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
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
Methanothermobacter thermautotrophicum
-
H2 + 5,10-methenyltetrahydromethanopterin = H+ + 5,10-methylenetetrahydromethanopterin
show the reaction diagram
stereoselective hydride transfer
Methanothermobacter thermautotrophicum
-
H2 + 5,10-methenyltetrahydromethanopterin = H+ + 5,10-methylenetetrahydromethanopterin
show the reaction diagram
mechanism
Methanothermobacter thermautotrophicum Marburg
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
oxidation
-
-
-
-
redox reaction
-
-
-
-
reduction
-
-
-
-
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
methanogenesis from H2 and CO2
-
-
methanogenesis from CO2
-
-
Methane metabolism
-
-
Metabolic pathways
-
-
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
COMMENTARY
LITERATURE
5,10-methylene-H4MPT dehydrogenase
-
-
-
-
Dehydrogenase, methylenetetrahydromethanopterin
-
-
-
-
EC 1.12.99.4
-
-
formerly
-
H2-forming methylenetetrahydromethanopterin dehydrogenase
-
-
H2-forming methylenetetrahydromethanopterin dehydrogenase
-
H2-forming methylenetetrahydromethanopterin dehydrogenase
Methanothermobacter marburgensis DSM 2133
-
-
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
UNIPROT
SEQUENCE DB
SOURCE
Methanopyrus kandleri DSM 6324
-
SwissProt
Manually annotated by BRENDA team
Methanothermobacter marburgensis DSM 2133
-
SwissProt
Manually annotated by BRENDA team
Methanothermobacter thermautotrophicum
-
-
-
Manually annotated by BRENDA team
Methanothermobacter thermautotrophicum
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 thermautotrophicum
strain Marburg
-
-
Manually annotated by BRENDA team
Methanothermobacter thermautotrophicum Marburg
strain Marburg
-
-
Manually annotated by BRENDA team
Methanothermobacter wolfeii DSM 2970
-
SwissProt
Manually annotated by BRENDA team
SUBSTRATE
PRODUCT                      
REACTION DIAGRAM
ORGANISM
UNIPROT
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
Methanothermobacter thermautotrophicum
-
-
-
?
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
Methanothermobacter thermautotrophicum
-
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
-
involved in methanogenesis, reverse reaction under argon atmosphere
-
r
5,10-methenyltetrahydromethanopterin + H2
5,10-methylenetetrahydromethanopterin + H+
show the reaction diagram
Hmd catalyzes a step in the hydrogenotrophic methanogenesis pathway in class I methanogens
-
?
H+ + 5,10-methylenetetrahydromethanopterin
H2 + 5,10-methenyltetrahydromethanopterin
show the reaction diagram
-
-
r
H+ + 5,10-methylenetetrahydromethanopterin
H2 + 5,10-methenyltetrahydromethanopterin
show the reaction diagram
the purified enzyme does not catalyze the reduction of viologen dyes, of methylene blue, of flavins, of pyridine nucleotides
-
r
H+ + 5,10-methylenetetrahydromethanopterin
H2 + 5,10-methenyltetrahydromethanopterin
show the reaction diagram
Methanothermobacter wolfeii DSM 2970
-
-
r
N5,N10-methylenetetrahydromethanopterin + H+
N5,N10-methenyltetrahydromethanopterin + H2
show the reaction diagram
Methanothermobacter thermautotrophicum
-
-
-
-
N5,N10-methylenetetrahydromethanopterin + H+
N5,N10-methenyltetrahydromethanopterin + H2
show the reaction diagram
Methanothermobacter thermautotrophicum
-
-
-
-
N5,N10-methylenetetrahydromethanopterin + H+
N5,N10-methenyltetrahydromethanopterin + H2
show the reaction diagram
Methanothermobacter thermautotrophicum
-
-
-
-
N5,N10-methylenetetrahydromethanopterin + H+
N5,N10-methenyltetrahydromethanopterin + H2
show the reaction diagram
Methanothermobacter thermautotrophicum
-
r
-
-
N5,N10-methylenetetrahydromethanopterin + H+
N5,N10-methenyltetrahydromethanopterin + H2
show the reaction diagram
Methanothermobacter thermautotrophicum
-
r
-
-
N5,N10-methylenetetrahydromethanopterin + H+
N5,N10-methenyltetrahydromethanopterin + H2
show the reaction diagram
Methanothermobacter thermautotrophicum
-
r
-
-
N5,N10-methylenetetrahydromethanopterin + H+
N5,N10-methenyltetrahydromethanopterin + H2
show the reaction diagram
Methanothermobacter thermautotrophicum, Methanothermococcus thermolithotrophicus
-
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
Methanothermobacter thermautotrophicum
-
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
Methanothermobacter thermautotrophicum
-
no reaction with viologen dyes
-
-
N5,N10-methylenetetrahydromethanopterin + H+
N5,N10-methenyltetrahydromethanopterin + H2
show the reaction diagram
Methanothermobacter thermautotrophicum Marburg
-
r
-
-
N5,N10-methylenetetrahydromethanopterin + H+
N5,N10-methenyltetrahydromethanopterin + H2
show the reaction diagram
Methanothermobacter thermautotrophicum Marburg
-
-
-
-
N5,N10-methylenetetrahydromethanopterin + H+
N5,N10-methenyltetrahydromethanopterin + H2
show the reaction diagram
Methanothermobacter thermautotrophicum Marburg
-
r
-
-
N5,N10-methylenetetrahydromethanopterin + H+
N5,N10-methenyltetrahydromethanopterin + H2
show the reaction diagram
Methanothermobacter thermautotrophicum Marburg
-
r, no reaction with: coenzyme F420, NAD+, NADP+, no reaction with viologen dyes
-
-
H+ + 5,10-methylenetetrahydromethanopterin
H2 + 5,10-methenyltetrahydromethanopterin
show the reaction diagram
Methanothermobacter marburgensis DSM 2133
the purified enzyme does not catalyze the reduction of viologen dyes, of methylene blue, of flavins, of pyridine nucleotides
-
r
additional information
?
