Information on EC 2.8.4.1 - coenzyme-B sulfoethylthiotransferase

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The expected taxonomic range for this enzyme is: Archaea, Bacteria

EC NUMBER
COMMENTARY
2.8.4.1
-
RECOMMENDED NAME
GeneOntology No.
coenzyme-B sulfoethylthiotransferase
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
methyl-CoM + CoB = CoM-S-S-CoB + methane
show the reaction diagram
ethyl CoM and difluoromethyl CoM are poor substrates. The sulfide sulfur can be replaced by selenium but not by oxygen; methylreductase complex mechanism suggested; the enzyme from methanogenic bacteria requires the hydroprophinoid nickel complex coenzyme F-430. Highly specific for coenzyme B with a geptanoyl chain
-
-
-
methyl-CoM + CoB = CoM-S-S-CoB + methane
show the reaction diagram
proposed reaction mechanism uses a radical intermediate and a nickel organic compound. Suggested solutions for enzyme state, structure, reaction cycle and binding mechanism for the enzyme are given
-
methyl-CoM + CoB = CoM-S-S-CoB + methane
show the reaction diagram
ternary complex type
-
methyl-CoM + CoB = CoM-S-S-CoB + methane
show the reaction diagram
mechanism, nucleophilic attack of Ni(I)-MCRred1 on the methyl group of methyl-SCoM generates a methyl-Ni intermediate; Two reaction mechanisms for methane formation distinguishable by the first step of catalysis, overview
-
methyl-CoM + CoB = CoM-S-S-CoB + methane
show the reaction diagram
in the active site region of both isozymes, modified amino acids occur determined by mass spectrometry: thioglycine alpha445, forming a thioxo peptide/thioamide bond with tyrosine alpha446, 2-(S)-methylglutamine alpha400, 1-N-methylhistidine alpha257 and 5-(S)-methylarginine alpha271
-
methyl-CoM + CoB = CoM-S-S-CoB + methane
show the reaction diagram
in the active site region of both isozymes, modified amino acids occur determined by mass spectrometry: thioglycine alpha445, forming a thioxo peptide/thioamide bond with tyrosine alpha446, S-methylcysteine alpha452, 2-(S)-methylglutamine alpha400, and 1-N-methylhistidine alpha257
-
methyl-CoM + CoB = CoM-S-S-CoB + methane
show the reaction diagram
in the active site region of both isozymes, modified amino acids occur determined by mass spectrometry: thioglycine alpha445, forming a thioxo peptide/thioamide bond with tyrosine alpha446, S-methylcysteine alpha452, 2-(S)-methylglutamine alpha400, and 5-(S)-methylarginine alpha271
-
methyl-CoM + CoB = CoM-S-S-CoB + methane
show the reaction diagram
in the active site region of both isozymes, modified amino acids occur determined by mass spectrometry: thioglycine alpha445, forming a thioxo peptide/thioamide bond with tyrosine alpha446, 2-(S)-methylglutamine alpha400, 1-N-methylhistidine alpha257 and 5-(S)-methylarginine alpha271
-, Q49605
methyl-CoM + CoB = CoM-S-S-CoB + methane
show the reaction diagram
in the active site region of both isozymes, modified amino acids occur determined by mass spectrometry: thioglycine alpha445, forming a thioxo peptide/thioamide bond with tyrosine alpha446, S-methylcysteine alpha452, 1-N-methylhistidine alpha257 and 5-(S)-methylarginine alpha271
-
methyl-CoM + CoB = CoM-S-S-CoB + methane
show the reaction diagram
in the active site region of both isozymes, five modified amino acids occur determined by mass spectrometry: thioglycine alpha445, forming a thioxo peptide/thioamide bond with tyrosine alpha446, S-methylcysteine alpha452, 2-(S)-methylglutamine alpha400, 1-N-methylhistidine alpha257 and 5-(S)-methylarginine alpha271
-
methyl-CoM + CoB = CoM-S-S-CoB + methane
show the reaction diagram
two possible catalytic mechanisms, overview
-
methyl-CoM + CoB = CoM-S-S-CoB + methane
show the reaction diagram
reaction mechanism, different varaints, the Ni(I) center is assumed to attack the thioether sulfur of CH3-S-CoM, generating -CH3 and the thiolate complex CoM-SNi(II)F430 as intermediates, detailed overview
-
methyl-CoM + CoB = CoM-S-S-CoB + methane
show the reaction diagram
the first step of the mechanism is proposed to involve a nucleophilic attack of the NiI active state, MCRred1, on Me-SCoM to form a NiIII-methyl intermediate, spectroscopic analysis and structures, overview
-
methyl-CoM + CoB = CoM-S-S-CoB + methane
show the reaction diagram
catalytic mechanism, the first step of the mechanism is proposed to involve a nucleophilic attack of the NiI active state, MCRred1, on Me-SCoM to form a NiIII-methyl intermediate, spectroscopic analysis and structures, overview
-
methyl-CoM + CoB = CoM-S-S-CoB + methane
show the reaction diagram
ternary complex type
Methanothermobacter thermautotrophicus Marburg
-
-
REACTION TYPE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
sulfo ethyl group transfer
-
-
-
-
PATHWAY
KEGG Link
MetaCyc Link
Metabolic pathways
-
Methane metabolism
-
methyl-coenzyme M reduction to methane
-
Microbial metabolism in diverse environments
-
SYSTEMATIC NAME
IUBMB Comments
methyl-CoM:CoB S-(2-sulfoethyl)thiotransferase
This enzyme catalyses the final step in methanogenesis, the biological production of methane. This important anaerobic process is carried out only by methanogenic archaea. The enzyme can also function in reverse, for anaerobic oxidation of methane. The enzyme requires the hydroporphinoid nickel complex coenzyme F430. Highly specific for coenzyme B with a heptanoyl chain; ethyl CoM and difluoromethyl CoM are poor substrates. The sulfide sulfur can be replaced by selenium but not by oxygen.
SYNONYMS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
2-(methylthio)ethanesulfonic acid reductase
-
-
-
-
Coenzyme-B sulfoethylthiotransferase alpha
-
-
-
-
Coenzyme-B sulfoethylthiotransferase beta
-
-
-
-
Coenzyme-B sulfoethylthiotransferase gamma
-
-
-
-
MCR
Methanococcus maripaludis DSM 2067
-
-
-
MCR
Methanosarcina mazei DSM 3318, Methanosarcina mazei DSM 3647
-
-
-
MCR
P11558 and P11560 and P11562
-
MCR
Methanothermobacter marburgensis DSM 2133, Methanothermobacter marburgensis OCM82
-
-
-
MCR
Methanothermobacter marburgensis OCM82
P11558 and P11560 and P11562
-
-
MCR
Methanothermobacter wolfeii DSM 2970
-
-
-
MCR
D1JBK2 and D1JBK3 and D1JBK4
-
MCR I alpha
-
-
-
-
MCR I beta
-
-
-
-
MCR I gamma
-
-
-
-
MCR II alpha
-
-
-
-
MCR II beta
-
-
-
-
MCR II gamma
-
-
-
-
methyl coenzyme M reductase
-
-
-
-
methyl coenzyme M reductase A
-
-
methyl coenzyme M reductase I
-
-
methyl coenzyme-M reductase
Methanogenic bacterium
-
-
methyl-coenzyme M reductase
-
-
methyl-coenzyme M reductase
-
-
methyl-coenzyme M reductase
-
-
methyl-coenzyme M reductase
Methanococcus maripaludis DSM 2067
-
-
-
methyl-coenzyme M reductase
Q49605
-
methyl-coenzyme M reductase
-
-
methyl-coenzyme M reductase
-
-
methyl-coenzyme M reductase
-
-
methyl-coenzyme M reductase
Methanosarcina mazei DSM 3318, Methanosarcina mazei DSM 3647
-
-
-
methyl-coenzyme M reductase
P11558 and P11560 and P11562
-
methyl-coenzyme M reductase
Methanothermobacter marburgensis DSM 2133, Methanothermobacter marburgensis OCM82
-
-
-
methyl-coenzyme M reductase
Methanothermobacter marburgensis OCM82
P11558 and P11560 and P11562
-
-
methyl-coenzyme M reductase
-
-
methyl-coenzyme M reductase
Methanothermobacter wolfeii DSM 2970
-
-
-
methyl-coenzyme M reductase
methanotrophic archaeon
-
-
methyl-coenzyme M reductase
D1JBK2 and D1JBK3 and D1JBK4
-
methyl-coenzyme M reductase A
-
-
methyl-coenzyme-M reductase
-
-
methyl-CoM reductase
-
-
-
-
methyl-ScoM reductase
-
-
-
-
methylcoenzyme M reductase
-
-
S-methyl-coenzyme M reductase
-
-
-
-
CAS REGISTRY NUMBER
COMMENTARY
53060-41-6
-
ORGANISM
COMMENTARY
LITERATURE
SEQUENCE CODE
SEQUENCE DB
SOURCE
M.o.H. and M.o.H.G.
