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Information on EC 1.5.99.15 - dihydromethanopterin reductase (acceptor)
for references in articles please use BRENDA:EC1.5.99.15
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EC Tree 1 Oxidoreductases
1.5 Acting on the CH-NH group of donors
1.5.99 With unknown physiological acceptors
1.5.99.15 dihydromethanopterin reductase (acceptor)
IUBMB Comments
This archaeal enzyme catalyses the last step in the biosynthesis of tetrahydromethanopterin, a coenzyme used in methanogenesis. The enzyme, characterized from the archaea Methanosarcina mazei and Methanocaldococcus jannaschii, is an iron-sulfur flavoprotein. cf. EC 1.5.1.47, dihydromethanopterin reductase [NAD(P)+].
The expected taxonomic range for this enzyme is: Archaea, Bacteria
Reaction Schemes
show+
oxidized acceptor
=
+
Synonyms
mm1854, mj0208, more
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
AfpA
archaeal-flavoprotein-like flavoprotein
DmrX
methylene H4MPT dehydrogenase B
MJ0208
MM1854
MtdB
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
5,6,7,8-tetrahydromethanopterin + oxidized acceptor = 7,8-dihydromethanopterin + reduced acceptor
5,6,7,8-tetrahydromethanopterin + oxidized acceptor = 7,8-dihydromethanopterin + reduced acceptor
-
-
-
-
5,6,7,8-tetrahydromethanopterin + oxidized acceptor = 7,8-dihydromethanopterin + reduced acceptor
DmrB uses a ping-pong mechanism to transfer reducing equivalents from FMN to the pterin substrate, modeling, overview
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PATHWAY SOURCE
PATHWAYS
BRENDA
KEGG
MetaCyc
tetrahydromethanopterin biosynthesis
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SYSTEMATIC NAME
IUBMB Comments
5,6,7,8-tetrahydromethanopterin:acceptor 5,6-oxidoreductase
This archaeal enzyme catalyses the last step in the biosynthesis of tetrahydromethanopterin, a coenzyme used in methanogenesis. The enzyme, characterized from the archaea Methanosarcina mazei and Methanocaldococcus jannaschii, is an iron-sulfur flavoprotein. cf. EC 1.5.1.47, dihydromethanopterin reductase [NAD(P)+].
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
LITERATURE
COMMENTARY
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
5,6,7,8-tetrahydromethanopterin + oxidized acceptor
7,8-dihydromethanopterin + reduced acceptor
Substrates: -
Products: -
Products: -
?
7,8-dihydromethanopterin + reduced acceptor
5,6,7,8-tetrahydromethanopterin + oxidized acceptor
7,8-dihydromethanopterin + reduced dithiothreitol
5,6,7,8-tetrahydromethanopterin + oxidized dithiothreitol
7,8-dihydromethanopterin + reduced ferredoxin
5,6,7,8-tetrahydromethanopterin + ferredoxin
7,8-dihydromethanopterin + FMNH2
5,6,7,8-tetrahydromethanopterin + FMN
Substrates: -
Products: -
Products: -
?
7,8-dihydromethanopterin + FMNH2
5,6,7,8-tetrahydromethanopterin + FMN
Substrates: DmrB uses a ping-pong mechanism to transfer reducing equivalents from FMN to the pterin substrate, identification of the 7,8-dihydromethanopterin binding site by computational docking
Products: -
Products: -
?
7,8-dihydromethanopterin + reduced acceptor
5,6,7,8-tetrahydromethanopterin + oxidized acceptor
Substrates: the enzyme catalyzes the last step of tetrahydromethanopterin biosynthesis
Products: -
Products: -
?
7,8-dihydromethanopterin + reduced acceptor
5,6,7,8-tetrahydromethanopterin + oxidized acceptor
Substrates: the enzyme catalyzes the last step of tetrahydromethanopterin biosynthesis
Products: -
Products: -
?
7,8-dihydromethanopterin + reduced acceptor
5,6,7,8-tetrahydromethanopterin + oxidized acceptor
Substrates: the enzyme catalyzes the last step of tetrahydromethanopterin biosynthesis
Products: -
Products: -
?
7,8-dihydromethanopterin + reduced acceptor
5,6,7,8-tetrahydromethanopterin + oxidized acceptor
Substrates: the enzyme catalyzes the last step of tetrahydromethanopterin biosynthesis
Products: -
Products: -
?
