PDBsum entry 2olo

Oxidoreductase

PDB id

2olo

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Contents

			Protein chain

					393 a.a. *

			Ligands

					FAD


					6PC


					MPD ×2

			Waters ×250

* Residue conservation analysis

PDB id:

2olo

Links

Name:

Oxidoreductase

Title:

Nikd, an unusual amino acid oxidase essential for nikkomycin biosynthesis: open form at 1.9a resolution

Structure:

Nikd protein. Chain: a. Engineered: yes. Other_details: open form

Source:

Streptomyces tendae. Organism_taxid: 1932. Strain: tu501. Gene: nikd. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.90Å

R-factor:

0.184

R-free:

0.212

Authors:

C.J.Carrell,R.C.Bruckner,D.Venci,G.Zhao,M.S.Jorns,F.S.Mathews

Key ref:

C.J.Carrell et al. (2007). NikD, an unusual amino acid oxidase essential for nikkomycin biosynthesis: structures of closed and open forms at 1.15 and 1.90 A resolution. Structure, 15, 928-941. PubMed id: 17697998

Date:

19-Jan-07

Release date:

31-Jul-07

PROCHECK

	Headers

	References

Protein chain

Q9X9P9 (Q9X9P9_STRTE) - NikD protein from Streptomyces tendae

Seq: Struc:					389 a.a. 393 a.a.

Key:

PfamA domain

Secondary structure

CATH domain

	Structure 15:928-941 (2007)
PubMed id: 17697998

NikD, an unusual amino acid oxidase essential for nikkomycin biosynthesis: structures of closed and open forms at 1.15 and 1.90 A resolution.
C.J.Carrell, R.C.Bruckner, D.Venci, G.Zhao, M.S.Jorns, F.S.Mathews.

ABSTRACT

NikD is an unusual amino-acid-oxidizing enzyme that contains covalently bound FAD, catalyzes a 4-electron oxidation of piperideine-2-carboxylic acid to picolinate, and plays a critical role in the biosynthesis of nikkomycin antibiotics. Crystal structures of closed and open forms of nikD, a two-domain enzyme, have been determined to resolutions of 1.15 and 1.9 A, respectively. The two forms differ by an 11 degrees rotation of the catalytic domain with respect to the FAD-binding domain. The active site is inaccessible to solvent in the closed form; an endogenous ligand, believed to be picolinate, is bound close to and parallel with the flavin ring, an orientation compatible with redox catalysis. The active site is solvent accessible in the open form, but the picolinate ligand is approximately perpendicular to the flavin ring and a tryptophan is stacked above the flavin ring. NikD also contains a mobile cation binding loop.

Literature references that cite this PDB file's key reference

PubMed id

Reference

20577996

M.Moon, and S.G.Van Lanen (2010).
Characterization of a dual specificity aryl acid adenylation enzyme with dual function in nikkomycin biosynthesis.

Biopolymers, 93, 791-801.

20353187

M.S.Jorns, Z.W.Chen, and F.S.Mathews (2010).
Structural characterization of mutations at the oxygen activation site in monomeric sarcosine oxidase .

Biochemistry, 49, 3631-3639.

PDB codes:

3m0o 3m12 3m13

19651103

P.F.Fitzpatrick (2010).
Oxidation of amines by flavoproteins.

Arch Biochem Biophys, 493, 13-25.

19438712

D.P.Heuts, N.S.Scrutton, W.S.McIntire, and M.W.Fraaije (2009).
What's in a covalent bond? On the role and formation of covalently bound flavin cofactors.

FEBS J, 276, 3405-3427.

19702312

P.R.Kommoju, R.C.Bruckner, P.Ferreira, C.J.Carrell, F.S.Mathews, and M.S.Jorns (2009).
Factors that affect oxygen activation and coupling of the two redox cycles in the aromatization reaction catalyzed by NikD, an unusual amino acid oxidase.

Biochemistry, 48, 9542-9555.

PDB code:

3hzl

19530706

P.R.Kommoju, R.C.Bruckner, P.Ferreira, and M.S.Jorns (2009).
Probing the role of active site residues in NikD, an unusual amino acid oxidase that catalyzes an aromatization reaction important in nikkomycin biosynthesis.

Biochemistry, 48, 6951-6962.

19354202

R.C.Bruckner, and M.S.Jorns (2009).
Spectral and kinetic characterization of intermediates in the aromatization reaction catalyzed by NikD, an unusual amino acid oxidase.

Biochemistry, 48, 4455-4465.

19233844

W.Chen, T.Huang, X.He, Q.Meng, D.You, L.Bai, J.Li, M.Wu, R.Li, Z.Xie, H.Zhou, X.Zhou, H.Tan, and Z.Deng (2009).
Characterization of the polyoxin biosynthetic gene cluster from Streptomyces cacaoi and engineered production of polyoxin H.

J Biol Chem, 284, 10627-10638.

18693755

G.Zhao, R.C.Bruckner, and M.S.Jorns (2008).
Identification of the oxygen activation site in monomeric sarcosine oxidase: role of Lys265 in catalysis.

Biochemistry, 47, 9124-9135.

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.