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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.
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