-
-
Manually annotated by BRENDA team
gene mcrA; isozyme MCR I
-
-
Manually annotated by BRENDA team
Methanococcus maripaludis DSM 2067
-
-
-
Manually annotated by BRENDA team
isozyme MCR I; isozymes MCR I, gene mcrA
-
-
Manually annotated by BRENDA team
Methanogenic bacterium
from bovine rumen fluid
-
-
Manually annotated by BRENDA team
; gene mcrA
-
-
Manually annotated by BRENDA team
; formerly Methanosarcina frisia
-
-
Manually annotated by BRENDA team
Methanosarcina mazei DSM 3318
formerly Methanosarcina frisia
-
-
Manually annotated by BRENDA team
Methanosarcina mazei DSM 3647
-
-
-
Manually annotated by BRENDA team
TM-1, acetate grown
-
-
Manually annotated by BRENDA team
formerly Methanobacterium thermoautotrophicum, strain Marburg
-
-
Manually annotated by BRENDA team
i.e. Methanothermobacter thermoautotrophicum strain Marburg
-
-
Manually annotated by BRENDA team
i.e. Methanothermobacter thermoautotrophicum strain Marburg, DSM 2133; or Methanothermobacter thermoautotrophicum strain Marburg, DSM 2133
-
-
Manually annotated by BRENDA team
isozymes MCR I and MCR II; isozymes MCR I and MCR II, gene mcrA
-
-
Manually annotated by BRENDA team
strain DSM 2133, gene mcrA
-
-
Manually annotated by BRENDA team
strain DSM 2133, MCR isoenzyme I
-
-
Manually annotated by BRENDA team
subunits alpha, beta and gamma
P11558 and P11560 and P11562
UniProt
Manually annotated by BRENDA team
Methanothermobacter marburgensis DSM 2133
formerly Methanobacterium thermoautotrophicum, strain Marburg
-
-
Manually annotated by BRENDA team
Methanothermobacter marburgensis OCM82
-
-
-
Manually annotated by BRENDA team
Methanothermobacter marburgensis OCM82
subunits alpha, beta and gamma
P11558 and P11560 and P11562
UniProt
Manually annotated by BRENDA team
a hydrogenotrophic methanogen, strain DELTAH DSM 1053, genes encoded in operons mrt and mcr
-
-
Manually annotated by BRENDA team
cells preincubated with 100% H2 before desintegration, prduces two isoenzymes; strain Marburg, DSM 2133
-
-
Manually annotated by BRENDA team
produces different isoenzymes under different growth conditions; strain Marburg, DSM 2133
-
-
Manually annotated by BRENDA team
Methanothermobacter thermautotrophicus Marburg
strain Marburg, DSM 2133
-
-
Manually annotated by BRENDA team
formerly Methanobacterium wolfei
-
-
Manually annotated by BRENDA team
Methanothermobacter wolfeii DSM 2970
formerly Methanobacterium wolfei
-
-
Manually annotated by BRENDA team
methanotrophic archaeon
-
-
-
Manually annotated by BRENDA team
no activity in Methanobrevibacter ruminantium
-
-
-
Manually annotated by BRENDA team
no activity in Methanobrevibacter ruminantium M-1
-
-
-
Manually annotated by BRENDA team
subunits alpha, beta and gamma; consortia of microorganisms collected from a Black Sea mat (ANME-1)
D1JBK2 and D1JBK3 and D1JBK4
UniProt
Manually annotated by BRENDA team
the methanogenic community in hydrothermally active sediments of Guaymas Basin (Gulf of California, Mexico) is analyzed by PCR amplification, cloning, and sequencing of methyl coenzyme M reductase genes. Members of the Methanomicrobiales and Methanosarcinales dominate the mcrA clone libraries from the upper 15 cm of the sediments. Within the H2 /CO2 - and formate-utilizing family Methanomicrobiales, two mcrA and 16S rRNA lineages are closely affiliated with cultured species of the genera Methanoculleus and Methanocorpusculum. The most frequently recovered mcrA PCR amplicons within the Methanomicrobiales does not branch with any cultured genera. Within the nutritionally versatile family Methanosarcinales, one 16S rRNA amplicon and most of the mcrA PCR amplicons are affiliated with the obligately acetate utilizing species Methanosaeta concilii. The mcrA clone libraries also includes phylotypes related to the methyl-disproportionating genus Methanococcoides. Two mcrA and two 16S rRNA lineages within the Methanosarcinales are unrelated to any cultured genus
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
metabolism
-
MCR catalyzes the terminal step in the formation of biological methane from methyl-coenzyme M and coenzyme B
SUBSTRATE
PRODUCT                      
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
2-(methylthio)ethanesulfonate + N-(7-mercaptoheptanoyl)threonine 3-O-phosphate
CoM-S-S-CoB + methane
show the reaction diagram
-
i.e. CoM and CoB
-
-
?
2-(methylthio)ethanesulfonate + N-(7-mercaptoheptanoyl)threonine 3-O-phosphate
CoM-S-S-CoB + methane
show the reaction diagram
-
i.e. CoM and CoB, the enzyme exists in the the inactive Ni(II) MCRox1-silent form and the active Ni(I) MCRred1 form with transition from MCRred1 to MCRred2 forms, the protein is able to undergo a conformational change upon binding of the second substrate. Analysis of the catalytic mechanism of the reduction at the nickel center using inhibitory fluorescent trifluoromethyl thio esters of the substrate CoB for spectroscopic analysis of the structure of the enzyme-cofactor complex, derivatives synthesis, overview
-
-
?
2-(methylthio)ethansulfonate + N-(7-mercaptoheptanoyl)threonine 3-O-phosphate
CoM-S-S-CoB + methane
show the reaction diagram
-
i.e. CoM and CoB
-
-
?
CH3-S-CoM + HS-CoB
CoM-S-S-CoB + methane
show the reaction diagram
-
-
-
-
?
CH3-S-CoM + HS-CoB
CoM-S-S-CoB + methane
show the reaction diagram
D1JBK2 and D1JBK3 and D1JBK4
-
-
-
r
CH3-S-CoM + HS-CoB
CoM-S-S-CoB + methane
show the reaction diagram
-
i.e. methyl-coenezyme M + coenzyme B
-
-
?
CH3-S-CoM + HS-CoB
CoM-S-S-CoB + methane
show the reaction diagram
-
i.e. methyl-coenzyme M + coenzyme B
-
-
?
CH3-S-CoM + HS-CoB
CoM-S-S-CoB + methane
show the reaction diagram
-
key step in the convertion of C1 substrates or acetate to methane thereby providing energy for the cell
-
-
?
CH3-S-CoM + HS-CoB
CoM-S-S-CoB + methane
show the reaction diagram
-
MCR catalyzes the first proposed step in anaerobic methane oxidation and terminal step in methanogenesis by using N-7-mercaptoheptanolyl-threonine phosphate, i.e. CoB-SH. as the two-electron donor to reduce 2-(methylthiol)-ethane sulfonate, i.e. methyl-SCoM, to methane, and producing the heterodisulfide, CoBS-SCoM
-
-
?
CH3-S-CoM + HS-CoB
CoM-S-S-CoB + methane
show the reaction diagram
-
MCR catalyzes the methane-forming step in methanogenic archaea
-
-
?
CH3-S-CoM + HS-CoB
CoM-S-S-CoB + methane
show the reaction diagram
Q49605
MCR catalyzes the methane-forming step in methanogenic archaea
-
-
?
CH3-S-CoM + HS-CoB
CoM-S-S-CoB + methane
show the reaction diagram
-
catalytic cycle and proton transfer mechanism and energetics, reaction complex formations and mechanism, detailed overview
-
-
?
