BRENDA - Enzyme Database
show all sequences of 1.5.99.15

Structure of dihydromethanopterin reductase, a cubic protein cage for redox transfer

McNamara, D.E.; Cascio, D.; Jorda, J.; Bustos, C.; Wang, T.C.; Rasche, M.E.; Yeates, T.O.; Bobik, T.A.; J. Biol. Chem. 289, 8852-8864 (2014)

Data extracted from this reference:

Cloned(Commentary)
Cloned (Commentary)
Organism
expressed in Escherichia coli BL21 (DE3)-RIL cells
Paraburkholderia xenovorans
gene dmrB, recombinant expression of N-terminally His6 -tagged enzyme in Escherichia coli strain BL21DE3 RIL
Paraburkholderia xenovorans
Crystallization (Commentary)
Crystallization (Commentary)
Organism
hanging drop vapor diffusion method, using 0.8-1.2 M ammonium sulfate as precipitant
Paraburkholderia xenovorans
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
Paraburkholderia xenovorans
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
ID
5,6,7,8-tetrahydromethanopterin + oxidized acceptor
Paraburkholderia xenovorans
-
7,8-dihydromethanopterin + reduced acceptor
-
-
?
7,8-dihydromethanopterin + FMNH2
Paraburkholderia xenovorans
-
5,6,7,8-tetrahydromethanopterin + FMN
-
-
?
Organism
Organism
UniProt
Commentary
Textmining
Paraburkholderia xenovorans
Q13QT8
-
-
Purification (Commentary)
Purification (Commentary)
Organism
HisTrap column chromatography and S200 gel filtration
Paraburkholderia xenovorans
recombinant N-terminally His6 -tagged enzyme from Escherichia coli strain BL21DE3 RIL cell-free extract by nickel affinity chromatography and gel filtration
Paraburkholderia xenovorans
Reaction
Reaction
Commentary
Organism
Reaction ID
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
Paraburkholderia xenovorans
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
Substrate Product ID
5,6,7,8-tetrahydromethanopterin + oxidized acceptor
-
742870
Paraburkholderia xenovorans
7,8-dihydromethanopterin + reduced acceptor
-
-
-
?
7,8-dihydromethanopterin + FMNH2
-
742870
Paraburkholderia xenovorans
5,6,7,8-tetrahydromethanopterin + FMN
-
-
-
?
7,8-dihydromethanopterin + FMNH2
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
742870
Paraburkholderia xenovorans
5,6,7,8-tetrahydromethanopterin + FMN
-
-
-
?
Subunits
Subunits
Commentary
Organism
homotetraicosamer
24 * 22100, His6-tagged enzyme, SDS-PAGE
Paraburkholderia xenovorans
homotrimer
enzyme crystal structure analysis
Paraburkholderia xenovorans
Synonyms
Synonyms
Commentary
Organism
dihydromethanopterin reductase
-
Paraburkholderia xenovorans
Dmr
-
Paraburkholderia xenovorans
DmrB
-
Paraburkholderia xenovorans
H2MPT reductase
-
Paraburkholderia xenovorans
Cofactor
Cofactor
Commentary
Organism
Structure
FMN
-
Paraburkholderia xenovorans
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
Paraburkholderia xenovorans
additional information
determination of FMN is the cofactor of DmrB, overview
Paraburkholderia xenovorans
Cloned(Commentary) (protein specific)
Commentary
Organism
expressed in Escherichia coli BL21 (DE3)-RIL cells
Paraburkholderia xenovorans
gene dmrB, recombinant expression of N-terminally His6 -tagged enzyme in Escherichia coli strain BL21DE3 RIL
Paraburkholderia xenovorans
Cofactor (protein specific)
Cofactor
Commentary
Organism
Structure
FMN
-
Paraburkholderia xenovorans
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
Paraburkholderia xenovorans
additional information
determination of FMN is the cofactor of DmrB, overview
Paraburkholderia xenovorans
Crystallization (Commentary) (protein specific)
Crystallization
Organism
hanging drop vapor diffusion method, using 0.8-1.2 M ammonium sulfate as precipitant
Paraburkholderia xenovorans
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
Paraburkholderia xenovorans
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
ID
5,6,7,8-tetrahydromethanopterin + oxidized acceptor
Paraburkholderia xenovorans
-
7,8-dihydromethanopterin + reduced acceptor
-
-
?
7,8-dihydromethanopterin + FMNH2
Paraburkholderia xenovorans
-
5,6,7,8-tetrahydromethanopterin + FMN
-
-
?
Purification (Commentary) (protein specific)
Commentary
Organism
HisTrap column chromatography and S200 gel filtration
Paraburkholderia xenovorans
recombinant N-terminally His6 -tagged enzyme from Escherichia coli strain BL21DE3 RIL cell-free extract by nickel affinity chromatography and gel filtration
Paraburkholderia xenovorans
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
ID
5,6,7,8-tetrahydromethanopterin + oxidized acceptor
