5N2A

METHYL-COENZYME M REDUCTASE III FROM METHANOTORRIS FORMICICUS TRIGONAL FORM

Summary for 5N2A

• Entry DOI: 10.2210/pdb5n2a/pdb
• Descriptor: Methyl-coenzyme M reductase subunit alpha, Methyl-coenzyme M reductase, beta subunit, Methyl-coenzyme M reductase, gamma subunit, ... (8 entities in total)
• Functional Keywords: transferase, post-translational modification, binding sites, catalysis, coenzymes, disulfides, hydrogen, hydrogen bonding, ligands, mesna, metalloporphyrins, methane, methanococcales, nickel, oxidation-reduction, oxidoreductases, phosphothreonine, protein conformation, protein folding, protein structure, thermophile, autotroph, hydroxy-tryptophane
• Biological source: Methanotorris formicicus Mc-S-70; More
• Total number of polymer chains: 3
• Total formula weight: 140508.13

Authors

Wagner, T.,Wegner, C.E.,Ermler, U.,Shima, S. (deposition date: 2017-02-07, release date: 2017-06-14, Last modification date: 2024-01-17)

Primary citation

Wagner, T.,Wegner, C.E.,Kahnt, J.,Ermler, U.,Shima, S.
Phylogenetic and Structural Comparisons of the Three Types of Methyl Coenzyme M Reductase from Methanococcales and Methanobacteriales.
J.Bacteriol., 199:-, 2017

PubMed Abstract: The phylogenetically diverse family of methanogenic archaea universally use methyl coenzyme M reductase (MCR) for catalyzing the final methane-forming reaction step of the methanogenic energy metabolism. Some methanogens of the orders and contain two isoenzymes. Comprehensive phylogenetic analyses on the basis of all three subunits grouped MCRs from and into three distinct types: (i) MCRs from , (ii) MCRs from and , and (iii) MCRs from The first and second types contain MCR isoenzymes I and II from , respectively; therefore, they were designated MCR type I and type II and accordingly; the third one was designated MCR type III. For comparison with the known MCR type I and type II structures, we determined the structure of MCR type III from and As predicted, the three MCR types revealed highly similar overall structures and virtually identical active site architectures reflecting the chemically challenging mechanism of methane formation. Pronounced differences were found at the protein surface with respect to loop geometries and electrostatic properties, which also involve the entrance of the active-site funnel. In addition, the C-terminal end of the γ-subunit is prolonged by an extra helix after helix γ8 in MCR type II and type III, which is, however, differently arranged in the two MCR types. MCR types I, II, and III share most of the posttranslational modifications which appear to fine-tune the enzymatic catalysis. Interestingly, MCR type III lacks the methyl-cysteine but possesses in subunit α of a 6-hydroxy-tryptophan, which thus far has been found only in the α-amanitin toxin peptide but not in proteins. Methyl coenzyme M reductase (MCR) represents a prime target for the mitigation of methane releases. Phylogenetic analyses of MCRs suggested several distinct sequence clusters; those from and were subdivided into three types: MCR type I from , MCR type II from and , and the newly designated MCR type III exclusively from We determined the first X-ray structures for an MCR type III. Detailed analyses revealed substantial differences between the three types only in the peripheral region. The subtle modifications identified and electrostatic profiles suggested enhanced substrate binding for MCR type III. In addition, MCR type III from contains 6-hydroxy-tryptophan, a new posttranslational modification that thus far has been found only in the α-amanitin toxin.

PubMed: 28559298
DOI: 10.1128/JB.00197-17

Experimental method

X-RAY DIFFRACTION (2.8 Å)