7,8-dihydromethanopterin + reduced dithiothreitol
5,6,7,8-tetrahydromethanopterin + oxidized dithiothreitol
Substrates: -
Products: -
Products: -
?
7,8-dihydromethanopterin + reduced dithiothreitol
5,6,7,8-tetrahydromethanopterin + oxidized dithiothreitol
Substrates: -
Products: -
Products: -
?
7,8-dihydromethanopterin + reduced dithiothreitol
5,6,7,8-tetrahydromethanopterin + oxidized dithiothreitol
Substrates: NAD(P)H is incapable of directly reducing the flavin cofactor, but dithionite eliminates the FMN peaks, indicating successful electron transfer to the enzyme. An electron transfer system of NADPH, spinach NADPH-ferredoxin oxidoreductase, and ferredoxin can also reduce the FMN peaks. A newly developed assay indicates that dithiothreitol-reduced enzyme can transfer electrons to dihydromethanopterin. Ferredoxin may serve as an electron donor
Products: -
Products: -
?
7,8-dihydromethanopterin + reduced dithiothreitol
5,6,7,8-tetrahydromethanopterin + oxidized dithiothreitol
Substrates: NAD(P)H is incapable of directly reducing the flavin cofactor, but dithionite eliminates the FMN peaks, indicating successful electron transfer to the enzyme. An electron transfer system of NADPH, spinach NADPH-ferredoxin oxidoreductase, and ferredoxin can also reduce the FMN peaks. A newly developed assay indicates that dithiothreitol-reduced enzyme can transfer electrons to dihydromethanopterin. Ferredoxin may serve as an electron donor
Products: -
Products: -
?
7,8-dihydromethanopterin + reduced ferredoxin
5,6,7,8-tetrahydromethanopterin + ferredoxin
Substrates: -
Products: -
Products: -
?
7,8-dihydromethanopterin + reduced ferredoxin
5,6,7,8-tetrahydromethanopterin + ferredoxin
Substrates: -
Products: -
Products: -
?
7,8-dihydromethanopterin + reduced ferredoxin
5,6,7,8-tetrahydromethanopterin + ferredoxin
Substrates: -
Products: -
Products: -
?
7,8-dihydromethanopterin + reduced ferredoxin
5,6,7,8-tetrahydromethanopterin + ferredoxin
Substrates: -
Products: -
Products: -
?
additional information
?
-
Substrates: NAD(P)H is incapable of directly reducing the flavin cofactor, but dithionite eliminates the FMN peaks, indicating successful electron transfer to MJ0208. An electron transfer system of NADPH, spinach NADPH-ferredoxin oxidoreductase, and ferredoxin can also reduce the FMN peaks. Dithiothreitol-reduced MJ0208 can transfer electrons to dihydromethanopterin
Products: -
Products: -
?
additional information
?
-
-
Substrates: NAD(P)H is incapable of directly reducing the flavin cofactor, but dithionite eliminates the FMN peaks, indicating successful electron transfer to MJ0208. An electron transfer system of NADPH, spinach NADPH-ferredoxin oxidoreductase, and ferredoxin can also reduce the FMN peaks. Dithiothreitol-reduced MJ0208 can transfer electrons to dihydromethanopterin
Products: -
Products: -
?
additional information
?
-
Substrates: NAD(P)H is incapable of directly reducing the flavin cofactor, but dithionite eliminates the FMN peaks, indicating successful electron transfer to MJ0208. An electron transfer system of NADPH, spinach NADPH-ferredoxin oxidoreductase, and ferredoxin can also reduce the FMN peaks. Dithiothreitol-reduced MJ0208 can transfer electrons to dihydromethanopterin
Products: -
Products: -
?
additional information
?
-
Substrates: NAD(P)H is incapable of directly reducing the flavin cofactor, but dithionite eliminates the FMN peaks, indicating successful electron transfer to MM1854. An electron transfer system of NADPH, spinach NADPH-ferredoxin oxidoreductase, and ferredoxin can also reduce the FMN peaks. Dithiothreitol-reduced MM1854 can transfer electrons to dihydromethanopterin
Products: -
Products: -
?
additional information
?
-
-
Substrates: NAD(P)H is incapable of directly reducing the flavin cofactor, but dithionite eliminates the FMN peaks, indicating successful electron transfer to MM1854. An electron transfer system of NADPH, spinach NADPH-ferredoxin oxidoreductase, and ferredoxin can also reduce the FMN peaks. Dithiothreitol-reduced MM1854 can transfer electrons to dihydromethanopterin
Products: -
Products: -
?
additional information
?
