction mechanism is proposed that uses a radical intermediate and a nickel organic compound.
 
  Selected figure(s)  
 
Figure 3.
Fig. 3. Structure of coenzyme F[430] (viewed toward the front face) and the final 2 F[obs] F[calc] electron density at 1.45 Å resolution contoured at the 2 level. The quality of the electron density is sufficiently high to determine the exact configuration of the^ coenzyme that is in agreement with previous results (5). The^ propionate substituents of rings A, B, and C are perpendicular to the tetrapyrrole plane pointing toward the apex, whereas the^ lactam ring is directed toward the mouth of the channel (Fig. 2B). The six-membered carbocyclic ring joined with ring D, and^ the protruding acetate and acetamide substituents lie approximately in the tetrapyrrole ring plane. Figures 3 and 5 were produced^ with SETOR (48).
Figure 4.
Fig. 4. (A) The active site region of the MCR[ox1-silent] structure. The binding positions of the coenzymes suggest the active^ site between the nickel of coenzyme F[430] and the sulfur atom of^ CoB. The active site is coated mostly by nonpolar and aromatic^ residues. Five mutually contacting phenylalanine and tyrosine^ side chains are arranged as ring forming a tunnel. (B) The active site region of the MCR[silent] structure. Compared with the MCR[ox1-silent] structure, CoM has moved through the tunnel to form with CoB a heterodisulfide, the oxidation product of the^ reaction. The sulfonate moiety of CoM lost its interactions to the protein matrix and is coordinated to the Ni atom.
 
  The above figures are reprinted by permission from the AAAs: Science (1997, 278, 1457-1462) copyright 1997.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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PDB code: 2qty
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18765671 R.M.Drevland, Y.Jia, D.R.Palmer, and D.E.Graham (2008).
Methanogen homoaconitase catalyzes both hydrolyase reactions in coenzyme B biosynthesis.
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Phylogenomic analysis of proteins that are distinctive of Archaea and its main subgroups and the origin of methanogenesis.
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17690920 D.I.Kern, M.Goenrich, B.Jaun, R.K.Thauer, J.Harmer, and D.Hinderberger (2007).
Two sub-states of the red2 state of methyl-coenzyme M reductase revealed by high-field EPR spectroscopy.
  J Biol Inorg Chem, 12, 1097-1105.  
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.
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17372351 K.Fukuyama, and T.Okada (2007).
Structures of cyanide, nitric oxide and hydroxylamine complexes of Arthromyces ramosusperoxidase at 100 K refined to 1.3 A resolution: coordination geometries of the ligands to the haem iron.
  Acta Crystallogr D Biol Crystallogr, 63, 472-477.
PDB codes: 2e39 2e3a 2e3b
17949432 S.E.Denman, N.W.Tomkins, and C.S.McSweeney (2007).
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Spectroscopic and computational studies of reduction of the metal versus the tetrapyrrole ring of coenzyme F430 from methyl-coenzyme M reductase.
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16391725 M.O.Senge (2006).
Exercises in molecular gymnastics--bending, stretching and twisting porphyrins.
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Posttranslational protein modification in Archaea.
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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.
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15643942 O.Nercessian, N.Bienvenu, D.Moreira, D.Prieur, and C.Jeanthon (2005).
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16242993 S.Shima, and R.K.Thauer (2005).
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16234924 U.Ermler (2005).
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PDB codes: 1q0d 1q0f 1q0g 1q0k 1q0m
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15300829 S.J.Kwon, R.Petri, A.L.DeBoer, and C.Schmidt-Dannert (2004).
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Nickel coordination is regulated by the DNA-bound state of NikR.
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Aliphatic epoxide carboxylation.
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Identification of methyl coenzyme M reductase A (mcrA) genes associated with methane-oxidizing archaea.
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A two-component signal transduction system involved in nickel sensing in the cyanobacterium Synechocystis sp. PCC 6803.
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Deconstructing F(430): quantum chemical perspectives of biological methanogenesis.
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Chloromethane utilization gene cluster from Hyphomicrobium chloromethanicum strain CM2(T) and development of functional gene probes to detect halomethane-degrading bacteria.
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Mineralogical biosignatures and the search for life on Mars.
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11544359 R.C.Fahey (2001).
Novel thiols of prokaryotes.
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11321536 T.Lueders, K.J.Chin, R.Conrad, and M.Friedrich (2001).
Molecular analyses of methyl-coenzyme M reductase alpha-subunit (mcrA) genes in rice field soil and enrichment cultures reveal the methanogenic phenotype of a novel archaeal lineage.
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10971575 H.Beinert (2000).
A tribute to sulfur.
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Novel cofactors via post-translational modifications of enzyme active sites.
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Structure/function relationships in nickel metallobiochemistry.
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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.