Information on EC 1.5.98.1 - methylenetetrahydromethanopterin dehydrogenase

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

EC NUMBER
COMMENTARY hide
1.5.98.1
-
RECOMMENDED NAME
GeneOntology No.
methylenetetrahydromethanopterin dehydrogenase
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REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
5,10-methylenetetrahydromethanopterin + oxidized coenzyme F420 = 5,10-methenyltetrahydromethanopterin + reduced coenzyme F420
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
oxidation
-
-
-
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redox reaction
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reduction
-
-
-
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
factor 420 biosynthesis
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methanogenesis from CO2
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Methane metabolism
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Metabolic pathways
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Microbial metabolism in diverse environments
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SYSTEMATIC NAME
IUBMB Comments
5,10-methylenetetrahydromethanopterin:coenzyme-F420 oxidoreductase
Coenzyme F420 is a 7,8-didemethyl-8-hydroxy-5-deazariboflavin derivative; methanopterin is a pterin analogue. The enzyme is involved in the formation of methane from CO2 in the methanogen Methanothermobacter thermautotrophicus.
CAS REGISTRY NUMBER
COMMENTARY hide
100357-01-5
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
chemolithoautotrophic
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-
Manually annotated by BRENDA team
chemolithoautotrophic
-
-
Manually annotated by BRENDA team
strain TM-1
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-
Manually annotated by BRENDA team
strain TM-1
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-
Manually annotated by BRENDA team
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UniProt
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
physiological function
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
5,10-methenyltetrahydromethanopterin + reduced coenzyme F420
5,10-methylenetetrahydromethanopterin + coenzyme F420
show the reaction diagram
hydrogenotrophic methanogenesis pathway in class I methanogens, enzyme of the methanogenic energy metabolism that catalyzes the hydride transfer between substrate and product using coenzyme F420 as hydride carrier
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-
r
5,10-Methylenetetrahydromethanopterin + coenzyme F420
5,10-Methenyltetrahydromethanopterin + reduced coenzyme F420
show the reaction diagram
5,10-Methylenetetrahydromethanopterin + coenzyme F420
?
show the reaction diagram
-
the enzyme is proposed to function in methanol oxidation step to CO2
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-
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5,10-methylenetetrahydromethanopterin + oxidized coenzyme F420
5,10-methenyltetrahydromethanopterin + reduced coenzyme F420
show the reaction diagram
methylenetetrahydromethanopterin + coenzyme F420
methenyltetrahydromethanopterin + reduced coenzyme F420
show the reaction diagram
additional information
?
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NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
5,10-methenyltetrahydromethanopterin + reduced coenzyme F420
5,10-methylenetetrahydromethanopterin + coenzyme F420
show the reaction diagram
P94951
hydrogenotrophic methanogenesis pathway in class I methanogens, enzyme of the methanogenic energy metabolism that catalyzes the hydride transfer between substrate and product using coenzyme F420 as hydride carrier
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-
r
5,10-Methylenetetrahydromethanopterin + coenzyme F420
?
show the reaction diagram
-
the enzyme is proposed to function in methanol oxidation step to CO2
-
-
-
5,10-methylenetetrahydromethanopterin + oxidized coenzyme F420
5,10-methenyltetrahydromethanopterin + reduced coenzyme F420
show the reaction diagram
methylenetetrahydromethanopterin + coenzyme F420
methenyltetrahydromethanopterin + reduced coenzyme F420
show the reaction diagram
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fourth step in the CO2 reduction to methane
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-
r
additional information
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
coenzyme F420
additional information
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
(NH4)2SO4
Cs+
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monovalent cations stimulate in the order K+ less than Cs+ less than Na+ less than NH4+ less than Li+
Li+
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monovalent cations stimulate in the order K+ less than Cs+ less than Na+ less than NH4+ less than Li+
NH4+
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monovalent cations stimulate in the order K+ less than Cs+ less than Na+ less than NH4+ less than Li+
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
(NH4)2SO4
-
0.15M-0.2M (NH4)2SO4 stimulates by a factor of 1.3. Higher concentrations are inhibitory
K2HPO4
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0.15M-0.2M K2HPO4 stimulates by a factor of 1.3. Higher concentrations are inhibitory
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
(NH4)2SO4
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stimulates
additional information
-
relatively high concentrations of lyotropic salt is required for activity, 200fold activation
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.005 - 0.08
5,10-methylenetetrahydromethanopterin
0.004 - 0.065
coenzyme F420
0.006 - 0.08
methylenetetrahydromethanopterin
0.005 - 0.08
oxidized coenzyme F420
0.013 - 0.065
reduced coenzyme F420
additional information
additional information
-
ternary complex kinetic mechanism
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.01
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pH 7.5, 65C, cell extract
0.24
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pH 7.5, 65C, cell extract
1.5
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pH 7.5, 65C
16.7
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pH 7.5, 65C, cell extract
1100
pH 6.0, 20C
3700
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1 M (NH4)2SO4, at 65C