-
Substrates: NAD(P)H is incapable of directly reducing the flavin cofactor, but dithionite eliminates the FMN peaks, indicating successful electron transfer to MM1854. An electron transfer system of NADPH, spinach NADPH-ferredoxin oxidoreductase, and ferredoxin can also reduce the FMN peaks. Dithiothreitol-reduced MM1854 can transfer electrons to dihydromethanopterin
Products: -
Products: -
?
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
LITERATURE
COMMENTARY
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
5,6,7,8-tetrahydromethanopterin + oxidized acceptor
7,8-dihydromethanopterin + reduced acceptor
Substrates: -
Products: -
Products: -
?
7,8-dihydromethanopterin + FMNH2
5,6,7,8-tetrahydromethanopterin + FMN
Substrates: -
Products: -
Products: -
?
7,8-dihydromethanopterin + reduced acceptor
5,6,7,8-tetrahydromethanopterin + oxidized acceptor
7,8-dihydromethanopterin + reduced ferredoxin
5,6,7,8-tetrahydromethanopterin + ferredoxin
7,8-dihydromethanopterin + reduced acceptor
5,6,7,8-tetrahydromethanopterin + oxidized acceptor
Substrates: the enzyme catalyzes the last step of tetrahydromethanopterin biosynthesis
Products: -
Products: -
?
7,8-dihydromethanopterin + reduced acceptor
5,6,7,8-tetrahydromethanopterin + oxidized acceptor
Substrates: the enzyme catalyzes the last step of tetrahydromethanopterin biosynthesis
Products: -
Products: -
?
7,8-dihydromethanopterin + reduced acceptor
5,6,7,8-tetrahydromethanopterin + oxidized acceptor
Substrates: the enzyme catalyzes the last step of tetrahydromethanopterin biosynthesis
Products: -
Products: -
?
7,8-dihydromethanopterin + reduced acceptor
5,6,7,8-tetrahydromethanopterin + oxidized acceptor
Substrates: the enzyme catalyzes the last step of tetrahydromethanopterin biosynthesis
Products: -
Products: -
?
7,8-dihydromethanopterin + reduced ferredoxin
5,6,7,8-tetrahydromethanopterin + ferredoxin
Substrates: -
Products: -
Products: -
?
7,8-dihydromethanopterin + reduced ferredoxin
5,6,7,8-tetrahydromethanopterin + ferredoxin
Substrates: -
Products: -
Products: -
?
7,8-dihydromethanopterin + reduced ferredoxin
5,6,7,8-tetrahydromethanopterin + ferredoxin
Substrates: -
Products: -
Products: -
?
7,8-dihydromethanopterin + reduced ferredoxin
5,6,7,8-tetrahydromethanopterin + ferredoxin
Substrates: -
Products: -
Products: -
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
FMN
bioinformatic analysis reveals the presence of one FMN-binding site. The purified protein shows an absorbance peaks at 380 and 460 nm, characteristic of oxidized FMN
FMN
the enzyme contains one flavin mononucleotide (FMN)-binding site
FMN
the enzyme contains one flavin mononucleotide (FMN)-binding site
FMN
within a homotrimer, each monomer-monomer interface exhibits an active site with two adjacently bound flavin mononucleotide (FMN) ligands, one deeply buried and tightly bound and one more peripheral. Computational docking suggests that the peripheral site binds either the observed FMN (the electron donor for the overall reaction) or the pterin, H2MPT (the electron acceptor for the overall reaction), in configurations ideal for electron transfer to and from the tightly bound FMN. Analysis of the FMN binding structure in the active site, and kinetics, overview
FMN
DmrB contains 2 FMN molecules on the active site at the monomer-monomer interface. The FMN-1 molecule shows ionic interactions with residues Ser110 and Asn116 along with some non-bonded contacts. The FMN-2 molecule shows ionic contacts with Lys123 and Gln120 and pi-pi stacking with the Tyr85 residue. FMN stabilizes and preserves the secondary and quaternary structure of DmrB against thermal insult
[4Fe-4S]-center
the enzyme contains two iron-sulfur cluster sites
[4Fe-4S]-center
the enzyme contains two iron-sulfur cluster sites
additional information
determination of FMN is the cofactor of DmrB, overview
-
additional information
NAD(P)H is incapable of directly reducing the flavin cofactor, but dithionite eliminates the FMN peaks, indicating successful electron transfer to MJ0208. An electron transfer system of NADPH, spinach NADPH-ferredoxin oxidoreductase, and ferredoxin can also reduce the FMN peaks. Dithiothreitol-reduced MJ0208 can transfer electrons to dihydromethanopterin
-
additional information
-