-
742870
Paraburkholderia xenovorans
7,8-dihydromethanopterin + reduced acceptor
-
-
-
?
7,8-dihydromethanopterin + FMNH2
-
742870
Paraburkholderia xenovorans
5,6,7,8-tetrahydromethanopterin + FMN
-
-
-
?
7,8-dihydromethanopterin + FMNH2
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
742870
Paraburkholderia xenovorans
5,6,7,8-tetrahydromethanopterin + FMN
-
-
-
?
Subunits (protein specific)
Subunits
Commentary
Organism
homotetraicosamer
24 * 22100, His6-tagged enzyme, SDS-PAGE
Paraburkholderia xenovorans
homotrimer
enzyme crystal structure analysis
Paraburkholderia xenovorans
General Information
General Information
Commentary
Organism
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
Paraburkholderia xenovorans
metabolism
the enzyme catalyzes the final step of methanopterin biosynthesis
Paraburkholderia xenovorans
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
Paraburkholderia xenovorans
General Information (protein specific)
General Information
Commentary
Organism
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
Paraburkholderia xenovorans
metabolism
the enzyme catalyzes the final step of methanopterin biosynthesis
Paraburkholderia xenovorans
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
Paraburkholderia xenovorans
Other publictions for EC 1.5.99.15
No.
1st author
Pub Med
title
organims
journal
volume
pages
year
Activating Compound
Application
Cloned(Commentary)
Crystallization (Commentary)
Engineering
General Stability
Inhibitors
KM Value [mM]
Localization
Metals/Ions
Molecular Weight [Da]
Natural Substrates/ Products (Substrates)
Organic Solvent Stability
Organism
Oxidation Stability
Posttranslational Modification
Purification (Commentary)
Reaction
Renatured (Commentary)
Source Tissue
Specific Activity [micromol/min/mg]
Storage Stability
Substrates and Products (Substrate)
Subunits
Synonyms
Temperature Optimum [°C]
Temperature Range [°C]
Temperature Stability [°C]
Turnover Number [1/s]
pH Optimum
pH Range
pH Stability
Cofactor
Ki Value [mM]
pI Value
IC50 Value
Activating Compound (protein specific)
Application (protein specific)
Cloned(Commentary) (protein specific)
Cofactor (protein specific)
Crystallization (Commentary) (protein specific)
Engineering (protein specific)
General Stability (protein specific)
IC50 Value (protein specific)
Inhibitors (protein specific)
Ki Value [mM] (protein specific)
KM Value [mM] (protein specific)
Localization (protein specific)
Metals/Ions (protein specific)
Molecular Weight [Da] (protein specific)
Natural Substrates/ Products (Substrates) (protein specific)
Organic Solvent Stability (protein specific)
Oxidation Stability (protein specific)
Posttranslational Modification (protein specific)
Purification (Commentary) (protein specific)
Renatured (Commentary) (protein specific)
Source Tissue (protein specific)
Specific Activity [micromol/min/mg] (protein specific)
Storage Stability (protein specific)
Substrates and Products (Substrate) (protein specific)
Subunits (protein specific)
Temperature Optimum [°C] (protein specific)
Temperature Range [°C] (protein specific)
Temperature Stability [°C] (protein specific)
Turnover Number [1/s] (protein specific)
pH Optimum (protein specific)
pH Range (protein specific)
pH Stability (protein specific)
pI Value (protein specific)
Expression
General Information
General Information (protein specific)
Expression (protein specific)
KCat/KM [mM/s]
KCat/KM [mM/s] (protein specific)
727782
Wang
Discovery and characterization ...
Methanocaldococcus jannaschii, Methanosarcina mazei, Methanosarcina mazei DSM 3647, Methanocaldococcus jannaschii DSM 2661
J. Bacteriol.
196
203-209
2014
-
-
2
-
-
1
-
-
-
2
1
4
-
17
-
-
2
-
-
-
-
1
8
1
4
-
-
-
-
-
-
-
2
-
-
-
-
-
2
2
-
-
1
-
-
-
-
-
2
1
4
-
-
-
2
-
-
-
1
8
1
-
-
-
-
-
-
-
-
-
2
2
-
-
-
742781
Wang
Discovery and characterizatio ...
Methanocaldococcus jannaschii, Methanosarcina mazei, Methanosarcina mazei DSM 3647, Methanocaldococcus jannaschii DSM 2661
J. Bacteriol.
196
203-209
2014
-
-
2
-
-
-
-
-
-
2
-
4
-
17
-
-
2
-
-
-
-
-
8
1
9
2
-
2
-
2
-
-
8
-
-
-
-
-
2
8
-
-
-
-
-
-
-
-
2
-
4
-
-
-
2
-
-
-
-
8
1
2
-
2
-
2
-
-
-
-
4
4
-
-
-
742870
McNamara
Structure of dihydromethanopt ...
Paraburkholderia xenovorans
J. Biol. Chem.
289
8852-8864
2014
-
-
2
2
-
-
-
-
-
-
-
2
-
1
-
-
2
1
-
-
-
-
3
2
4
-
-
-
-
-
-
-
3
-
-
-
-
-
2
3
2
-
-
-
-
-
-
-
-
-
2
-
-
-
2
-
-
-
-
3
2
-
-
-
-
-
-
-
-
-
3
3
-
-
-