CH3-S-CoM + HS-CoB
CoM-S-S-CoB + methane
show the reaction diagram
-
i.e. methyl-coenezyme M + coenzyme B, selectivity of the MCR reaction toward nucleophilic attack by Ni(I)
-
-
?
CH3-S-CoM + HS-CoB
CoM-S-S-CoB + methane
show the reaction diagram
-
i.e. methyl-coenzyme M or 2-methylmercaptoethanesulfonate + coenzyme B or N-7-mercaptoheptanoylthreonine phosphate
-
-
?
CH3-S-CoM + HS-CoB
CoM-S-S-CoB + methane
show the reaction diagram
-
MCR contains a thioxo peptide bond and methylated amino acids in the active site region, the number of methylated amino acids varies between species, overview
-
-
?
CH3-S-CoM + HS-CoB
CoM-S-S-CoB + methane
show the reaction diagram
Q49605
MCR contains a thioxo peptide bond and methylated amino acids in the active site region, the number of methylated amino acids varies between species, overview
-
-
?
CH3-S-CoM + HS-CoB
CoM-S-S-CoB + methane
show the reaction diagram
-
the active enzyme is in the MCRred1c form, coordinated ligands of the two paramagnetic MCRred2 states, reduction and oxidation states and critical bond activation step, detailed overview
-
-
?
CH3-S-CoM + HS-CoB
CoM-S-S-CoB + methane
show the reaction diagram
P11558 and P11560 and P11562
HS-CoB is N-5-mercaptoheptanoylthreonine phosphate
-
-
?
CH3-S-CoM + HS-CoB
CoM-S-S-CoB + methane
show the reaction diagram
-
i.e. N-7-mercaptoheptanoylthreonine phosphate, Ni(III)-methyl is an intermediate in methane formation
-
-
?
CH3-S-CoM + HS-CoB
CoM-S-S-CoB + methane
show the reaction diagram
Methanothermobacter marburgensis OCM82
P11558 and P11560 and P11562
HS-CoB is N-5-mercaptoheptanoylthreonine phosphate
-
-
?
CH3-S-CoM + HS-CoB6
CoM-S-S-CoB6 + methane
show the reaction diagram
-
i.e. N-7-mercaptohexanoylthreonine phosphate
-
-
?
CH3-S-CoM + HS-CoB8
CoM-S-S-CoB8 + methane
show the reaction diagram
-
a two-electron transfer reaction
-
-
?
CH3-S-CoM + HS-CoB9
CoM-S-S-CoB9 + methane
show the reaction diagram
-
-
-
-
?
CH3-S-CoM + SH-CoB
CoM-S-S-CoB + methane
show the reaction diagram
Methanothermobacter marburgensis, Methanothermobacter marburgensis OCM82
-
-
-
-
?
CH3-S-CoM + SH-CoB5
CoM-S-S-CoB5 + methane
show the reaction diagram
-
-
-
-
?
CH3-S-CoM + SH-CoB5
CoM-S-S-CoB5 + methane
show the reaction diagram
P11558 and P11560 and P11562
i.e. N-5-mercaptopentanoylthreonine phosphate
-
-
?
CH3-S-CoM + SH-CoB5
CoM-S-S-CoB5 + methane
show the reaction diagram
Methanothermobacter marburgensis OCM82
-
-
-
-
?
CH3-S-CoM + SH-CoB5
CoM-S-S-CoB5 + methane
show the reaction diagram
Methanothermobacter marburgensis OCM82
P11558 and P11560 and P11562
i.e. N-5-mercaptopentanoylthreonine phosphate
-
-
?
CH3-S-CoM + SH-CoB6
CoM-S-S-CoB6 + methane
show the reaction diagram
P11558 and P11560 and P11562
i.e. N-6-mercaptohexanoylthreonine phosphate, slow substrate
-
-
?
CH3-S-CoM + SH-CoB6
CoM-S-S-CoB6 + methane
show the reaction diagram
Methanothermobacter marburgensis, Methanothermobacter marburgensis OCM82
-
methanogenesis occurs 1000fold more slowly than with SH-CoB
-
-
?
CH3-S-CoM + SH-CoB6
CoM-S-S-CoB6 + methane
show the reaction diagram
Methanothermobacter marburgensis OCM82
P11558 and P11560 and P11562
i.e. N-6-mercaptohexanoylthreonine phosphate, slow substrate
-
-
?
CH3-S-CoM + SH-CoB8
CoM-S-S-CoB8 + methane
show the reaction diagram
Methanothermobacter marburgensis, Methanothermobacter marburgensis OCM82
P11558 and P11560 and P11562
i.e. N-8-mercaptooctanoylthreonine phosphate
-
-
?
CH3-S-CoM + SH-CoB9
CoM-S-S-CoB9 + methane
show the reaction diagram
Methanothermobacter marburgensis, Methanothermobacter marburgensis OCM82
P11558 and P11560 and P11562
i.e. N-9-mercaptononanoylthreonine phosphate
-
-
?
CH3-S-CoM3 + HS-CoB8
CoM3-S-S-CoB8 + methane
show the reaction diagram
-
-
-
-
?
ethyl coenzyme M + coenzyme B
ethane + CoM-S-S-CoB
show the reaction diagram
-
1% of the activity with methyl coenzyme M
-
-
?
methyl coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
-
-
-
?
methyl coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
-
-
-
-
?
methyl coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
-
methanogenesis
-
?
methyl coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
-
strictly anaerobic conditions
-
?
methyl coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
-
reductive methylation
-
?
methyl coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
-
rate limiting step in methanogenesis
-
?
methyl coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
-
final step in methane formation in all methanogenic archaea
-
?
methyl coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
-
final step in methane formation in all methanogenic archaea
-
?
methyl coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
-
final step in methane formation in all methanogenic archaea
-
?
methyl coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
-
final step in methane formation in all methanogenic archaea
-
?
methyl coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
-
energy metabolism of all methanogenic archaea
-
?
methyl coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
-
energy metabolism of all methanogenic archaea
-
?
methyl coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
-
key enzyme in methane formation by methanogenic Archaea
-
?
methyl coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
-
key enzyme in methane formation by methanogenic Archaea
-
?
methyl coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
-
the enzyme catalyzes the final step in methanogenesis
-
-
?
methyl coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
-
discussion of mechanism
-
-
?
methyl coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
-
the enzyme is essential in Methanosarcina acetivorans C2A
-
-
?
methyl coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
Methanothermobacter thermautotrophicus Marburg
-
methanogenesis
-
?
methyl coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
Methanothermobacter thermautotrophicus Marburg
-
rate limiting step in methanogenesis, energy metabolism of all methanogenic archaea
-
?
methyl coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
Methanothermobacter thermautotrophicus Marburg
-
final step in methane formation in all methanogenic archaea
-
?
methyl coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
Methanothermobacter thermautotrophicus Marburg
-
energy metabolism of all methanogenic archaea
-
?
methyl coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
Methanothermobacter thermautotrophicus Marburg
-
final step in methane formation in all methanogenic archaea
-
?
methyl coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
Methanothermobacter thermautotrophicus Marburg
-
final step in methane formation in all methanogenic archaea
-
?
methyl coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
Methanothermobacter thermautotrophicus Marburg
-
final step in methane formation in all methanogenic archaea
-
?
methyl-coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
-
-
-
?
methyl-coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
-
-
-
?
methyl-coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
-
-
-
?
methyl-coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
-
-
-
?
methyl-coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
-
-
-
?
methyl-coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
-
-
-
-
?
methyl-coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
-
methane formation only under H2 not under N2 atmosphere. ATP and FAD also required. Ti(III) citrate can be used as electron source under N2 atmosphere. Dithiothreitol and CN-B12 under H2 can also be used for methanogenesis
-
?
methyl-coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
-
in presence of H2 as source of electrons, requires Mg2+ and catalytic ATP
-
-
methyl-coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
-
specific for L-enantiomer of coenzyme B
-
?
methyl-coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
-
spin density and coenzyme M coordination geometry of the ox1 form of methyl-coenzyme M reductase
-
-
?
methyl-coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
Methanothermobacter thermautotrophicus Marburg
-
-
-
?
methyl-coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
Methanothermobacter thermautotrophicus Marburg
-
-
-
?
methyl-coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
Methanothermobacter thermautotrophicus Marburg
-
-
-
?
