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Information on EC 1.5.98.1 - methylenetetrahydromethanopterin dehydrogenase and Organism(s) Methanopyrus kandleri and UniProt Accession P94951

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IUBMB Comments
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.
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Methanopyrus kandleri
UNIPROT: P94951
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The taxonomic range for the selected organisms is: Methanopyrus kandleri
The expected taxonomic range for this enzyme is: Archaea, Bacteria
Synonyms
n5,n10-methylenetetrahydromethanopterin dehydrogenase, methylenetetrahydromethanopterin dehydrogenase, f420-dependent methylenetetrahydromethanopterin dehydrogenase, methylene-h(4)mpt dehydrogenase, f420h2-dependent methylenetetrahydromethanopterin dehydrogenase, coenzyme-f420-dependent n5,n10-methylenetetrahydromethanopterin dehydrogenase, f420-dependent methylene-tetrahydromethanopterin dehydrogenase, methylene tetrahydromethanopterin:coenzyme f420 oxidoreductase, coenzyme f420-dependent methylenetetrahydromethanopterin dehydrogenase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
coenzyme F420-dependent methylenetetrahydromethanopterin dehydrogenase
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coenzyme-F420-dependent N5,N10-methylenetetrahydromethanopterin dehydrogenase
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F420-dependent methylenetetrahydromethanopterin dehydrogenase
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Coenzyme F420 dependent N5,N10-methylenetetrahydromethanopterin dehydrogenase
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-
-
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Dehydrogenase, methylenetetrahydromethanopterin
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-
-
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Methylene tetrahydromethanopterin:coenzyme F420 oxidoreductase
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-
-
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Methylene-H4MPT:coenzyme F420 oxidoreductase
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-
-
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N5,N10-Methylenetetrahydromethanopterin dehydrogenase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
5,10-methylenetetrahydromethanopterin + oxidized coenzyme F420 = 5,10-methenyltetrahydromethanopterin + reduced coenzyme F420
show the reaction diagram
ternary complex mechanism
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
oxidation
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-
-
-
reduction
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-
-
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PATHWAY SOURCE
PATHWAYS
-
-, -, -, -, -
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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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 + oxidized coenzyme F420
5,10-methenyltetrahydromethanopterin + reduced coenzyme F420
show the reaction diagram
5,10-methylenetetrahydromethanopterin + oxidized coenzyme F420
5,10-methenyltetrahydromethanopterin + reduced coenzyme F420
show the reaction diagram
additional information
?
-
-
enzyme is involved in CO2 reduction to CH4
-
-
?
NATURAL SUBSTRATE
NATURAL 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
-
-
r
5,10-methylenetetrahydromethanopterin + oxidized coenzyme F420
5,10-methenyltetrahydromethanopterin + reduced coenzyme F420
show the reaction diagram
the enzyme catalyzes the fourth reaction step of CO2-reduction to methane in methanogenic archaea
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-
?
5,10-methylenetetrahydromethanopterin + oxidized coenzyme F420
5,10-methenyltetrahydromethanopterin + reduced coenzyme F420
show the reaction diagram
-
fourth step in the CO2 reduction to methane
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-
r
additional information
?
-
-
enzyme is involved in CO2 reduction to CH4
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
coenzyme F420
additional information
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
(NH4)2SO4
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very high salt concentration are required for high activity. Highest specific acitivity in presence of 2 M (NH4)2SO4. Other salts including NaH2PO4, KH2PO4 and NaCl are also effective in stimulating the enzyme activity
K+
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very high salt concentration is required for high activity. Highest specific acitivity in presence of 2 M (NH4)2SO4. Other salts including NaH2PO4, KH2PO4 and NaCl are also effective in stimulating the enzyme activity
Na+
-
very high salt concentration is required for high activity. Highest specific acitivity in presence of 2 M (NH4)2SO4. Other salts including NaH2PO4, KH2PO4 and NaCl are also effective in stimulating the enzyme activity
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
(NH4)2SO4
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
0.02 - 0.04
5,10-methylenetetrahydromethanopterin
0.03
coenzyme F420
1 M (NH4)2SO4, at 65°C
0.04 - 0.08
oxidized coenzyme F420
0.08
5,10-methylenetetrahydromethanopterin
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-
0.02
coenzyme F420
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-
0.08
methylenetetrahydromethanopterin
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native enzyme, pH 6.0, 65°C, N2-atmosphere
0.02
oxidized coenzyme F420
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native enzyme, pH 6.0, 65°C, N2-atmosphere
additional information
additional information
-
ternary complex kinetic mechanism
-
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
3700
1 M (NH4)2SO4, at 65°C
additional information
-
-
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6
-
assay at, substrate methylenetetrahydromethanopterin, forward reaction
8
-
assay at, substrate methenyltetrahydromethanopterin, reverse reaction
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
4.2
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deduced from amino acid sequence
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
additional information
-
optimal growth on H2 and CO2 at 98°C
Manually annotated by BRENDA team
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
31383
x * 31383, calculated from sequence
34000
x * 34000, enzyme from Methanopyrus kandleri
36000
x * 36000, recombinant enzyme expressed in Escherichia coli
300000
-
gel filtration
31383
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8 * 36000, approximately, SDS-PAGE, 8 * 31383, sequence calculation
36000
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
hexamer
an X-ray structure of methylenetetrahydromethanopterin dehydrogenase at 1.54 A resolution reveals a homohexameric complex organized as a dimer of trimers
hexamer
octamer
additional information
-
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
the selenomethionine-labelled form of the enzyme is structurally characterized at 1.54 A resolution
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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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
OXIDATION STABILITY
ORGANISM
UNIPROT
LITERATURE
moderately stable against inactivation by air. 50% loss of activity within 12 h at 4°C under aerobic conditions
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13755
O2 causes slow inactivation
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486097
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20°C, anaerobically stored, 50% loss of activity after several weeks
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-20°C, purified recombinant enzyme, N2-atmosphere, stable for at least 4 weeks
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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
overexpression 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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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Klein, A.R.; Thauer, R.K.
