4KCF

X-ray Structure of a KijD3 in Complex with FMN and dTDP-3-amino-2,3,6-trideoxy-4-keto-3-methyl-D-glucose

Summary for 4KCF

• Entry DOI: 10.2210/pdb4kcf/pdb
• Related: 3M9V
• Descriptor: FAD-dependent oxidoreductase, [(2R,4S,6R)-4-azanyl-4,6-dimethyl-5,5-bis(oxidanyl)oxan-2-yl] [[(2R,3S,5R)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] hydrogen phosphate, FLAVIN MONONUCLEOTIDE, ... (4 entities in total)
• Functional Keywords: kijd3, fatty acyl-coa dehydrogenase family, kijanose, kijanimicin, fad, flavoprotein, oxidoreductase, class d flavin containing monooxygenases, n-oxygenase, nucleotide linked sugar, dtdp-3-amino-2, 3, 6-trideoxy-4-keto-3-methyl-d-glucose, fmn
• Biological source: Actinomadura kijaniata
• Total number of polymer chains: 1
• Total formula weight: 49345.13

Authors

Holden, H.M.,Thoden, J.B.,Branch, M.C.,Zimmer, A.L.,Bruender, N.A. (deposition date: 2013-04-24, release date: 2013-05-22, Last modification date: 2023-09-20)

Primary citation

Thoden, J.B.,Branch, M.C.,Zimmer, A.L.,Bruender, N.A.,Holden, H.M.
Active site architecture of a sugar N-oxygenase.
Biochemistry, 52:3191-3193, 2013

PubMed Abstract: KijD3 is a flavin-dependent N-oxygenase implicated in the formation of the nitro-containing sugar d-kijanose, found attached to the antibiotic kijanimicin. For this investigation, the structure of KijD3 in complex with FMN and its dTDP-sugar substrate was solved to 2.1 Å resolution. In contrast to the apoenzyme structure, the C-terminus of the protein becomes ordered and projects into the active site cleft [Bruender, N. A., Thoden, J. B., and Holden, H. M. (2010) Biochemistry 49, 3517-3524]. The amino group of the dTDP-aminosugar that is oxidized is located 4.9 Å from C4a of the flavin ring. The model provides a molecular basis for understanding the manner in which KijD3 catalyzes its unusual chemical transformation.

PubMed: 23621882
DOI: 10.1021/bi400407x

Experimental method

X-RAY DIFFRACTION (2.098 Å)