methyl-coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
Methanothermobacter thermautotrophicus Marburg
-
specific for L-enantiomer of coenzyme B
-
?
methyl-coenzyme M + N-(7-mercaptoheptanoyl)threonine 3-O-phosphate (coenzyme B)
methane + CoM-S-S-CoB
show the reaction diagram
-
i.e. methyl-SCoM
a the mixed disulfide
-
?
methyl-coenzyme M + N-(7-mercaptoheptanoyl)threonine 3-O-phosphate (coenzyme B)
methane + CoM-S-S-CoB
show the reaction diagram
Q49605
i.e. methyl-SCoM
a the mixed disulfide
-
?
methyl-coenzyme M + N-(7-mercaptoheptanoyl)threonine 3-O-phosphate (coenzyme B)
methane + CoM-S-S-CoB
show the reaction diagram
-
i.e. methyl-SCoM
a the mixed disulfide
-
?
methyl-coenzyme M + N-(7-mercaptoheptanoyl)threonine 3-O-phosphate (coenzyme B)
methane + CoM-S-S-CoB
show the reaction diagram
-
i.e. methyl-SCoM
a the mixed disulfide
-
?
methyl-coenzyme M + N-(7-mercaptoheptanoyl)threonine 3-O-phosphate (coenzyme B)
methane + CoM-S-S-CoB
show the reaction diagram
-
the enzyme catalyzes the methane forming step in methane biosynthesis by methanogenic archaea
a the mixed disulfide
-
?
methyl-coenzyme M + N-(7-mercaptoheptanoyl)threonine 3-O-phosphate (coenzyme B)
methane + CoM-S-S-CoB
show the reaction diagram
Q49605
the enzyme catalyzes the methane forming step in methane biosynthesis by methanogenic archaea
a the mixed disulfide
-
?
methyl-coenzyme M + N-(7-mercaptoheptanoyl)threonine 3-O-phosphate (coenzyme B)
methane + CoM-S-S-CoB
show the reaction diagram
-
the enzyme catalyzes the methane forming step in methane biosynthesis by methanogenic archaea
a the mixed disulfide
-
?
methyl-coenzyme M + N-(7-mercaptoheptanoyl)threonine 3-O-phosphate (coenzyme B)
methane + CoB-S-S-CoM
show the reaction diagram
-
i.e. methyl-SCoM
a the mixed disulfide
-
?
methylmercaptopropionate + HS-CoB
?
show the reaction diagram
-
is about 110fold less reactive than the natural substrate methyl-SCoM
-
-
?
additional information
?
-
-
dual requirement for electron donors
-
-
-
additional information
?
-
-
ability of the hydrogenase to reduce a number of artificial and naturally occurring electron acceptors is examined
-
-
-
additional information
?
-
-
several bifunctional substrates tested, substrates contain both an aliphatic thiol and a methyl thioether function
-
-
-
additional information
?
-
-
MCR also appears to initiate anaerobic methane oxidation, the reverse methanogenesis
-
-
-
additional information
?
-
-
the enzyme catalyzes the final step in methane biosynthesis by methanogenic archaea
-
-
-
additional information
?
-
-
the enzyme catalyzes the formation of methane from methyl-coenzyme M and coenzyme B in methanogenic archaea
-
-
-
additional information
?
-
-
conversion of MCRox1 toMCRred1 by Ti(III)citrate, bromopropanesulfonate is an alternative substrate of MCR in an ionic reaction that is coenzyme B-independent and leads to debromination of bromopropanesulfonate and formation of a distinct state with an EPR signal that is assigned to a Ni(III)-propylsulfonate species, propanesulfonate formation also occurs in steady-state reactions in the presence of Ti(III) citrate
-
-
-
additional information
?
-
-
the enzyme performs reactions with brominated acid, 4-bromobutyric acid to 16-bromohexadecanoic acid, analogously to the reaction of MCRred1, the active Ni(I)-F430 containing enzyme form, to generate a methyl-Ni(III) intermediate in methane formation with the natural substrate, methyl-SCoM, substrate specificity and acivities, overview, MCR catalyzes the final step in the biological synthesis of methane. Using coenzyme B, CoBSH, as the two-electron donor, MCR reduces methyl-coenzyme M, methyl-SCoM, to methane and the mixed disulfide, CoB-S-S-CoM. MCR contains coenzyme F430, an essential redox-active nickel tetrahydrocorphin, at its active site. The active form of MCR, MCRred1, contains Ni(I)-F430
-
-
-
additional information
?
-
-
MCR reduction/oxidation state, electron paramagnetic resonance status analysis, detailed overview
-
-
-
additional information
?
-
-
MCR substrate specificity and reactivation activity of different thiols, e.g. 2-mercaptoethanol, DTT, Na2S, and cysteine, kinetics, overview
-
-
-
additional information
?
-
-
three general mechanisms for the catalytic production of methane by MCR: (1) the Ni-Me/Ragsdale pathway, (2) the Ni-Me/Thauer pathway, (3) the methyl radical pathway. Density functional calculations and electronic-structure calculations and analysis by computational methods, homolytic Ni-S/Ni-C bonds energies, overview
-
-
-
additional information
?
-
-
MCR is the key enzyme in methane formation by methanogenic Archaea. It converts the thioether methyl-coenzyme M and the thiol coenzyme B into methane and the heterodisulfide of coenzyme M and coenzyme B
-
-
-
additional information
?
-
-
The active form of the enzyme, referred to as MCRred1, features the tetracoordinate dx2y2 nickel(I) state of the cofactor, simulations of enzyme nickel intermediate states in synthetic complexes, mechanism and modeling, pyriporphyrin-based model and isoporphyrin-based model, overview
-
-
-
additional information
?
-
Methanothermobacter marburgensis, Methanothermobacter marburgensis OCM82
-
no activity with SH-CoB8 or SH-CoB9
-
-
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
2-(methylthio)ethanesulfonate + N-(7-mercaptoheptanoyl)threonine 3-O-phosphate
CoM-S-S-CoB + methane
show the reaction diagram
-
i.e. CoM and CoB
-
-
?
2-(methylthio)ethansulfonate + N-(7-mercaptoheptanoyl)threonine 3-O-phosphate
CoM-S-S-CoB + methane
show the reaction diagram
-
i.e. CoM and CoB
-
-
?
CH3-S-CoM + HS-CoB
CoM-S-S-CoB + methane
show the reaction diagram
-
-
-
-
?
CH3-S-CoM + HS-CoB
CoM-S-S-CoB + methane
show the reaction diagram
D1JBK2 and D1JBK3 and D1JBK4
-
-
-
r
CH3-S-CoM + HS-CoB
CoM-S-S-CoB + methane
show the reaction diagram
-
i.e. methyl-coenezyme M + coenzyme B
-
-
?
CH3-S-CoM + HS-CoB
CoM-S-S-CoB + methane
show the reaction diagram
-
i.e. methyl-coenzyme M + coenzyme B
-
-
?
CH3-S-CoM + HS-CoB
CoM-S-S-CoB + methane
show the reaction diagram
-
key step in the convertion of C1 substrates or acetate to methane thereby providing energy for the cell
-
-
?
CH3-S-CoM + HS-CoB
CoM-S-S-CoB + methane
show the reaction diagram
-
MCR catalyzes the first proposed step in anaerobic methane oxidation and terminal step in methanogenesis by using N-7-mercaptoheptanolyl-threonine phosphate, i.e. CoB-SH. as the two-electron donor to reduce 2-(methylthiol)-ethane sulfonate, i.e. methyl-SCoM, to methane, and producing the heterodisulfide, CoBS-SCoM
-
-
?
CH3-S-CoM + HS-CoB
CoM-S-S-CoB + methane
show the reaction diagram
-
MCR catalyzes the methane-forming step in methanogenic archaea
-
-
?
CH3-S-CoM + HS-CoB
CoM-S-S-CoB + methane
show the reaction diagram
Q49605
MCR catalyzes the methane-forming step in methanogenic archaea
-
-
?
CH3-S-CoM + HS-CoB
CoM-S-S-CoB + methane
show the reaction diagram
P11558 and P11560 and P11562
HS-CoB is N-5-mercaptoheptanoylthreonine phosphate
-
-
?
CH3-S-CoM + HS-CoB
CoM-S-S-CoB + methane
show the reaction diagram
-
i.e. N-7-mercaptoheptanoylthreonine phosphate, Ni(III)-methyl is an intermediate in methane formation
-
-
?
