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PDBsum entry 1e6v
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Oxidoreductase
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PDB id
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1e6v
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Contents |
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545 a.a.
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436 a.a.
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248 a.a.
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Comparison of three methyl-Coenzyme m reductases from phylogenetically distant organisms: unusual amino acid modification, Conservation and adaptation.
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Authors
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W.Grabarse,
F.Mahlert,
S.Shima,
R.K.Thauer,
U.Ermler.
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Ref.
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J Mol Biol, 2000,
303,
329-344.
[DOI no: ]
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PubMed id
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Abstract
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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.
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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].
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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].
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2000,
303,
329-344)
copyright 2000.
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