Literature summary for 1.14.13.187 extracted from

Sartor, L.; Ibarra, C.; Al-Mestarihi, A.; Bachmann, B.O.; Vey, J.L.
Structure of DnmZ, a nitrososynthase in the Streptomyces peucetius anthracycline biosynthetic pathway (2015), Acta Crystallogr. Sect. F, 71, 1205-1214 .

Search for more literature for 1.14.13.187

Crystallization (Commentary)

Crystallization (Comment)	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

Crystallization (Comment)

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	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
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	Comment	Textmining
Streptomyces peucetius	A0A0R4I990	-	-

Reaction

Reaction	Comment	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	a

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
dTDP-beta-L-evernosamine + 2 NADPH + 2 H+ + 2 O2	overall reaction	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	Streptomyces peucetius	?	-	?

Subunits

Subunits	Comment	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	Comment	Organism
DnmZ	-	Streptomyces peucetius

Cofactor

Cofactor	Comment	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

General Information

General Information	Comment	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