CH3-S-CoM + HS-CoB
CoM-S-S-CoB + methane
show the reaction diagram
Methanothermobacter marburgensis OCM82
P11558 and P11560 and P11562
HS-CoB is N-5-mercaptoheptanoylthreonine phosphate
-
-
?
CH3-S-CoM + SH-CoB
CoM-S-S-CoB + methane
show the reaction diagram
Methanothermobacter marburgensis, Methanothermobacter marburgensis OCM82
-
-
-
-
?
methyl coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
-
-
-
?
methyl coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
-
methanogenesis
-
?
methyl coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
-
strictly anaerobic conditions
-
?
methyl coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
-
reductive methylation
-
?
methyl coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
-
rate limiting step in methanogenesis
-
?
methyl coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
-
final step in methane formation in all methanogenic archaea
-
?
methyl coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
-
final step in methane formation in all methanogenic archaea
-
?
methyl coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
-
final step in methane formation in all methanogenic archaea
-
?
methyl coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
-
final step in methane formation in all methanogenic archaea
-
?
methyl coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
-
energy metabolism of all methanogenic archaea
-
?
methyl coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
-
energy metabolism of all methanogenic archaea
-
?
methyl coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
-
key enzyme in methane formation by methanogenic Archaea
-
?
methyl coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
-
key enzyme in methane formation by methanogenic Archaea
-
?
methyl coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
-
the enzyme catalyzes the final step in methanogenesis
-
-
?
methyl coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
Methanothermobacter thermautotrophicus Marburg
-
methanogenesis
-
?
methyl coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
Methanothermobacter thermautotrophicus Marburg
-
rate limiting step in methanogenesis, energy metabolism of all methanogenic archaea
-
?
methyl coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
Methanothermobacter thermautotrophicus Marburg
-
final step in methane formation in all methanogenic archaea
-
?
methyl coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
Methanothermobacter thermautotrophicus Marburg
-
energy metabolism of all methanogenic archaea
-
?
methyl coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
Methanothermobacter thermautotrophicus Marburg
-
final step in methane formation in all methanogenic archaea
-
?
methyl coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
Methanothermobacter thermautotrophicus Marburg
-
final step in methane formation in all methanogenic archaea
-
?
methyl coenzyme M + coenzyme B
methane + CoM-S-S-CoB
show the reaction diagram
Methanothermobacter thermautotrophicus Marburg
-
final step in methane formation in all methanogenic archaea
-
?
methyl-coenzyme M + N-(7-mercaptoheptanoyl)threonine 3-O-phosphate (coenzyme B)
methane + CoM-S-S-CoB
show the reaction diagram
-
the enzyme catalyzes the methane forming step in methane biosynthesis by methanogenic archaea
a the mixed disulfide
-
?
methyl-coenzyme M + N-(7-mercaptoheptanoyl)threonine 3-O-phosphate (coenzyme B)
methane + CoM-S-S-CoB
show the reaction diagram
Q49605
the enzyme catalyzes the methane forming step in methane biosynthesis by methanogenic archaea
a the mixed disulfide
-
?
methyl-coenzyme M + N-(7-mercaptoheptanoyl)threonine 3-O-phosphate (coenzyme B)
methane + CoM-S-S-CoB
show the reaction diagram
-
the enzyme catalyzes the methane forming step in methane biosynthesis by methanogenic archaea
a the mixed disulfide
-
?
methyl-coenzyme M + N-(7-mercaptoheptanoyl)threonine 3-O-phosphate (coenzyme B)
methane + CoB-S-S-CoM
show the reaction diagram
-
i.e. methyl-SCoM
a the mixed disulfide
-
?
additional information
?
-
-
MCR also appears to initiate anaerobic methane oxidation, the reverse methanogenesis
-
-
-
additional information
?
-
-
the enzyme catalyzes the final step in methane biosynthesis by methanogenic archaea
-
-
-
additional information
?
-
-
the enzyme catalyzes the formation of methane from methyl-coenzyme M and coenzyme B in methanogenic archaea
-
-
-
additional information
?
-
-
MCR catalyzes the final step in the biological synthesis of methane. Using coenzyme B, CoBSH, as the two-electron donor, MCR reduces methyl-coenzyme M, methyl-SCoM, to methane and the mixed disulfide, CoB-S-S-CoM. MCR contains coenzyme F430, an essential redox-active nickel tetrahydrocorphin, at its active site. The active form of MCR, MCRred1, contains Ni(I)-F430
-
-
-
COFACTOR
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
coenzyme F430
-
a redox-active nickel tetrahydrocorphin bound at the active site, contains low-spin Ni(II), determination of the cofactor reduction site at the exocyclic ketone group by NMR study, mass spectrometry, and QM/MM computations, conversion of F430 to F330 reduces the hydrocorphin ring but not the metal, reduction of F430 with Ti(III) citrate to generate F380, corresponding to the active MCRred1 state, reduces the Ni(II) to Ni(I) but does not reduce the tetrapyrrole ring system, overview
coenzyme F430
-
an essential redox-active nickel tetrahydrocorphin, bound at the active site, the active form of MCR, MCRred1, contains Ni(I)-F430
coenzyme F430
-
2 mol of the nickel tetrapyrrole coenzyme F430, tightly bound, per enzyme hexamer, nickel is in the Ni(I) state in the active enzyme
coenzyme F430
Q49605
2 mol of the nickel tetrapyrrole coenzyme F430, tightly bound, per enzyme hexamer, nickel is in the Ni(I) state in the active enzyme
coenzyme F430
-
2 mol of the nickel tetrapyrrole coenzyme F430, tightly bound, per enzyme hexamer, nickel is in the Ni(I) state in the active enzyme
coenzyme F430
-
structure analysis using crystal structure PDB code 1MRO, and conformational changes during catalysis, free cofactor F430 is thermally unstable, it first epimerizes to 13-epi F430 and then in a second epimerization to 12,13-diepi F430, nonplanar deformations, overview
coenzyme F430
-
the nickel-containing tetrapyrrole is essential for the reaction, and is bound to the active site
coenzyme F430
-
each active site has the nickel porphyrinoid F430 as a prosthetic group, in the active state, F430 contains the transition metal in the Ni(I) oxidation state
F-430
-
2 mol nickel porphinoid/mol enzyme, prosthetic group
F-430
-
2 mol coenzyme F-430/mol enzyme; 2 mol nickel porphinoid/mol enzyme, prosthetic group; nickel porphinoid coenzyme M
F-430
-
1 mol coenzyme F-430/mol enzyme
F-430
-
contains two tightly bound molecules of coenzyme F-430
F-430
-
2 mol coenzyme F-430/mol enzyme; 2 mol nickel porphinoid/mol enzyme, prosthetic group
F-430
-
2 mol coenzyme F-430/mol enzyme; the extracted form in aqueous solution and protein-bound form are studied by using low-temperature magnetic-circular-dichroism spectroscopy. Tightly bound nickel tetrapyrrole cofactor
F-430
-
1.6.1.8 mol F-430/mol enzyme; nickel porphinoid coenzyme M
F-430
-
2 mol coenzyme F-430/mol enzyme
F-430
-
cofactor F430 undergoes a significant conformational change when it binds to the enzyme. Conversion from MCRox1 to MCRred1 involves major conformational rearrangements, which are propose to be due to a 2-electron reversible reduction of the hydrocorphin ring of F430
F-430
-
tightly bound nickel porphinol. The enzyme is active only when its prosthetic group in in the NI(I)-reduced state
F-430
-
nickel-containing porphinoid cofactor F-430. Comparison of the free cofactor in the (+)1, (+)2 and (+)3 oxidation states with the cofactor bound to methyl-coenzyme M reductase in the silent, red and ox forms
F-430
-
