PDBsum entry 1dfh

Oxidoreductase

PDB id: 1dfh

Contents

Protein chains

257 a.a. *

Ligands

NAD-TDB ×2

* Residue conservation analysis

References listed in PDB file

Key reference

Title

A mechanism of drug action revealed by structural studies of enoyl reductase.

Authors

C.Baldock, J.B.Rafferty, S.E.Sedelnikova, P.J.Baker, A.R.Stuitje, A.R.Slabas, T.R.Hawkes, D.W.Rice.

Ref.

Science, 1996, 274, 2107-2110. [DOI no: 10.1126/science.274.5295.2107]

PubMed id

8953047

Abstract

Enoyl reductase (ENR), an enzyme involved in fatty acid biosynthesis, is the target for antibacterial diazaborines and the front-line antituberculosis drug isoniazid. Analysis of the structures of complexes of Escherichia coli ENR with nicotinamide adenine dinucleotide and either thienodiazaborine or benzodiazaborine revealed the formation of a covalent bond between the 2' hydroxyl of the nicotinamide ribose and a boron atom in the drugs to generate a tight, noncovalently bound bisubstrate analog. This analysis has implications for the structure-based design of inhibitors of ENR, and similarities to other oxidoreductases suggest that mimicking this molecular linkage may have generic applications in other areas of medicinal chemistry.

Figure 1.
Fig. 1. The E. coli ENR tetramer is made up of four subunits, each consisting of a single domain of approximate dimensions 55 by 45 by 45 Å com- posed of a parallel b sheet of seven strands (b1 to b7), flanked on one side by helices a1, a2, and a7 and on the other by helices a3 to a5, with a further helix, a6, lying along the top of the b sheet. (A) Schematic diagram of a single subunit of the ENR-NAD 1 -thienodiazaborine complex. The ribbon trace of E. coli ENR is shown in red; NAD 1 (blue) and diazaborine (cyan) are shown in an all-atom represen- tation. The loop that orders on diazaborine binding is highlighted in green. [Produced using MIDAS (25).] (B and C) Initial Fourier maps of the NAD 1 -thienodiazaborine complex at 2.2 Å resolution (B) and of the NAD 1 -benzodiazaborine complex at 2.5 Å resolution (C) with the final refined structures superimposed. The density (contoured at 1.2s and 0.9s, respectively) was calculated with coefficients 2uFobsu 2 uFcalcu and phases that were calculated from the refined structure from the molecular replacement solution that had been generated with the model of the E. coli ENR-NAD 1 complex, which contained no information about the inhibitor. [Produced using BOBSCRIPT (26), a modified version of MOLSCRIPT (27).] (D) The superposition (based on the nicotinamide and its associated ribose) of the nucleotide-inhibitor complex of ENR into the active site of the nucleotide-substrate complex of DHFR [PDB entry 7DFR (13)]. The Ca backbone trace for DHFR is shown in green, with bound NADP and folate colored turquoise and by atom, respectively; the superimposed NAD 1 and thienodiazaborine of ENR are shown in red and all atom colors, respectively (red, oxygen; white, carbon; blue, nitrogen; yellow, sulfur; green, boron). The covalent bond between the 29 hydroxyl of the nicotinamide ribose and the boron of the diazaborine in ENR is represented by a dotted yellow line. [Produced using MIDAS (25).] When the NAD 1 -thienodi- azaborine complex is fitted into the active site of DHFR, there are some steric clashes between the sulfonyl group and the propyl tail of the diazaborine with parts of the enzyme surface. Nonetheless, there is sufficient space around the 29OH of the nicotinamide ribose to envisage the formation of a linker between the ribose and a folate analog.

Figure 2.
Fig. 2. Schematic repre- sentation of the interac- tions made by the NAD 1 - thienodiazaborine com- plex with the enzyme sur- face and ordered solvent molecules. For NAD 1 , only the nicotinamide ring and the nicotinamide ri- bose are shown. Hydro- gen bonds are represent- ed by dashed lines, hy- drophobic contacts are shown as semicircular arcs, and Wat 1 and Wat 2 are two ordered solvent molecules. [Produced using LIGPLOT (28).]

The above figures are reprinted by permission from the AAAs: Science (1996, 274, 2107-2110) copyright 1996.

Secondary reference #1

Title

Crystallization of escherichia coli enoyl reductase and its complex with diazaborine.

Authors

C.Baldock, J.B.Rafferty, S.E.Sedelnikova, S.Bithell, A.R.Stuitje, A.R.Slabas, D.W.Rice.

Ref.

Acta Crystallogr D Biol Crystallogr, 1996, 52, 1181-1184. [DOI no: 10.1107/S0907444996005458]

PubMed id

15299580

Figure 1.
Fig. 1. section through the translation­function solution lb ENR from E. coli crystal form A in space group /"21 calculated using Tf'TC ICollaborative omputational Project. Number 4, 1994) and a tetramer of ENR from B. hal?us as lhe search model. This seclion is a! v = 0 and covers the range from x: 0­4 and ..­= 0 ~ and is contoured from 1.2 to 7 by 1.2.

Figure 3.
Fig. 3. A 12 ° rotation diffraction pattern from a crystal of ENR from E. coli form A. This image was taken on a MAR research image plate on station 9.5 at DRAL and at a resolution of 1.8 A at the edge of the plate.

The above figures are reproduced from the cited reference with permission from the IUCr