PDBsum entry 1vyr

Oxidoreductase

PDB id: 1vyr

Contents

Protein chain

363 a.a. *

Ligands

FMN

TNF

Waters ×784

* Residue conservation analysis

PDB id:

1vyr

Name:

Oxidoreductase

Title:

Structure of pentaerythritol tetranitrate reductase complexed with picric acid

Structure:

Pentaerythritol tetranitrate reductase. Chain: a. Fragment: residues 2-365. Engineered: yes. Other_details: 2,4,6 trinitrophenol is bound in the active site

Source:

Enterobacter cloacae. Organism_taxid: 550. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: ncbi u68759. Recombinant

Resolution:

0.90Å R-factor: 0.116 R-free: 0.140

Authors:

T.Barna,P.C.E.Moody

Key ref:

H.Khan et al. (2004). Atomic resolution structures and solution behavior of enzyme-substrate complexes of Enterobacter cloacae PB2 pentaerythritol tetranitrate reductase. Multiple conformational states and implications for the mechanism of nitroaromatic explosive degradation. J Biol Chem, 279, 30563-30572. PubMed id: 15128738 DOI: 10.1074/jbc.M403541200

Date:

05-May-04 Release date: 10-Jun-04

Protein chain

P71278  (P71278_ENTCL) -  Pentaerythritol tetranitrate reductase from Enterobacter cloacae

Seq: 365 a.a.

Struc: 363 a.a.

DOI no: 10.1074/jbc.M403541200

J Biol Chem 279:30563-30572 (2004)

PubMed id: 15128738

Atomic resolution structures and solution behavior of enzyme-substrate complexes of Enterobacter cloacae PB2 pentaerythritol tetranitrate reductase. Multiple conformational states and implications for the mechanism of nitroaromatic explosive degradation.

H.Khan, T.Barna, R.J.Harris, N.C.Bruce, I.Barsukov, A.W.Munro, P.C.Moody, N.S.Scrutton.

ABSTRACT

The structure of pentaerythritol tetranitrate (PETN) reductase in complex with the nitroaromatic substrate picric acid determined previously at 1.55 A resolution indicated additional electron density between the indole ring of residue Trp-102 and the nitro group at C-6 of picrate. The data suggested the presence of an unusual bond between substrate and the tryptophan side chain. Herein, we have extended the resolution of the PETN reductase-picric acid complex to 0.9 A. This high-resolution analysis indicates that the active site is partially occupied with picric acid and that the anomalous density seen in the original study is attributed to the population of multiple conformational states of Trp-102 and not a formal covalent bond between the indole ring of Trp-102 and picric acid. The significance of any interaction between Trp-102 and nitroaromatic substrates was probed further in solution and crystal complexes with wild-type and mutant (W102Y and W102F) enzymes. Unlike with wild-type enzyme, in the crystalline form picric acid was bound at full occupancy in the mutant enzymes, and there was no evidence for multiple conformations of active site residues. Solution studies indicate tighter binding of picric acid in the active sites of the W102Y and W102F enzymes. Mutation of Trp-102 does not impair significantly enzyme reduction by NADPH, but the kinetics of decay of the hydride-Meisenheimer complex are accelerated in the mutant enzymes. The data reveal that decay of the hydride-Meisenheimer complex is enzyme catalyzed and that the final distribution of reaction products for the mutant enzymes is substantially different from wild-type enzyme. Implications for the mechanism of high explosive degradation by PETN reductase are discussed.

Selected figure(s)

Figure 1.
FIG. 1. Resonance forms of TNT. Panel A, structure of TNT as the resonance hybrid of several canonical forms, illustrating the enhancement in the electrophilicity of C3 and C5, the site of hydride ion addition. Panel B, reduction of TNT by PETN reductase to form the Meisenheimer-hydride complex.

Figure 2.
FIG. 2. Multiple conformational states of Trp-102 in PETN reductase. Panel A, stereo pair of the electron density of Trp-102, picrate, and FMN observed at 1.55 Å, showing the apparent formation of a bond between the nitro group of picrate and the indole of Trp-102. The 6-membered ring appears to have puckered, consistent with the loss of aromatic character. Panel B, same view of electron density observed at 0.9 Å, showing that the side chain of Trp-102 adopts two conformations, each with partial occupancy, thus avoiding a steric clash with the partially occupied picrate.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 30563-30572) copyright 2004.

Figures were selected by an automated process.