PDBsum entry 1v4b

Oxidoreductase

PDB id: 1v4b

Contents

Protein chain

197 a.a. *

Ligands

FMN

EDO

IPA

Waters ×140

* Residue conservation analysis

PDB id:

1v4b

Name:

Oxidoreductase

Title:

The crystal structure of azor (azo reductase) from escherichia coli: oxidized form

Structure:

Nadh-azoreductase, fmn-dependent. Chain: a. Synonym: azo reductase, azor. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PDB file)

Resolution:

1.80Å R-factor: 0.194 R-free: 0.234

Authors:

K.Ito,M.Tanokura

Key ref:

K.Ito et al. (2006). Three-dimensional structure of AzoR from Escherichia coli. An oxidereductase conserved in microorganisms. J Biol Chem, 281, 20567-20576. PubMed id: 16684776 DOI: 10.1074/jbc.M513345200

Date:

12-Nov-03 Release date: 18-Jan-05

Protein chain

P41407  (AZOR_ECOLI) -  FMN-dependent NADH:quinone oxidoreductase from Escherichia coli (strain K12)

Seq: 201 a.a.

Struc: 197 a.a.

Enzyme reactions

• Enzyme class 2: E.C.1.6.5.- - ?????
• Enzyme class 3: E.C.1.7.1.17 - FMN-dependent NADH-azoreductase.
• Reaction: N,N-dimethyl-1,4-phenylenediamine + anthranilate + 2 NAD⁺ = 2-(4-dimethylaminophenyl)diazenylbenzoate + 2 NADH + 2 H⁺
• Cofactor: FMN

FMN (Bound ligand (Het Group name = FMN) corresponds exactly)

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1074/jbc.M513345200

J Biol Chem 281:20567-20576 (2006)

PubMed id: 16684776

Three-dimensional structure of AzoR from Escherichia coli. An oxidereductase conserved in microorganisms.

K.Ito, M.Nakanishi, W.C.Lee, H.Sasaki, S.Zenno, K.Saigo, Y.Kitade, M.Tanokura.

ABSTRACT

The crystal structure of AzoR (azoreductase) has been determined in complex with FMN for two different crystal forms at 1.8 and 2.2 A resolution. AzoR is an oxidoreductase isolated from Escherichia coli as a protein responsible for the degradation of azo compounds. This enzyme is an FMN-dependent NADH-azoreductase and catalyzes the reductive cleavage of azo groups by a ping-pong mechanism. The structure suggests that AzoR acts in a homodimeric state forming the two identical catalytic sites to which both monomers contribute. The structure revealed that each monomer of AzoR has a flavodoxin-like structure, without the explicit overall amino acid sequence homology. Superposition of the structures from the two different crystal forms revealed the conformational change and suggested a mechanism for accommodating substrates of different size. Furthermore, comparison of the active site structure with that of NQO1 complexed with substrates provides clues to the possible substrate-binding mechanism of AzoR.

Selected figure(s)

Figure 2.
FIGURE 2. Interactions between FMN and amino acid residues in the active site. a, schematic diagram showing contacts of the FMN cofactor to amino acid residues. Hydrogen bonds are shown as broken green lines (red residue numbers) and van der Waals' interactions by red shading (black residue numbers). Each atom element is represented by a sphere of different colors with a chemical symbol. b, SIGMAA-weighted 2mF[o] - DF[c] electron density maps surrounding the FMN. The map was calculated using the data of P4[2]2[1]2 crystal structure and is contoured at 1.2 . c, the electrostatic potential of AzoR is mapped onto the solvent-accessible surface, as calculated with GRASP. The FMN molecules shown in a and b are represented by a stick model, with color coding identical to that in Fig. 1.

Figure 5.
FIGURE 5. Comparison of the active site of AzoR with that of NQO1. One active site is shown for each of AzoR (a) and rat NQO1 (b) (Protein Data Bank accession code 1QRD). The flavin cofactors, duroquinone, and the side chains of conserved amino acid residues in both enzymes are represented by a stick model, with carbon atoms in gray, oxygen atoms in red, nitrogen atoms in blue, and phosphorous atoms in orange. The polypeptide moieties of one subunit for each enzyme are drawn as C traces in yellow and green.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 20567-20576) copyright 2006.

Figures were selected by an automated process.