prosthetic group has to be in the Ni(I) oxidation state for the enzyme to be active
F-430
-
with Ni(I) oxidation state, selectivity of the MCR reaction toward nucleophilic attack by Ni(I)
F-430
Q49605
with Ni(I) oxidation state
F-430
-
with Ni(I) oxidation state
F-430
-
the enzyme has two structurally interlinked active sites embedded in an alpha2beta2gamma2 subunit structure. Each active site has the nickel porphyrinoid F430 as a prosthetic group. In the active state, F430 contains the transition metal in the Ni(I) oxidation state
F-430
-
the active site of MCR includes a noncovalently bound Ni tetrapyrrolic coenzyme F430, which is in the Ni(I) state in the active enzyme, MCRred1
F-430
-
active in Ni(I) oxidation state, inactive in Ni(II) state, binding structure and oxidation states, hyperfine interactions of protons, detailed overview
F-430
-
with Ni(I) oxidation state
F-430
-
binding structure, and different oxidation states F430 (Ni(I)/Ni(II)/Ni(III)), Ni(I) is the active state, overview
F-430
-
nickel corphin coenzyme F430, structure of the free coenzyme, overview
F-430
-
the Ni-F430 cofactor is bound to the active site and exists in two oxidation states
F-430
-
an active site Ni cofactor
F-430
-
a nickel hydrocorphin coenzyme F430, the Ni(I) MCRred1 form and the inactive Ni(II) MCRox1-silent form, no formation of an MCRis dependent methyl-Ni(F430) species, analysis of the catalytic mechanism of the reduction at the nickel center using inhibitory fluorescent trifluoromethyl thio esters of the substrate CoB for spectroscopic analysis of the structure of the enzyme-cofactor complex, derivatives synthesis, overview
F-430
-
the active site of the enzyme contains an essential redox-active nickel tetrapyrrole cofactor, coenzyme F430, which is active in the Ni(I) state
F-430
P11558 and P11560 and P11562
the enzyme contains the highly reduced nickel-tetrapyrrole coenzyme F430
F-430
D1JBK2 and D1JBK3 and D1JBK4
the enzyme contains the Ni porphinoid F430 as prosthetic group
additional information
-
enzyme consists of 2 symmetry-equivalent active sites containing one molecule of the hydroporphinoid nickel complex coenzyme F-430, enzyme is active only if the metal center of coenzyme F-430 is in the nickel(I) form
-
additional information
-
2 molecules of the nickel porphinoid coenzyme F-430 are embedded between the subunits, forming 2 structurally identical active sites
-
METALS and IONS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
Ni
-
the niuckel porphinoid F-430 must be in the Ni(I) oxidation state for the enzyme to be active. The active enzyme exhibits an axial Ni(I)-based electron paramagnetic resonance signal and a UV-vis spectrum with an absorption maximum at 385 nM. This state is called the MCR-red1 state. When the temperature is lowered below 20C the perecentage of MCR in the red2 state decreases and that in the red1 state increases. These changes with temperature are fully reversible. At most 50% of the enzyme is converted to the MCR-red2 state under all experimental conditions
Ni
-
enzyme contains the tightly-bound nickel porphinol F-430 as prosthetic group
Ni
-
the active purified enzyme exhibits the axial EPR signal MCR-red1 and in the presence of coenzyme M and coenzyme B the rhombic signal MCR-red2, both derived from Ni(I). Two other EPR-detectable states of the enzyme, observed in vivo and in vitro designated MCR-ox1 and MCR-ox2 have quite different nickel EPR signals and are inactive. In vitro the MCR-red2 state is converted into the MCR-ox1 state by the addition of polysulfide and into a light-sensitive MCR-ox2 state by the addition of sulfite. In the presence of O2 the MCR-red2 state is converted into a novel third state designated MCR-ox3 and exhibits two EPR signals similar but not identical to MCR-ox1 and MCR-ox2
Ni
-
contains the nickel-containing porphinoid cofactor F-430
Ni(2+)
-
2 mol Ni/mol enzyme
Ni(2+)
-
involved in catalytic mechanism
Ni(2+)
-
nickel-porphinoid-containing protein
Ni2+
-
high-spin paramagnetic nickel(II) state for both, extracted and protein-bound form
Ni2+
-
in the coenzyme F430, a redox-active nickel tetrahydrocorphin bound at the active site
Ni2+
-
each active site has the nickel porphyrinoid F430 as a prosthetic group, in the active state, F430 contains the transition metal in the Ni(I) oxidation state
Ni2+
-
in the Ni-F430 cofactor, which is bound to the active site and exists in two oxidation states
Ni2+
-
nickel center in the ox1 form of methylcoenzyme M reductase, MCRox1
Ni3+
-
the enzyme contains nickel, Ni(III)-methyl is an intermediate in methane formation
Nickel
-
the active site of the enzyme contains an essential redox-active nickel tetrapyrrole cofactor, coenzyme F430, which is active in the Ni(I) state
Nickel
P11558 and P11560 and P11562
the enzyme contains nickel
INHIBITORS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
(+)-(2S,3R)-N-[7-(methylthio)heptanoyl]-O-phospho-L-threonine
-
CoB substrate thioester derivative, synthesis, spectral analysis and binding structure, overview
(+)-(2S,3R)-N-[7-(trifluoromethylthio)heptanoyl]-O-phospho-L-threonine
-
fluorescent CoB substrate thioester derivative, synthesis, spectral analysis and binding structure, overview
1-butanesulfonate
-
-
-
1-propanesulfonate
-
-
-
2-azidoethanesulfonate
-
competitive, reversible
2-bromoethanesulfonate
-
competitive with methyl coenzyme M
2-bromoethanesulfonate
-
reversible
2-bromoethanesulfonate
-
-
3-bromopropane sulfonate
-
-
3-bromopropane sulfonate
-
BPS, forms an alkyl-Ni(III) species with MCRred1is that elicits the MCRPS EPR signal; irreversible inhibition
3-bromopropanesulfonate
-
most potent inhibitor, competitive with respect to methyl-coenzyme M
3-bromopropanesulfonate
-
complete inhibition at 0.02 mM; most potent inhibitor, competitive with respect to methyl-coenzyme M
3-bromopropanesulfonate
-
competitive, reversible, 50% inhibition at 0.00007 mM
3-bromopropanesulfonate
-
irreversible, strong inibitior and competitive substrate
3-Bromopropionate
-
irreversible
3-chloropropanesulfonyl chloride
-
-
3-iodopropane sulfonate
-
-
3-mercapto-1-propanesulfonate
-
-
-
4-bromobutanesulfonate
-
-
4-bromobutyrate sulfonate
-
when reacted with 4-bromobutyrate, MCRred1 forms the alkyl-Ni(III) MCRXA state and then self-reactivation to regenerate the Ni(I) MCRred1 state and a bromocarboxy ester
-
7-bromoheptanoylthreonine phosphate
-
substrate analogue of coenzyme B in which the thiol group is substituted by bromine, potent inhibitor, competitive with respect to methyl-coenzyme M and B
allyl-coenzyme M
-
reversible
-
bromoethane sulfonate
D1JBK2 and D1JBK3 and D1JBK4
-
-
bromopropanesulfonate
-
BPS, a potent inhibitor and reversible redox inactivator that reacts with MCRred1 to form an EPR-active state called MCRPS, which is an alkyl-nickel species. Treatment of MCRPS with free thiol containing compounds leads to reconvertion to the active MCRred1 state
CO
-
little blocking effect on the hydrogenase function of component A
CoB5SH
P11558 and P11560 and P11562
-
-
CoB6SH
P11558 and P11560 and P11562
-
-
Coenzyme M
-
a competitive inhibitor
CoM-S-S-CoB
-
50% inhibition at 0.6 mM
cyano-coenzyme M
-
irreversible
-
ethanol
-
concentrations above 0.005 ml/0.2 ml assay
N-6-mercaptohexanoylthreonine phosphate
-
competitive with coenzyme B
N-7(methylthio)-heptanoylthreonine phosphate
-
competitive with coenzyme B
N-8-mercaptooctanoylthreonine phosphate
-
competitive with coenzyme B
O2
-
total loss of activity of hydrogenase activity of component A
propyl-coenzyme M
-
reversible
-
seleno-coenzyme M
-
irreversible
-
trifluoromethyl coenzyme M
-
irreversible
-
HS-CoM
-
the unmethylated coenzyme M is a reversible competitive inhibitor
additional information
-
inhibitors are substrate analogues
-
additional information
-
