Information on EC 1.12.98.2 - 5,10-methenyltetrahydromethanopterin hydrogenase

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The expected taxonomic range for this enzyme is: Euryarchaeota

EC NUMBER
COMMENTARY
1.12.98.2
-
RECOMMENDED NAME
GeneOntology No.
5,10-methenyltetrahydromethanopterin hydrogenase
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
H2 + 5,10-methenyltetrahydromethanopterin = H+ + 5,10-methylenetetrahydromethanopterin
show the reaction diagram
-
-
-
-
H2 + 5,10-methenyltetrahydromethanopterin = H+ + 5,10-methylenetetrahydromethanopterin
show the reaction diagram
mechanism
-
H2 + 5,10-methenyltetrahydromethanopterin = H+ + 5,10-methylenetetrahydromethanopterin
show the reaction diagram
stereoselective hydride transfer
-
H2 + 5,10-methenyltetrahydromethanopterin = H+ + 5,10-methylenetetrahydromethanopterin
show the reaction diagram
mechanism
Methanothermobacter thermautotrophicus Marburg
-
-
REACTION TYPE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
oxidation
-
-
-
-
redox reaction
-
-
-
-
reduction
-
-
-
-
PATHWAY
KEGG Link
MetaCyc Link
Metabolic pathways
-
Methane metabolism
-
methanogenesis from CO2
-
Microbial metabolism in diverse environments
-
SYSTEMATIC NAME
IUBMB Comments
hydrogen:5,10-methenyltetrahydromethanopterin oxidoreductase
Does not catalyse the reduction of artificial dyes. Does not by itself catalyse a H2/H+ exchange reaction. Does not contain nickel or iron-sulfur clusters.
SYNONYMS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
5,10-methylene-H4MPT dehydrogenase
-
-
-
-
Dehydrogenase, methylenetetrahydromethanopterin
-
-
-
-
EC 1.12.99.4
-
-
formerly
-
H2-forming methylenetetrahydromethanopterin dehydrogenase
-
-
H2-forming N5,N10-Methenyltetrahydromethanopterin dehydrogenase
-
-
-
-
Hmd
-
-
-
-
methylenetetrahydromethanopterin dehydrogenase
-
-
-
-
N5,N10-methenyltetrahydromethanopterin hydrogenase
-
-
-
-
N5,N10-Methylenetetrahydromethanopterin dehydrogenase
-
-
-
-
N5,N10-methylenetetrahydromethanopterin dehydrogenase (H2-forming)
-
-
-
-
CAS REGISTRY NUMBER
COMMENTARY
100357-01-5
-
ORGANISM
COMMENTARY
LITERATURE
SEQUENCE CODE
SEQUENCE DB
SOURCE
formerly Methanobacterium thermoautotrophicum, strains deltaH and TM, two different isoforms of enzyme, first isoform in early and middle stages of cultivation and is F420 dependent (mtd-isoform), second isoform in late stages of cultivation is H2-dependent (mth-isoform)
-
-
Manually annotated by BRENDA team
Methanothermobacter thermautotrophicus Marburg
strain Marburg
-
-
Manually annotated by BRENDA team
SUBSTRATE
PRODUCT                      
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
5,10-methenyltetrahydromethanopterin + H2
5,10-methylenetetrahydromethanopterin + H+
show the reaction diagram
-
-
-
-
?
5,10-methenyltetrahydromethanopterin + H2
5,10-methylenetetrahydromethanopterin + H+
show the reaction diagram
-
-
-
-
r
5,10-methenyltetrahydromethanopterin + H2
5,10-methylenetetrahydromethanopterin + H+
show the reaction diagram
-
-
-
-
r
5,10-methenyltetrahydromethanopterin + H2
5,10-methylenetetrahydromethanopterin + H+
show the reaction diagram
-
involved in methanogenesis
-
-
?
