ISDA: 4KCF

Deposition Date 2013-04-24

Release Date 2013-05-22

Last Version Date 2023-09-20

Entry Detail

PDB ID:

4KCF

Keywords:

OXIDOREDUCTASE

Title:

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

Biological Source:

Source Organism:

Actinomadura kijaniata (Taxon ID: 46161)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.10 Å

R-Value Free:

0.22

R-Value Work:

0.17

R-Value Observed:

0.17

Space Group:

I 2 2 2

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Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:FAD-dependent oxidoreductase
Gene (Uniprot):KijD3
Chain IDs:A
Chain Length:454
Number of Molecules:1
Biological Source:Actinomadura kijaniata

UniProt ID:B3TMR1 Pfam ID:PF02771, PF02770, PF00441, PF08028

Ligand Molecules

AKM

FMN

Primary Citation

Active site architecture of a sugar N-oxygenase.

Thoden, J.B, Branch, M.C, Zimmer, A.L, Bruender, N.A, Holden, H.M.Show

Biochemistry 52 3191 3193 (2013)

PMID: 23621882 DOI: 10.1021/bi400407x

Abstact

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.

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