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6
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assay at, substrate methylenetetrahydromethanopterin, forward reaction
8
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assay at, substrate methenyltetrahydromethanopterin, reverse reaction
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
20 - 80
20C: about 55% of maximal activity, 80C: about 75% of maximal activity
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6
-
deduced from amino acid sequnce
6.1
calculated from sequence
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
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8% of the activity
Manually annotated by BRENDA team
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85% of the activity
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Manually annotated by BRENDA team
PDB
SCOP
CATH
ORGANISM
UNIPROT
Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938)
Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938)
Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938)
Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938)
Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938)
Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938)
Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
140000
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gel filtration
200000
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gel filtration
216000
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native PAGE
300000
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gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
hexamer
homohexamer
octamer
tetramer
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4 * 32000, approximately, SDS-PAGE, 4 * 29644, sequence calculation
additional information
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structural adaption to extreme environment
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
crystallization trials are performed with the hanging drop vapor diffusion method using a sparse matrix crystallization kit under anaerobic and red light conditions, determination the structures of the Mtd-5,10-methylenetetrahydromethanopterin-, Mtd-5,10-methenyltetrahydromethanopterin- and the Mtd-5,10-methenyltetrahydromethanopterin-F420H2 complexes at 2.1, 2.0, and 1.8 A resolution, both substrate and cofactor bind in a face to face arrangement to an active site cleft, thereby ensuring a direct hydride transfer between their C14a and C5 atoms
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purified recombinant selenomethionine-labeled enzyme, hanging drop vapour diffusion method, 0.001 ml protein solution containing 12 mg/ml enzyme and 10 mM MOPS-KOH, pH 7.0, mixed with 0.001 ml reservoir solution containing 13% v/v 2-methyl-2,4-pentanediol, 0.1 M sodium phosphate, pH 8.0, and 0.2 M magnesium acetate, X-ray diffraction structure determination and analysis at 1.54 A resolution by single wavelength anomalous dispersion method, or at 2.4 A resolution by multiwavelength anomalous dispersion method
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selenomethionine-labeled enzyme: X-ray diffraction structure determination and analysis at 1.54 A resolution, atomic displacement B factor pattern, native enzyme: X-ray diffraction structure determination and analysis at 2.0-2.4 A resolution, the native enzyme shows a crystallographic superstructure of the selenomethionine-labeled enzyme
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the selenomethionine-labelled form of the enzyme is structurally characterized at 1.54 A resolution
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hanging drop vapour diffusion method, crystal structure of the enzyme in complex with cytochrome F420 at 2.6 A resolution
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
10
enzyme diluted in 120 mM potassium phosphate buffer pH 6.0 at temperature below 10C shows a half-life of less than 1 h. Higher concentrations of potassium phosphate stabilize, the optimum concentration being 0.5-0.8 M
25
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stable for more than 70 h, native and recombinant enzyme
40
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stable for more than 70 h, native and recombinant enzyme
65
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45% loss of activity in 1.5 h, 93% loss of activity in 24 h, recombinant enzyme. 35% loss of activity after 2 h, 96% loss of activity after 27 h
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
stable in phosphate buffer with or without glycerol or ammonium sulfate under both aerobic and anaerobic conditions
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thermostable up to 90C, only in the presence of salts. Complete stability in presence of 0.4-0.5 M K2HPO4
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OXIDATION STABILITY
ORGANISM
UNIPROT
LITERATURE
moderately stable against inactivation by air. 50% loss of activity within 12 h at 4C under aerobic conditions
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13755
O2 causes slow inactivation
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486097
stable under air
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13749
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20C, anaerobically stored, 50% loss of activity after several weeks
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-20C, purified recombinant enzyme, N2-atmosphere, stable for at least 4 weeks
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-20C, stable for several weeks
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4C, 0.5 mM 3-[(3-cholamidopropyl)dimethylammonio]1-propanesulfonate, stable for more than 6 months
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
gel filtration
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native enzyme, multistep procedure involving ammonium sulfate fractionation and several chromatographic steps, recombinant from Escherichia coli strain BL21(DE3)
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
gene mtd, DNA and amino acid sequence determination and analysis, functional overexpression in Escherichia coli strain BL21(DE3)
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overexpression in Escherichia coli
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