5,10-methenyltetrahydromethanopterin + H2
5,10-methylenetetrahydromethanopterin + H+
show the reaction diagram
-
involved in methanogenesis
-
-
r
5,10-methenyltetrahydromethanopterin + H2
5,10-methylenetetrahydromethanopterin + H+
show the reaction diagram
-
involved in methanogenesis
-
-
r
5,10-methenyltetrahydromethanopterin + H2
5,10-methylenetetrahydromethanopterin + H+
show the reaction diagram
-
reverse reaction under argon atmosphere
-
-
r
N5,N10-methylenetetrahydromethanopterin + H+
N5,N10-methenyltetrahydromethanopterin + H2
show the reaction diagram
-
-
-
-
-
N5,N10-methylenetetrahydromethanopterin + H+
N5,N10-methenyltetrahydromethanopterin + H2
show the reaction diagram
-
r
-
-
-
N5,N10-methylenetetrahydromethanopterin + H+
N5,N10-methenyltetrahydromethanopterin + H2
show the reaction diagram
-
r
-
-
N5,N10-methylenetetrahydromethanopterin + H+
N5,N10-methenyltetrahydromethanopterin + H2
show the reaction diagram
-
r
-
-
-
N5,N10-methylenetetrahydromethanopterin + H+
N5,N10-methenyltetrahydromethanopterin + H2
show the reaction diagram
-
no reaction with: coenzyme F420, NAD+, NADP+
-
-
-
N5,N10-methylenetetrahydromethanopterin + H+
N5,N10-methenyltetrahydromethanopterin + H2
show the reaction diagram
-
no reaction with: coenzyme F420, NAD+, NADP+, reverse reaction is favoured under alkaline conditions
-
-
-
N5,N10-methylenetetrahydromethanopterin + H+
N5,N10-methenyltetrahydromethanopterin + H2
show the reaction diagram
-
no reaction with viologen dyes
-
-
-
N5,N10-methylenetetrahydromethanopterin + H+
N5,N10-methenyltetrahydromethanopterin + H2
show the reaction diagram
Methanothermobacter thermautotrophicus Marburg
-
r
-
-
-
N5,N10-methylenetetrahydromethanopterin + H+
N5,N10-methenyltetrahydromethanopterin + H2
show the reaction diagram
Methanothermobacter thermautotrophicus Marburg
-
-
-
-
-
N5,N10-methylenetetrahydromethanopterin + H+
N5,N10-methenyltetrahydromethanopterin + H2
show the reaction diagram
Methanothermobacter thermautotrophicus Marburg
-
r
-
-
-
N5,N10-methylenetetrahydromethanopterin + H+
N5,N10-methenyltetrahydromethanopterin + H2
show the reaction diagram
Methanothermobacter thermautotrophicus Marburg
-
no reaction with: coenzyme F420, NAD+, NADP+, no reaction with viologen dyes
-
-
-
5,10-methenyltetrahydromethanopterin + H2
5,10-methylenetetrahydromethanopterin + H+
show the reaction diagram
Q58194
Hmd catalyzes a step in the hydrogenotrophic methanogenesis pathway in class I methanogens
-
-
?
additional information
?
-
-
the enzyme is involved in methanogenesis from CO2 and H2
-
-
-
additional information
?
-
-
under conditions of nickel limitation, the reduction of F420 with H2 is catalyzed by the metal-free methylenetetrahydromethanopterin dehydrogenase system which is composed of H2-forming methylenetetrahydromethanopterin dehydrogenase and F420-dependent methylenetetrahydromethanopterin dehydrogenase
-
-
-
additional information
?
-
-
no reduction of methyl viologen or methyl blue
-
-
-
additional information
?
-
-
no reduction of viologen dyes in the presence of H2
-
-
-
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
5,10-methenyltetrahydromethanopterin + H2
5,10-methylenetetrahydromethanopterin + H+
show the reaction diagram
-
involved in methanogenesis
-
-
?