NAD(P)H is incapable of directly reducing the flavin cofactor, but dithionite eliminates the FMN peaks, indicating successful electron transfer to MJ0208. An electron transfer system of NADPH, spinach NADPH-ferredoxin oxidoreductase, and ferredoxin can also reduce the FMN peaks. Dithiothreitol-reduced MJ0208 can transfer electrons to dihydromethanopterin
-
additional information
NAD(P)H is incapable of directly reducing the flavin cofactor, but dithionite eliminates the FMN peaks, indicating successful electron transfer to MM1854. An electron transfer system of NADPH, spinach NADPH-ferredoxin oxidoreductase, and ferredoxin can also reduce the FMN peaks. Dithiothreitol-reduced MM1854 can transfer electrons to dihydromethanopterin
-
additional information
-
NAD(P)H is incapable of directly reducing the flavin cofactor, but dithionite eliminates the FMN peaks, indicating successful electron transfer to MM1854. An electron transfer system of NADPH, spinach NADPH-ferredoxin oxidoreductase, and ferredoxin can also reduce the FMN peaks. Dithiothreitol-reduced MM1854 can transfer electrons to dihydromethanopterin
-
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Fe2+
Iron-sulfur cluster
Iron-sulfur cluster
bioinformatic analysis reveals the presence of two iron-sulfur cluster sites
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
7 - 7.5
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
22
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
Highest Expressing Human Cell Lines
Cell Line LinksPlease wait a moment until the data is sorted. This message will disappear when the data is sorted.
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
sequence comparisons suggested that the catalytic mechanism is conserved among the bacterial homologues of DmrB and partially conserved in archaeal homologues, where an alternate electron donor is likely used
metabolism
physiological function
metabolism
the enzyme catalyzes the final step of methanopterin biosynthesis
metabolism
the microbial production of methane by methanogenic archaea is dependent on the synthesis of the pterin-containing cofactor tetrahydromethanopterin (H4MPT). The enzyme catalyzing the last step of H4MPT biosynthesis is dihydromethanopterin reductase
metabolism
the microbial production of methane by methanogenic archaea is dependent on the synthesis of the pterin-containing cofactor tetrahydromethanopterin (H4MPT). The enzyme catalyzing the last step of H4MPT biosynthesis is dihydromethanopterin reductase
metabolism
-
the microbial production of methane by methanogenic archaea is dependent on the synthesis of the pterin-containing cofactor tetrahydromethanopterin (H4MPT). The enzyme catalyzing the last step of H4MPT biosynthesis is dihydromethanopterin reductase
-
metabolism
-
the microbial production of methane by methanogenic archaea is dependent on the synthesis of the pterin-containing cofactor tetrahydromethanopterin (H4MPT). The enzyme catalyzing the last step of H4MPT biosynthesis is dihydromethanopterin reductase
-
physiological function
the enzyme catalyzes the last step of tetrahydromethanopterin biosynthesis
physiological function
the enzyme catalyzes the last step of tetrahydromethanopterin biosynthesis
physiological function
dihydromethanopterin reductase (Dmr) is a redox enzyme that plays a key role in generating tetrahydromethanopterin (H4MPT) for use in one-carbon metabolism. DmrB is a bacterial enzyme that reduces dihydromethanopterin (H2MPT) to H4MPT using flavins as the source of reducing equivalents
physiological function
MJ0208 functions as an archaeal dihydromethanopterin reductase (DmrX) and ferredoxin may serve as an electron donor
physiological function
MM1854 functions as an archaeal dihydromethanopterin reductase (DmrX) and ferredoxin may serve as an electron donor
physiological function
-
the enzyme catalyzes the last step of tetrahydromethanopterin biosynthesis
-
physiological function
-
MM1854 functions as an archaeal dihydromethanopterin reductase (DmrX) and ferredoxin may serve as an electron donor
-
physiological function
-
the enzyme catalyzes the last step of tetrahydromethanopterin biosynthesis
-
physiological function
-
MJ0208 functions as an archaeal dihydromethanopterin reductase (DmrX) and ferredoxin may serve as an electron donor
-
Show AA Sequence and Transmembrane Helices (129 entries)
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Please use the AA Sequence and Transmembrane Helices Search for a specific query.