Re-face specificity at C14a of methylenetetrahydromethanopterin and si-face specificity at C5 of coenzyme F420 for coenzyme F420-dependent methylenetetrahydromethanopterin dehydrogenase from methanogenic archaea
Eur. J. Biochem.
227
169-174
1995
Methanopyrus kandleri, Methanothermobacter thermautotrophicus
Manually annotated by BRENDA team
Klein, A.R.; Koch, J.; Stetter, K.O.; Thauer, R.K.
Two N5,N10-methylenetetrahydromethanopterin dehydrogenases in the extreme thermophile Methanopyrus kandleri: characterization of the coenzyme F420-dependent enzyme
Arch. Microbiol.
160
186-192
1993
Methanopyrus kandleri
Manually annotated by BRENDA team
Shima, S.; Thauer, R.K.
Tetrahydromethanopterin-specific enzymes from Methanopyrus kandleri
Methods Enzymol.
331
317-353
2001
Archaeoglobus fulgidus, Methanocaldococcus jannaschii, Methanopyrus kandleri, Methanosarcina barkeri, Methanothermobacter thermautotrophicus
Manually annotated by BRENDA team
Hagemeier, C.H.; Shima, S.; Warkentin, E.; Thauer, R.K.; Ermler, U.
Coenzyme F420-dependent methylenetetrahydromethanopterin dehydrogenase from Methanopyrus kandleri: the selenomethionine-labelled and non-labelled enzyme crystallized in two different forms
Acta Crystallogr. Sect. D
59
1653-1655
2003
Methanopyrus kandleri
Manually annotated by BRENDA team
Warkentin, E.; Hagemeier, C.H.; Shima, S.; Thauer, R.K.; Ermler, U.
The structure of F420-dependent methylenetetrahydromethanopterin dehydrogenase: a crystallographic 'superstructure' of the selenomethionine-labelled protein crystal structure
Acta Crystallogr. Sect. D
61
198-202
2005
Methanopyrus kandleri
Manually annotated by BRENDA team
Ceh, K.; Demmer, U.; Warkentin, E.; Moll, J.; Thauer, R.K.; Shima, S.; Ermler, U.
Structural basis of the hydride transfer mechanism in F(420)-dependent methylenetetrahydromethanopterin dehydrogenase
Biochemistry
48
10098-10105
2009
Methanopyrus kandleri (P94951), Methanopyrus kandleri
Manually annotated by BRENDA team
Klein, A.R.; Thauer, R.K.
Overexpression of the coenzyme-F420-dependent N5,N10-methylenetetrahydromethanopterin dehydrogenase gene from the hyperthermophilic Methanopyrus kandleri
Eur. J. Biochem.
245
386-391
1997
Methanopyrus kandleri (P94951), Methanopyrus kandleri, Methanopyrus kandleri DSM 6324 (P94951)
Manually annotated by BRENDA team
Hagemeier, C.H.; Shima, S.; Thauer, R.K.; Bourenkov, G.; Bartunik, H.D.; Ermler, U.
Coenzyme F420-dependent methylenetetrahydromethanopterin dehydrogenase (Mtd) from Methanopyrus kandleri: a methanogenic enzyme with an unusual quarternary structure
J. Mol. Biol.
332
1047-1057
2003
Methanopyrus kandleri (P94951), Methanopyrus kandleri, Methanopyrus kandleri DSM 6324 (P94951)
Manually annotated by BRENDA team