5,10-methenyltetrahydromethanopterin + H2
5,10-methylenetetrahydromethanopterin + H+
show the reaction diagram
-
involved in methanogenesis
-
-
r
5,10-methenyltetrahydromethanopterin + H2
5,10-methylenetetrahydromethanopterin + H+
show the reaction diagram
-
involved in methanogenesis
-
-
r
5,10-methenyltetrahydromethanopterin + H2
5,10-methylenetetrahydromethanopterin + H+
show the reaction diagram
Q58194
Hmd catalyzes a step in the hydrogenotrophic methanogenesis pathway in class I methanogens
-
-
?
additional information
?
-
-
the enzyme is involved in methanogenesis from CO2 and H2
-
-
-
additional information
?
-
-
under conditions of nickel limitation, the reduction of F420 with H2 is catalyzed by the metal-free methylenetetrahydromethanopterin dehydrogenase system which is composed of H2-forming methylenetetrahydromethanopterin dehydrogenase and F420-dependent methylenetetrahydromethanopterin dehydrogenase
-
-
-
COFACTOR
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
additional information
-
enzyme contains iron bound to a cofactor of unknown structure
-
additional information
-
enzyme contains iron bound to a mercaptoethanol-extractable cofactor of unknown structure
-
additional information
-
enzyme contains iron bound to a mercaptoethanol-extractable cofactor of unknown structure, contains intrinsic CO bound to iron
-
additional information
-
tightly binds an iron-containing cofactor. The iron is coordinated by two CO molecules, one sulfur and a pyridone derivative, which is linked via a phosphodiester bond to a guanosine base
-
METALS and IONS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
Fe
-
tightly binds an iron-containing cofactor. The iron is coordinated by two CO molecules, one sulphur and a pyridone derivative, which is linked via a phosphodiester bond to a guanosine base
Fe
-
tightly binds an iron-containing cofactor. The iron is coordinated by two CO molecules, one sulfur and a pyridone derivative, which is linked via a phosphodiester bond to a guanosine base
Fe
Q58194
Hmd holoenzyme is comprised of 2 iron atoms, each iron atom coordinates the reduction of methenyltetrahydromethanopterin and oxidation of H2 while bound to both Hmd and a cofactor molecule
Iron
-
contains approximately 1 mol of iron per mol of enzyme
Iron
-
enzyme contains iron bound to a cofactor of unknown structure, one iron per monomer, iron is released from cofactor upon light inactivation
Iron
-
enzyme contains iron bound to a mercaptoethanol-extractable cofactor of unknown structure, one iron per monomer, iron is released from cofactor upon light inactivation
Iron
-
enzyme contains iron bound to an mercaptoethanol-extractable cofactor of unknown structure, contains intrinsic CO bound to iron
NaCl
-
the enzyme requires the presence of salts, 50% of maximal activity is reached at 100 mM potassium phosphate, KCl or NaCl
Nickel
-
contains less than 0.1 mol Ni per mol of enzyme
potassium phosphate
-
the enzyme requires the presence of salts, 50% of maximal activity is reached at 100 mM potassium phosphate, KCl or NaCl
KCl
-
the enzyme requires the presence of salts, 50% of maximal activity is reached at 100 mM potassium phosphate, KCl or NaCl
additional information
-
metal-free protein
additional information
-
the enzyme does not contain nickel or iron/sulfur clusters
additional information
-
no iron-sulfur-cluster or nickel
additional information
-
lack of redoxactive transition metals
additional information
-
no iron-sulfur-cluster
INHIBITORS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
CO
-
high concentrations
CO
-
high concentrations, reversible
H2
-
inhibits formation of N5,N10-methenyltetrahydromethanopterin
KM VALUE [mM]
KM VALUE [mM] Maximum
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.002
-
H+
-
pH 5.7
0.85
-
N5,N10-methenyltetrahydromethanopterin
-
-
0.02
-
N5,N10-methylenetetrahydromethanopterin
-
-