inhibition mechanism, brominated carboxylic acids, with carbon chain lengths of 4-16, all give rise to an alkyl-Ni intermediate with an EPR signal similar to that of the MCRPS species, brominated carboxylic acids mimic the interactions of BPS and methyl-SCoM at the MCR active site, overview
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
ADP
-
in absence of reducing agents
arsenate
-
in absence of reducing agents
ATP
-
stimulates the reactivation
ATP
-
absolute requirement, activation of the methylreductase system and not at the catalytic level
coenzyme F-420
-
enzyme system ist stimulated
EDTA
-
in absence of reducing agents
phosphate
-
in absence of reducing agents
reduced ferredoxin
-
reactivation after purification
sulfate
-
in absence of reducing agents
Ti(III) citrate
-
activation of the oxidized state of enzyme
Ti(III) citrate
-
conversion from the ox1 to the red1 state, maximal activation after 30 min, 20 mM Ti(III) at pH 9.0 and room temperature or pH 7.0 and 60C, optimal pH for activation of isoenzyme II is 10.0, enzyme is activated when the enzyme bound coenzyme F-430 is reduced to the Ni(I) state
Ti(III) citrate
-
reactivation after isolation
Ti(III) citrate
-
prevents enzyme inactivation by oxygen
Ti(III) citrate
-
artificial electron donor, if used as electron source component A1 is no longer required
Ti(III) citrate
-
nickel tetrahydrocorphin
vitamin B12
-
enzyme system ist stimulated
H2
-
suggested to be involved in the activation of the methylreductase, preincubation
additional information
-
activated enzyme immediately loses 97% of activity when assayed in the absence of Ti(III) citrate, dithiothreitol and cobalamin, that shows the requirement of these reductants for maximal activity
-
additional information
-
maximal stimulation with 0.3 mM aquocobalamin and 0.15 mM Ti(III) citrate
-
additional information
-
omission of the component A, B or C, as well as methyl coenzyme M, H2, Mg2+ or ATP leads to complete loss of activity and methane biosynthesis
-
KM VALUE [mM]
KM VALUE [mM] Maximum
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.03
-
CH3-S-CoM
-
with SH-CoB6 as cosubstrate, pH not specified in the publication, at 25C
-
0.28
-
CH3-S-CoM
-
with SH-CoB5 as cosubstrate, pH not specified in the publication, at 25C
-
3.5
-
CH3-S-CoM
-
pH 10.0, 25C
-
62
-
CH3-S-CoM3
-
pH 10.0, 25C
0.023
-
coenzyme B
-
-
0.059
-
coenzyme B
-
-
0.1
0.3
coenzyme B
-
isoenzyme I
0.4
0.6
coenzyme B
-
isoenzyme II
0.016
-
HS-CoB8
-
pH 10.0, 25C
0.46
-
HS-CoB9
-
pH 10.0, 25C
0.0033
-
methyl coenzyme M
-
-
0.6
0.8
methyl coenzyme M
-
isoenzyme I
1.3
1.5
methyl coenzyme M
-
isoenzyme II
0.34
-
SH-CoB5
-
pH not specified in the publication, at 25C
-
0.08
-
SH-CoB6
-
pH not specified in the publication, at 25C
-
2
-
methyl-coenzyme M
-
-
additional information
-
additional information
-
steady-state kinetics of MCRred1 with brominated acids, overview; transient kinetics study, overview
-
additional information
-
additional information
-
steady-state and rapid kinetics, MCRred1-catalyzed cleavage of the C-S bond of methyl-SCoM requires the other substrate, HSCoB, even under single turnover conditions
-
additional information
-
additional information
-
stopped flow kinetics, overview
-
Ki VALUE [mM]
Ki VALUE [mM] Maximum
INHIBITOR
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.001
-
2-azidoethanesulfonate
-
-
0.004
-
2-bromoethanesulfonate
-
-
0.1
-
2-bromoethanesulfonate
-
-
0.04
-
3-azidopropanesulfonate
-
-
0.00005
-
3-bromopropane sulfonate
-
-
0.00005
-
3-bromopropanesulfonate
-
-
0.0001
-
3-bromopropanesulfonate
-
for both isoenzymes
0.05
-
3-fluoropropanesulfonate
-
below
4
-
3-hydroxypropanesulfonate
-
-
0.001
-
3-iodopropanesulfonate
-
below
0.006
-
4-bromobutanesulfonate
-
-
0.005
-
7-bromoheptanoylthreonine phosphate
-
-
2
-
allyl-coenzyme M
-
-
-
0.25
-
chloromethanesulfonate
-
-
0.0001
-
CoB6SH
P11558 and P11560 and P11562
pH and temperature not specified in the publication
-
0.0001
-
N-6-mercaptohexanoylthreonine phosphate
-
competitive with coenzyme B
5
-
propyl-coenzyme M
-
-
-
SPECIFIC ACTIVITY [µmol/min/mg]
SPECIFIC ACTIVITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
0.5
2
-
in presence of dithiothreitol and of reduced corrinoids or Ti(III) citrate
0.72
-
-
CO2-oxidized cells
1
2
-
in presence of 15 mM dithiothreitol and 0.3 mM aquocobalamin or 0.15 mM Ti(III) citrate
2.5
-
-
purified, addition of Ti(III) citrate, dithiothreitol and cobalamin
3
5
-
cell extract; drops to 1% after cell breakage
3
-
-
extract of H2-reduced cells
20.1
-
-
purification from H2-reduced cells
additional information
-
-
activity measured at 92% N2, 8% H2
additional information
-
-
the active state of the enzyme is the reduced state
additional information
-
-
enzyme shows only little activity in ox1 state, highly active in red1 or red2 form
additional information
-
-
purified protein shows less than 1% of the activity predictable from rates of formation of methane in vivo
pH OPTIMUM
pH MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
7
-
-
60 nmol of methane are formed per minute per mg protein
7
-
-
for hydrogenase of component A
additional information
-
-
pH 10.0 is optimal for activation of MCRox1 to MCRred1 with Ti(III) citrate
TEMPERATURE OPTIMUM
TEMPERATURE OPTIMUM MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
37
-
-
assay at
60
-
-
assay; for hydrogenase of component A
TEMPERATURE RANGE
TEMPERATURE MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
SOURCE TISSUE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
SOURCE
additional information
-
growth temperature 65C
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
Methanococcus maripaludis DSM 2067, Methanosarcina mazei DSM 3318, Methanosarcina mazei DSM 3647, Methanothermobacter marburgensis DSM 2133
-
-
-
Manually annotated by BRENDA team
Methanothermobacter thermautotrophicus Marburg
-
; soluble
-
Manually annotated by BRENDA team
Methanothermobacter wolfeii DSM 2970
-
-
-
Manually annotated by BRENDA team
-
facultative membrane association under growth limiting conditions on nickel-depleted media
-
Manually annotated by BRENDA team
Methanococcus maripaludis DSM 2067, Methanosarcina mazei DSM 3318, Methanosarcina mazei DSM 3647, Methanothermobacter marburgensis DSM 2133, Methanothermobacter wolfeii DSM 2970
-
facultative membrane association under growth limiting conditions on nickel-depleted media
-
-
Manually annotated by BRENDA team
-
on the inner surface of the cytoplasmic membrane
Manually annotated by BRENDA team
Methanothermobacter thermautotrophicus Marburg
-
on the inner surface of the cytoplasmic membrane; on the inner surface of the cytoplasmic membrane
-
Manually annotated by BRENDA team
additional information
-
no activity found in membrane fraction
-
Manually annotated by BRENDA team
PDB
SCOP
CATH
ORGANISM
Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938)
Methanosarcina barkeri (strain Fusaro / DSM 804)
MOLECULAR WEIGHT
MOLECULAR WEIGHT MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
132000
-
-
nondenaturing slab gel electrophoresis
141000
-
-
gel filtration
280000
-
-
gel filtration
280000
-
D1JBK2 and D1JBK3 and D1JBK4
gel filtration
300000
-
Q49605
-
additional information
-
-
operon contains two additional polypeptides of 15752 and 21210 Da with unknown functions
SUBUNITS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
heterohexamer
-
2 * 65000 + 2 * 49000 + 2 * 38000, SDS-PAGE
heterohexamer
D1JBK2 and D1JBK3 and D1JBK4
-
heterohexamer
Methanosarcina mazei DSM 3318, Methanosarcina mazei DSM 3647
-
2 * 65000 + 2 * 49000 + 2 * 38000, SDS-PAGE
-
heterotrimer
Methanococcus maripaludis DSM 2067, Methanosarcina mazei DSM 3318, Methanosarcina mazei DSM 3647, Methanothermobacter marburgensis DSM 2133, Methanothermobacter wolfeii DSM 2970
-
1 * 65000 + 1 * 49000 + 1 * 38000, SDS-PAGE
-
hexamer
-
2 * 66000, 2 * 48000, 2 * 37000, SDS-PAGE; alpha2,beta2,gamma2
hexamer
-
(alphabetagamma)2
hexamer
Q49605
alpha2beta2gamma2
trimer
-
1 * 69000, 1 * 42000 and 1 * 33000, alpha, beta and gamma
