BRENDA - Enzyme Database
show all sequences of 1.14.13.187

Structure of DnmZ, a nitrososynthase in the Streptomyces peucetius anthracycline biosynthetic pathway

Sartor, L.; Ibarra, C.; Al-Mestarihi, A.; Bachmann, B.O.; Vey, J.L.; Acta Crystallogr. Sect. F 71, 1205-1214 (2015)

Data extracted from this reference:

Crystallization (Commentary)
Crystallization (Commentary)
Organism
purified enzyme, hanging drop vapor diffusion method, mixing of 0.001 ml protein solution containing 6 mg/ml of protein DnmZ with 0.001 ml crystallization solution containing 0.05 M glycine pH 9.5, 0.2 M ammonium sulfate, 10% w/v, and PEG 4000, and equilibration against 0.75 ml crystallization solution, 26°C, X-ray diffraction structure determination and analysis at 2.74-3.0 A resolution, molecular replacement using crystal structure PDB ID 3mxl as search model. Cocrystallization of DnmZ complexed with dTDP-L-epi-vancosamine, FAD, FMN or combinations of the amino sugar and flavin are unsuccessful
Streptomyces peucetius
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
ID
dTDP-beta-L-evernosamine + 2 NADPH + 2 H+ + 2 O2
Streptomyces peucetius
overall reaction
dTDP-2,3,6-trideoxy-3-C-methyl-4-O-methyl-3-nitroso-beta-L-arabino-hexopyranose + 2 NADP+ + 3 H2O
-
-
?
Organism
Organism
UniProt
Commentary
Textmining
Streptomyces peucetius
A0A0R4I990
-
-
Reaction
Reaction
Commentary
Organism
Reaction ID
dTDP-beta-L-evernosamine + 2 NADPH + 2 H+ + 2 O2 = dTDP-2,3,6-trideoxy-3-C-methyl-4-O-methyl-3-nitroso-beta-L-arabino-hexopyranose + 2 NADP+ + 3 H2O
reaction mechanism, overview. Once formed, the product undergoes retro oxime-aldol cleavage at the C3'-C40'bond before incorporation into baumycin
Streptomyces peucetius
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
Substrate Product ID
dTDP-beta-L-evernosamine + 2 NADPH + 2 H+ + 2 O2
overall reaction
743958
Streptomyces peucetius
dTDP-2,3,6-trideoxy-3-C-methyl-4-O-methyl-3-nitroso-beta-L-arabino-hexopyranose + 2 NADP+ + 3 H2O
-
-
-
?
additional information
thymine is recognized by interactions between the C4 carbonyl O atom and Arg332, and between both N3 and the C4 carbonyl O atom and a water molecule that hydrogen-bonds to the backbone carbonyl of Ala322. The ribose 3' hydroxyl group is hydrogen-bonded by Glu117, which is suitably positioned to form a salt bridge with Arg243. The dTDP diphosphate makes no apparent interactions with the protein
743958
Streptomyces peucetius
?
-
-
-
?
Subunits
Subunits
Commentary
Organism
More
enzyme DnmZ adopts a tetrameric ACAD quaternary fold. The site of catalysis, where the substrate deoxy amino sugar and flavin isoalloxazine come into contact, is centrally located, it is located directly adjacent to a loop containing two tandem cis-peptide bonds (residues His387-Tyr389) that connects helices alpha9 and alpha10. The cis-peptide loop is a unique feature of the nitrososynthases
Streptomyces peucetius
tetramer
dTDP-DnmZ tetramer, crystal structure analysis
Streptomyces peucetius
Synonyms
Synonyms
Commentary
Organism
DnmZ
-
Streptomyces peucetius
Cofactor
Cofactor
Commentary
Organism
Structure
FMN
the predicted flavin-binding site is formed by residues emanating from all three DnmZ domains and the loop connecting alpha8 and alpha9 from a neighboring chain. Numerous nonpolar amino-acid side chains form a hydrophobic pocket that can accommodate the dimethylbenzene portion of the flavin cofactor. A hydrogen-bonding network including Ser174, Ser223, Ser225 and Trp215 holds the protein surface in the correct conformation to allow hydrogenbonding interactions with the flavin isoalloxazine, including a hydrogen bond between the flavin N5 atom and Ser174. This interaction is conserved in the flavin monooxygenases and is thought to play a role in stabilizing the hydroperoxyflavin intermediate
Streptomyces peucetius
NADPH
-
Streptomyces peucetius
Cofactor (protein specific)
Cofactor
Commentary
Organism
Structure
FMN
the predicted flavin-binding site is formed by residues emanating from all three DnmZ domains and the loop connecting alpha8 and alpha9 from a neighboring chain. Numerous nonpolar amino-acid side chains form a hydrophobic pocket that can accommodate the dimethylbenzene portion of the flavin cofactor. A hydrogen-bonding network including Ser174, Ser223, Ser225 and Trp215 holds the protein surface in the correct conformation to allow hydrogenbonding interactions with the flavin isoalloxazine, including a hydrogen bond between the flavin N5 atom and Ser174. This interaction is conserved in the flavin monooxygenases and is thought to play a role in stabilizing the hydroperoxyflavin intermediate
Streptomyces peucetius
NADPH
-
Streptomyces peucetius
Crystallization (Commentary) (protein specific)
Crystallization
Organism
