PDBsum entry 1vfr

Oxidoreductase

PDB id: 1vfr

Contents

Protein chains

217 a.a. *

Ligands

FMN ×2

Waters ×183

* Residue conservation analysis

PDB id:

1vfr

Name:

Oxidoreductase

Title:

The major NAD(p)h:fmn oxidoreductase from vibrio fischeri

Structure:

NAD(p)h\:fmn oxidoreductase. Chain: a, b. Synonym: frase i, fmn reductase. Engineered: yes

Source:

Aliivibrio fischeri. Organism_taxid: 668. Atcc: atcc 7744. Collection: atcc 7744. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PDB file)

Resolution:

1.80Å R-factor: 0.187 R-free: 0.213

Authors:

H.Koike,H.Sasaki,T.Kobori,S.Zenno,K.Saigo,M.E.P.Murphy,E.T.Adman, M.Tanokura

Key ref:

H.Koike et al. (1998). 1.8 A crystal structure of the major NAD(P)H:FMN oxidoreductase of a bioluminescent bacterium, Vibrio fischeri: overall structure, cofactor and substrate-analog binding, and comparison with related flavoproteins. J Mol Biol, 280, 259-273. PubMed id: 9654450 DOI: 10.1006/jmbi.1998.1871

Date:

09-Jan-98 Release date: 16-Feb-99

Protein chains

P46072  (FRA1_ALIFS) -  Major NAD(P)H-flavin oxidoreductase from Aliivibrio fischeri

Seq: 218 a.a.

Struc: 217 a.a.

Enzyme reactions

• Enzyme class: E.C.1.6.99.- - ?????

DOI no: 10.1006/jmbi.1998.1871

J Mol Biol 280:259-273 (1998)

PubMed id: 9654450

1.8 A crystal structure of the major NAD(P)H:FMN oxidoreductase of a bioluminescent bacterium, Vibrio fischeri: overall structure, cofactor and substrate-analog binding, and comparison with related flavoproteins.

H.Koike, H.Sasaki, T.Kobori, S.Zenno, K.Saigo, M.E.Murphy, E.T.Adman, M.Tanokura.

ABSTRACT

We have solved the crystal structure of FRase I, the major NAD(P)H:FMN oxidoreductase of Vibrio fischeri, by the multiple isomorphous replacement method (MIR) at 1.8 A resolution with the conventional R factor of 0.187. The crystal structure of FRase I complexed with its competitive inhibitor, dicoumarol, has also been solved at 2.2 A resolution with the conventional R factor of 0.161. FRase I is a homodimer, having one FMN cofactor per subunit, which is situated at the interface of two subunits. The overall fold can be divided into two domains; 80% of the residues form a rigid core and the remaining, a small flexible domain. The overall core folding is similar to those of an NADPH-dependent flavin reductase of Vibrio harveyi (FRP) and the NADH oxidase of Thermus thermophilus (NOX) in spite of the very low identity in amino acid sequences (10% with FRP and 21% with NOX). 56% of alpha-carbons of FRase I core residues could be superposed onto NOX counterparts with an r.m.s. distance of 1.2 A. The remaining residues have relatively high B-values and may be essential for defining the substrate specificity. Indeed, one of them, Phe124, was found to participate in the binding of dicoumarol through stacking to one of the rings of dicoumarol. Upon binding of dicoumarol, most of the exposed re-face of the FMN cofactor is buried, which is consistent with the ping pong bi bi catalytic mechanism.

Selected figure(s)

Figure 3.
Figure 3. (a) The network of hydrogen bonds between the cofactor FMN and protein. The enzyme is drawn by a ball and stick model. Hydrogen atoms are omitted from this Figure for clarity. Each atom is colored according to atom type (carbon of protein in silver, carbon of FMN in yellow). Protein residues and N5 and N1 atoms of FMN are labeled. Hydrogen bonds are indicated with red broken lines. (b) Electron density of FMN and surrounding residues from a 2 F[o]−F[c]map contoured at one σ. The FMN and its phosphate atom as well as some surrounding residues are labeled. In this and all subsequent Figures, the one letter code for amino acid names is used for enhanced clarity.

Figure 4.
Figure 4. (a) Stereoview of dicoumarol bound to FRase I, highlighting the trans-conformation of dicoumarol such that the corresponding keto-oxygens of the two coumarols point in opposite directions. Residues within 4 Å from the buried half of dicoumarol are also shown and labeled, highlighting hydrophobic interaction with the inhibitor and protein. (b) A chemical structure of dicoumarol.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1998, 280, 259-273) copyright 1998.

Figures were selected by an automated process.