-
-
the enzyme is involved in methanogenesis from CO2 and H2
-
-
-
additional information
?
-
Methanothermobacter thermautotrophicum
-
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
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
Methanothermobacter thermautotrophicum
-
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
-
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
?
-
Methanothermobacter thermautotrophicum
-
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
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
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
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
Methanothermobacter thermautotrophicum
-
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
Methanothermobacter thermautotrophicum
-
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
Zn2+
the zinc content varies from preparation to preparation between 0.5-4 mol zinc/mol enzyme
KCl
-
the enzyme requires the presence of salts, 50% of maximal activity is reached at 100 mM potassium phosphate, KCl or NaCl
additional information
Methanothermobacter thermautotrophicum
-
metal-free protein
additional information
Methanothermobacter thermautotrophicum
-
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
additional information
the enzyme does not contain iron-sulfur clusters, nickel, or flavins
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
CO
-
high concentrations
CO
-
high concentrations, reversible
cyanide
1 mM, 50% inhibition
H2
Methanothermobacter thermautotrophicum
-
inhibits formation of N5,N10-methenyltetrahydromethanopterin
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.05
5,10-methenyltetrahydromethanopterin
pH 7.5, 60C
0.07
5,10-methenyltetrahydromethanopterin
pH and temperature not specified in the publication
0.02
5,10-methylenetetrahydromethanopterin
pH and temperature not specified in the publication
0.04
5,10-methylenetetrahydromethanopterin
pH 6.5, 60C
0.85
N5,N10-methenyltetrahydromethanopterin
-
-
0.02
N5,N10-methylenetetrahydromethanopterin
Methanothermobacter thermautotrophicum
-
-
0.04
N5,N10-methylenetetrahydromethanopterin
Methanothermobacter thermautotrophicum
-
-
0.05
N5,N10-methylenetetrahydromethanopterin
-
-
0.06
N5,N10-methylenetetrahydromethanopterin
-
-
0.002
H+
-
pH 5.7
additional information
H2
the apparent Km for H2 is estimated to be approximately 60% H2 in the gas phase
additional information
H2
apparent Km for H2 is 60%
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
975
5,10-methenyltetrahydromethanopterin
Methanothermobacter marburgensis
P32440
pH 7.5, 60C
1462
5,10-methylenetetrahydromethanopterin
Methanothermobacter marburgensis
P32440
pH 6.5, 60C
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
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]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
610
-
purified enzyme, pH 6.0, 40C, under N2
750
Methanothermobacter thermautotrophicum
-
-
800
Methanothermobacter thermautotrophicum
-
-
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
6.5
Methanothermobacter thermautotrophicum
-
-
pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
4.5 - 7
-
reaction rate increases hyperbolically with the proton concentration between pH 7 and pH 4.5
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
60
Methanothermobacter thermautotrophicum
-
-
60
in 120 mM potassium phosphate pH 6
additional information
-
-
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
40 - 65
-
2.5-fold higher activity at 65C than at 40C
pI VALUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
4.4
isoelectric focussing
PDB
SCOP
CATH
ORGANISM
UNIPROT
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
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
38000
the Hmd holoenzyme is comprised of a homodimer of 38 kDa subunits, 2 pyridone derivative cofactor molecules and 2 iron atoms
696971
45000
Methanothermobacter thermautotrophicum
-
gradient PAGE
394694
150000
-
gel filtration
394696
170000
-
gel filtration
394697
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
-
2 * 40000, SDS-PAGE
dimer
2 * 43000, SDS-PAGE
dimer
Methanothermobacter wolfeii DSM 2970
-
2 * 43000, SDS-PAGE
-
homodimer
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
homodimer
Methanothermobacter marburgensis DSM 2133
-
-
-
monomer
Methanothermobacter thermautotrophicum
-
x * 43000, SDS-PAGE
monomer
Methanothermobacter thermautotrophicum 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
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
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
60
30 min, 50% inactivation
727402
90
-
60 min, stable, enzyme in cell extract; rapid inactivation of purified enzyme
394697
GENERAL STABILITY
ORGANISM
UNIPROT
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
LITERATURE
enzyme is rapidly inactivated upon exposure to oxygen
-
658635
rapidly inactivated in the presence of molecular oxygen. The rate of inactivation increases in the presence of dithiothreitol (2 mM) or of mercaptoethanol (5 mM)
727402
stable to O2
Methanothermobacter thermautotrophicum
-
394691
the enzyme is much more sensitive towards inactivation by O2 than the enzyme from Methanothermobacter marburgensis
727402
purified enzyme is very labile even under strictly anoxic conditions
-
394696
STORAGE STABILITY
ORGANISM
UNIPROT
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
Methanothermobacter thermautotrophicum
-
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
all purification steps are performed in the dark
-
-
Methanothermobacter thermautotrophicum
-
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli
-