0.04
-
N5,N10-methylenetetrahydromethanopterin
-
-
0.05
-
N5,N10-methylenetetrahydromethanopterin
-
-
0.06
-
N5,N10-methylenetetrahydromethanopterin
-
-
Ki VALUE [mM]
Ki VALUE [mM] Maximum
INHIBITOR
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.1
-
CN-
-
pH 6.0, 40C, under N2, substrate concentration of 0.003 mM
0.1
-
CN-
-
pH 6.0, 40C, under N2
0.2
-
CN-
-
pH 6.0, 40C, under N2, substrate concentration of 0.01 mM
0.01
-
CO
-
pH 6.0, 40C, under N2
SPECIFIC ACTIVITY [µmol/min/mg]
SPECIFIC ACTIVITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
610
-
-
purified enzyme, pH 6.0, 40C, under N2
pH OPTIMUM
pH MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
pH RANGE
pH RANGE MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
4.5
7
-
reaction rate increases hyperbolically with the proton concentration between pH 7 and pH 4.5
TEMPERATURE OPTIMUM
TEMPERATURE OPTIMUM MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
additional information
-
-
-
TEMPERATURE RANGE
TEMPERATURE MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
40
65
-
2.5-fold higher activity at 65C than at 40C
PDB
SCOP
CATH
ORGANISM
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)
Methanothermobacter marburgensis (strain DSM 2133 / 14651 / NBRC 100331 / OCM 82 / Marburg)
Methanothermobacter marburgensis (strain DSM 2133 / 14651 / NBRC 100331 / OCM 82 / Marburg)
MOLECULAR WEIGHT
MOLECULAR WEIGHT MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
38000
-
Q58194
the Hmd holoenzyme is comprised of a homodimer of 38 kDa subunits, 2 pyridone derivative cofactor molecules and 2 iron atoms
170000
-
-
gel filtration
SUBUNITS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
dimer
-
2 * 40000, SDS-PAGE
homodimer
Q58194
2 * 38000, structural modeling of Hmd enzyme reveals a common structural arrangement comprised of one large N-terminal domain containing alpha-helices and beta-sheets and one smaller C-terminal domain containing only alpha-helices
monomer
Methanothermobacter thermautotrophicus Marburg
-
x * 43000, SDS-PAGE; x * 43000, SDS-PAGE; x * 43000, SDS-PAGE
-
tetramer
-
4 * 37992, calculation from nucleotide sequence; 4 * 38038, MALDI-TOF-MS analysis of peptides obtained by BrCN cleavage; 4 * 43000, SDS-PAGE
tetramer
-
4 * 44000, SDS-PAGE
Crystallization/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
hanging-drop or sitting-drop, vapour diffusion method. Crystal structure of the Hmd apoenzyme from Methanocaldococcus jannaschii at 1.75 A resolution
-
hanging-drop or sitting-drop, vapour diffusion method. Crystal structure of the Hmd apoenzyme from Methanocaldococcus jannaschii at 2.4 A resolution
-
TEMPERATURE STABILITY
TEMPERATURE STABILITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
90
-
-
60 min, stable, enzyme in cell extract; rapid inactivation of purified enzyme
GENERAL STABILITY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
sensitive to UV-A/blue light, CO protects from inactivation
-
enzyme and cofactor are light sensitive
-
sensitive to UV-A/blue light, CO protects from inactivation
-
50% loss of activity after freezing and thawing
-
the rate of inactivation increases upon dilution and in the presence of O2 and decreases upon the addition of 5 mg/ml albumin
-
OXIDATION STABILITY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
enzyme is rapidly inactivated upon exposure to oxygen
-
658635
purified enzyme is very labile even under strictly anoxic conditions
-
394696
STORAGE STABILITY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
-20C, under N2 gas phase, 20% loss of activity within 2 weeks
-
4C, pH 7.6, 50 mM Tris-HCl, 20% glycerol, under N2 gas phase, 50% loss of activity after 1 week
-
Purification/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
all purification steps are performed in the dark
-
Cloned/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
expressed in Escherichia coli
-