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Figure 1 | BMC Genomics

Figure 1

From: In silico characterization of the family of PARP-like poly(ADP-ribosyl)transferases (pARTs)

Figure 1

Schematic illustration of the distinguishing structural features of the PARP-1/DT vs. the ART2/VIP2 subfamilies of ADP-ribosyltransferases. Two abutting sheets of anti-parallel β strands form the upper and lower jaws of a Pacman-like NAD-binding crevice in all known structures of ADP-ribosyltransferases. The distinguishing structural features of the PARP/DT and ART2/VIP2 subfamilies are depicted schematically on top and are highlighted in the structures of chicken PARP-1 (3pax), diphtheria toxin (DT) (1tox), an archael tRNA:NAD 2'-phosphotransferase (TpT) (1wfx), rat ART2 (1og3) and B. cereus VIP2 toxin (1qs2) below. The structures are depicted from the "front view" with a full view of the ligands bound in the active site crevice. The ligands NAD and 3MB are colored cyan and are depicted as stick models. The central four β-strands (from top to bottom: β 5, β 2, β 1, β 3, colored orange) are conserved in all mARTs and pARTs. The β strands at the edges of the respective sheets (β 4 and β 6, colored pink) show greater structural variation than the central β strands. The H-Y-E motif residues are depicted in red and their side chains are shown as sticks. The glutamic acid residue at the front edge of β 5 is the critical catalytic residue in both diphtheria toxin and PARP-1 – a corresponding glutamic acid residue is observed also in the 3D structures of rat ART2 and numerous bacterial mARTs. Diphtheria toxin (1tox), pseudomonas exotoxin A (1aer), PARP-1 (3pax), and PARP-2 (1gs0) share the following structural features which are not conserved in either rat ART2 (1og3) or most other bacterial mARTs: the orientation of β 6, the alpha helix between β 2 and β 3 (colored yellow) and the conserved histidine and tyrosine amino acid residues in β 1 and β 3. The loop between β 4 and β 5 (colored magenta) is thought to play a role in the recognition of target proteins and ADP-ribose polymers. Distinguishing features of ART2, VIP2, iota toxin (1gir), and the C3 exoenzymes (1g24, 1ojz) include three conserved alpha helices upstream of β strand 1, a seventh β strand that displaces β strand 6 and an R-S-E- motif instead of the H-Y-E motif of PARP-1 and DT. (Note that the depicted ART2 structure carries a site directed mutation of the catalytic glutamic acid residue E189I). The recently determined 3D structure of the tRNA:NAD 2'-phosphotransferase (1wfx) bears striking resemblance to that of DT and PARP-1 and carries an H-H-V variant of the H-Y-E motif. Note that the structure of the diphtheria toxin catalytic domain shown here in complex with NAD is truncated C-terminally at the proteolytic cleavage site that separates this domain from the translocation domain. The PARP-1 catalytic domain shown here is truncated N-terminally at the position of the phase 0 intron that separates this domain from a neighboring helical domain. The TpT catalytic domain is truncated N-terminally at the point of fusion to a winged-helix domain.

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