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
homodimer
homotetraicosamer
24 * 22100, His6-tagged enzyme, SDS-PAGE
multimer
enzyme has a didodecamer (24mer) structure consisting of 8 trimeric subunits, cysallization data
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
hanging drop vapor diffusion method, using 0.8-1.2 M ammonium sulfate as precipitant
purified recombinant N-terminally His6 -tagged enzyme by hanging drop vapor diffusion method, mixing of 0.003 ml of 13 mg/ml protein in 20 mM Tris-HCl, pH 8.0, 100 mM NaCl, 5% glycerol, and 4 mM DTT, with reservori solution containing FMN, method optimization, 7-14 days at room temperature, X-ray diffraction structure determination and analysis at 1.9 A resolution
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
100
55
apo-form of DmrB retains the secondary structure till 55°C
84
holo-form of DmrB retains the secondary structure till a temperature of 84°C
100
purified recombinant His-tagged enzyme, pH 7.0, 15 min, inactivation
100
purified recombinant His-tagged enzyme, pH 7.0, 15 min, inactivation
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GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
labile when exposed to cold storage at 4°C and 20°C or liquid nitrogen temperatures
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His6-tagged enzyme from Escherichia col strain BE100 [BL21(DE3) RIL] in an anaerobic chamber by heat treatement at 65°C for 5 min, the supernatant is a second time heat treated at 85°C for 15 min,
recombinant His6-tagged enzyme from Escherichia coli strain BE100 [BL21(DE3) RIL] in an anaerobic chamber by nickel affinity chromatography, ultrafiltration, and gel filtration
recombinant N-terminally His6 -tagged enzyme from Escherichia coli strain BL21DE3 RIL cell-free extract by nickel affinity chromatography and gel filtration
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
gene dmrB, recombinant expression of N-terminally His6 -tagged enzyme in Escherichia coli strain BL21DE3 RIL
gene dmrX, recombinant expression of His6-tagged enzyme in Escherichia coli strain BE100 [BL21(DE3) RIL]
gene dmrX, recombinant expression of the codon-optimized gene encoding His6-tagged enzyme in Escherichia col strain BE100 [BL21(DE3) RIL]
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RENATURED/Commentary
ORGANISM
UNIPROT
LITERATURE
enzyme displays a concentration-dependant self-assembly which is mediated by ionic interactions. The cofactor FMN stabilizes and preserves the secondary and quaternary structure of DmrB against thermal insult
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Wang, S.; Tiongson, J.; Rasche, M.E.
Discovery and characterization of the first archaeal dihydromethanopterin reductase, an iron-sulfur flavoprotein from Methanosarcina mazei
J. Bacteriol.
196
203-209
2014
Methanocaldococcus jannaschii (Q57661), Methanocaldococcus jannaschii, Methanocaldococcus jannaschii DSM 2661 (Q57661), Methanosarcina mazei (Q8PVV3), Methanosarcina mazei, Methanosarcina mazei DSM 3647 (Q8PVV3)
brenda
Wang, S.; Tiongson, J.; Rasche, M.E.
Discovery and characterization of the first archaeal dihydromethanopterin reductase, an iron-sulfur flavoprotein from Methanosarcina mazei
J. Bacteriol.
196
203-209
2014
Methanocaldococcus jannaschii (Q57661), Methanocaldococcus jannaschii, Methanocaldococcus jannaschii DSM 2661 (Q57661), Methanosarcina mazei (Q8PVV3), Methanosarcina mazei, Methanosarcina mazei DSM 3647 (Q8PVV3)
brenda
McNamara, D.E.; Cascio, D.; Jorda, J.; Bustos, C.; Wang, T.C.; Rasche, M.E.; Yeates, T.O.; Bobik, T.A.
Structure of dihydromethanopterin reductase, a cubic protein cage for redox transfer
J. Biol. Chem.
289
8852-8864
2014
Paraburkholderia xenovorans (Q13QT8)
brenda
Garg, A.; Sinha, S.
Factors deciding the assembly and thermostability of the DmrB cage
Int. J. Biol. Macromol.
182
959-967
2021
Paraburkholderia xenovorans (Q13QT8)
brenda
EXTERNAL LINKS (specific for EC-Number 1.5.99.15)
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Release 2023.1 (January 2023)
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