trimer
-
1 * 63900, 1 * 41700, 1 * 30400, SDS-PAGE
hexamer
Methanothermobacter thermautotrophicus Marburg
-
2 * 66000, 2 * 48000, 2 * 37000, SDS-PAGE; 2 * 66000, 2 * 48000, 2 * 37000, SDS-PAGE; alpha2,beta2,gamma2; alpha2,beta2,gamma2; alpha2,beta2,gamma2; alpha2,beta2,gamma2; alpha2,beta2,gamma2; alpha2,beta2,gamma2; alpha2,beta2,gamma2
-
additional information
-
four protein components: A1 (coenzyme F-420-reducing hydrogenase), A2, A3 (methylviologen-reducing hydrogenase) and C as well as catalytic amounts of ATP, vitamin B12 and the disulfide of 7-mercaptoheptanoylthreonine in addition to Ti(III) citrate, component A1 is no longer required, component A1 and A3 500000 Da from gel-filtration
additional information
-
three components: A 500000 Da hydrogenase activity for reduction of viologen dyes, coenzyme F-420 or flavins, B 1000 Da oxygen labile and C 130000 Da, gel-filtration
additional information
-
enzyme structure analysis in reduced and oxidized state, the enzyme has two structurally interlinked active sites embedded in an a2b2c2 subunit structure, overview; the enzyme has two structurally interlinked active sites embedded in an alpha2beta2gamma2 subunit structure. Each active site has the nickel porphyrinoid F430 as a prosthetic group
additional information
-
structure of the holoenzyme, overview
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
side-chain modification
-
methylation of residues in the active site, e.g. at His257, 5fold methylation in isozyme MCR I, overview
side-chain modification
-
methylation of residues in the active site, e.g. at His257, overview
side-chain modification
-
methylation of residues in the active site, e.g. at His257, 5fold methylation in isozyme MCR I, overview
side-chain modification
-, Q49605
methylation of residues in the active site, e.g. at His257, overview
side-chain modification
-
methylation of residues in the active site, e.g. at His257, overview
side-chain modification
-
methylation of residues in the active site, e.g. at His257, 5fold methylation in isozyme MCR I, overview
Crystallization/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
enzyme alone and in complex with substrates, sitting drop vapor diffusion method, using 100 mM Na-HEPES, pH 7.3-8.0, 150 mM magnesium acetate, and 20-22% (w/v) PEG 400
P11558 and P11560 and P11562
hanging drop vapor diffusion method, crystal form M obtained with 2-methyl-2,4-pentanediol grown within two months, form P grows from polyethylene glycol 400 within two weeks at 4C, both crystal forms have one molecule per assymetric unit
-
sitting drop vapor diffusion method, using 25% (w/v) PEG 400, 0.1M Tris pH 8.5 and 0.2 M Li2SO4
D1JBK2 and D1JBK3 and D1JBK4
pH STABILITY
pH STABILITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
9
-
-
above this pH value and 60C isoenzyme I is slowly denatured
TEMPERATURE STABILITY
TEMPERATURE STABILITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
4
-
-
11 h, fully active
23
-
-
N2 atmosphere, 2 h, 28% loss of original activity
60
-
-
pH above 9.0 isoenzyme I is slowly denatured
95
-
-
10 min under anaerobic conditions, heat-labile components A and C lose activity
121
-
-
1-2 h, heat-stable component B, no loss of activity
GENERAL STABILITY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
activity is stabilized by high concentrations of ammonium sulfate
-
methyl-coenzyme M stabilizes enzyme activity
-
OXIDATION STABILITY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
high concentrations of both H2 and CO2 favour the expression of isoenzyme II, low concentrations favour the expression of isoenzyme I
-
393248
oxygen causes irreversible loss of methane forming activity, component C is oxygen-stable
-
393259
STORAGE STABILITY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
-20C, stored under N2 atmosphere, 50 mM anaerobic Tris-HCl, pH 7.6, 150 mM NaCl, 1 mM Ti(III) citrate
-
4C, 11 h, fully active
-
liquid N2, 50 mM potassium phosphate buffer, pH 7.0, 1 M potassium acetate, 10 mM 2-mercaptoethanol, 10% w/v glycerol
-
three freeze-thaw cycles, fully active
-
-20C, 50 mM potassium PIPES buffer, pH 6.2, 15 mM MgCl2, 10 mM 2-mercaptoethanol
-
-70C, rapidly frozen, yellow precipitate, suspended in 100%-saturated ammonium sulfate, stored unter N2, remains active
-
-80C, under N2 atmosphere, 50 mM PIPES, pH 7.2, 40% v/v glycerol, placed in H2 gas phase, stable for weeks
-
0C, enzyme preparation, 100% H2
-
4C, component C, 96% homogeneous, under N2 atmosphere, several months without any loss of activity in multicomponent assay
-
4C, pH 7.0, 4 h, 50% loss of activity of red1 form
-
4C, under N2 atmosphere, 50 mM potassium phosphate, pH 6.7, 50% decrease of specific acitivity within 12 hours
-
ice bath temperature, hydrogenase stable 3-4 weeks
-
storage in frozen stage not possible, thawing leads to a rapid loss of activity
-
Purification/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
Q-Sepharose, Phenyl-Superose HR 5/5, Superose 6 HR 10/30 column
-
sucrose density gradient cetrifugation, Q-Sepharose, Phenyl-Superose 5/5 column, anaerobic
-
active native enzyme to homogeneity
-
active native isozyme MCR I in presence of HS-CoM
-
active native MCR; native enzyme, during purification the enzyme lost its MCR-red2 signal owing to the removal of HS-CoB
-
in the silent, red1c, or ox1 states
-
purification of native MCRox1, and of native MCRred1, the latter by ammonium sulfate fractionation and ion exchange chromatography
-
4C, strictly anaerobic conditions, fractional ammonium-sulfate precipitation; copurification of isoenzymes, separation of isoenzymes by anion-exchange chromatography
-
all buffers that are used during purification process are supplemented with stabilising methyl coenzyme M, further chromatography steps with phenyl-superose, Mono-Q and Sephadex G25 result in 90% loss of specific activity; under 5% H2/95% N2 condition, fractionated ammonium sulfate precipitation
-
anaerobic conditions, ion-exchange column, gel-filtration
-
anaerobic, different components purified seperately, component C ion-exchange chromatography, hydrophobic interaction chromatography, component A2 affinity chromatography, ion-exchange chromatography, component A1 and A3 are obtained by gel filtration, hydrophobic interaction chromatography
-
copurification of isoenzymes, separation of isoenzymes by anion-exchange chromatography; hydrophobic interaction chromatography, Sepharose beads which contain antibodies specific for each isoenzyme, immunoadsorption method; under 5% H2/95% N2 condition, fractionated ammonium sulfate precipitation
-
membrane filtration, on Mono Q, Superose-6 and Phenyl-Superose column
-
under 5% H2/95% N2 condition, fractionated ammonium sulfate precipitation
-
-
D1JBK2 and D1JBK3 and D1JBK4
Cloned/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
expression of two ORF gene products in Escherichia coli DS 410, expressed proteins are suggested to be important for enzyme activity, but neither stimulatory nor inhibitory effects of these gene products are determined
-
genes in operons mrt and mcr, DNA and amino acid sequence determination, promoter region, determination of operator regions of the mcr and mrt operons, and of cis elements and trans-acting factors responsible for the gene expression of MCRs by using electrophoretic mobility shift assay and affinity particle purification. IMP dehydrogenase-related protein VII, IMPDH VII encoded by MTH126, is a plausible candidate for the transcriptional regulator of the mcr operon in this methanogen, the binding site of IMPDH VII mostly overlaps the factor B-responsible element-TATA box of the mcr operon, overview. Expression in Escherichia coli strain BL21(DE3)
-
APPLICATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
analysis
-
methanogen diversity evidenced by molecular characterization of methyl coenzyme M reductase A genes in hydrothermal sediments of the Guaymas Basin