purified enzyme, hanging drop vapor diffusion method, mixing of 0.001 ml protein solution containing 6 mg/ml of protein DnmZ with 0.001 ml crystallization solution containing 0.05 M glycine pH 9.5, 0.2 M ammonium sulfate, 10% w/v, and PEG 4000, and equilibration against 0.75 ml crystallization solution, 26°C, X-ray diffraction structure determination and analysis at 2.74-3.0 A resolution, molecular replacement using crystal structure PDB ID 3mxl as search model. Cocrystallization of DnmZ complexed with dTDP-L-epi-vancosamine, FAD, FMN or combinations of the amino sugar and flavin are unsuccessful
Streptomyces peucetius
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
ID
dTDP-beta-L-evernosamine + 2 NADPH + 2 H+ + 2 O2
Streptomyces peucetius
overall reaction
dTDP-2,3,6-trideoxy-3-C-methyl-4-O-methyl-3-nitroso-beta-L-arabino-hexopyranose + 2 NADP+ + 3 H2O
-
-
?
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
ID
dTDP-beta-L-evernosamine + 2 NADPH + 2 H+ + 2 O2
overall reaction
743958
Streptomyces peucetius
dTDP-2,3,6-trideoxy-3-C-methyl-4-O-methyl-3-nitroso-beta-L-arabino-hexopyranose + 2 NADP+ + 3 H2O
-
-
-
?
additional information
thymine is recognized by interactions between the C4 carbonyl O atom and Arg332, and between both N3 and the C4 carbonyl O atom and a water molecule that hydrogen-bonds to the backbone carbonyl of Ala322. The ribose 3' hydroxyl group is hydrogen-bonded by Glu117, which is suitably positioned to form a salt bridge with Arg243. The dTDP diphosphate makes no apparent interactions with the protein
743958
Streptomyces peucetius
?
-
-
-
?
Subunits (protein specific)
Subunits
Commentary
Organism
More
enzyme DnmZ adopts a tetrameric ACAD quaternary fold. The site of catalysis, where the substrate deoxy amino sugar and flavin isoalloxazine come into contact, is centrally located, it is located directly adjacent to a loop containing two tandem cis-peptide bonds (residues His387-Tyr389) that connects helices alpha9 and alpha10. The cis-peptide loop is a unique feature of the nitrososynthases
Streptomyces peucetius
tetramer
dTDP-DnmZ tetramer, crystal structure analysis
Streptomyces peucetius
General Information
General Information
Commentary
Organism
metabolism
in the anthracycline biosynthetic pathway, the enzyme's specific role involves the synthesis of the seven-carbon acetal moiety attached to C4 of l-daunosamine observed in the anthracycline baumycin
Streptomyces peucetius
additional information
enzyme structure and active site structure analysis, overview
Streptomyces peucetius
physiological function
DnmZ is an N-hydroxylating flavin monooxygenase and a nitrososynthase that catalyzes the oxidation of the exocyclic amine of the sugar nucleotide dTDP-L-epi-vancosamine to its nitroso form. Its specific role in the anthracycline biosynthetic pathway involves the synthesis of the seven-carbon acetal moiety attached to C4 of l-daunosamine observed in the anthracycline baumycin
Streptomyces peucetius
General Information (protein specific)
General Information
Commentary
Organism
metabolism
in the anthracycline biosynthetic pathway, the enzyme's specific role involves the synthesis of the seven-carbon acetal moiety attached to C4 of l-daunosamine observed in the anthracycline baumycin
Streptomyces peucetius
additional information
enzyme structure and active site structure analysis, overview
Streptomyces peucetius
physiological function
DnmZ is an N-hydroxylating flavin monooxygenase and a nitrososynthase that catalyzes the oxidation of the exocyclic amine of the sugar nucleotide dTDP-L-epi-vancosamine to its nitroso form. Its specific role in the anthracycline biosynthetic pathway involves the synthesis of the seven-carbon acetal moiety attached to C4 of l-daunosamine observed in the anthracycline baumycin
Streptomyces peucetius
Other publictions for EC 1.14.13.187
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)
743958
Sartor
Structure of DnmZ, a nitrosos ...
Streptomyces peucetius
Acta Crystallogr. Sect. F
71
1205-1214
2015
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727686
Al-Mestarihi
Nitrososynthase-triggered oxid ...
Streptomyces peucetius
J. Am. Chem. Soc.
135
11457-11460
2013
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728170
Li
MD and QM/MM study on catalyti ...
Micromonospora sp., Micromonospora sp. ATCC 39149
J. Mol. Graph. Model.
44
9-16
2013
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726951
Vey
Structure and mechanism of ORF ...
Micromonospora carbonacea, Micromonospora carbonacea ATCC 39149
Biochemistry
49
9306-9317
2010
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725191
Hu
A unifying nitrososynthase inv ...
Micromonospora carbonacea, Micromonospora carbonacea var. africana
J. Am. Chem. Soc.
130
15756-15757
2008
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