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The DNA-binding domain of human PARP-1 interacts with DNA single-strand breaks as a monomer through its second zinc finger.

Eustermann S, Videler H, Yang JC, Cole PT, Gruszka D, Veprintsev D, Neuhaus D - J. Mol. Biol. (2011)

Bottom Line: Poly(ADP-ribose)polymerase-1 (PARP-1) is a highly abundant chromatin-associated enzyme present in all higher eukaryotic cell nuclei, where it plays key roles in the maintenance of genomic integrity, chromatin remodeling and transcriptional control.F2 interacts much more strongly with nicked or gapped DNA ligands than does F1, and we present a mutational study that suggests origins of this difference.Our data suggest that different DNA lesions are recognized by the DNA-binding domain of PARP-1 in a highly similar conformation, helping to rationalize how the full-length protein participates in multiple steps of DNA single-strand breakage and base excision repair.

View Article: PubMed Central - PubMed

Affiliation: MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.

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Solution structures of the N-terminal zinc fingers F1 and F2 of human PARP-1. (a) Ensemble views of the 30 accepted structures of F1 (backbone rmsd 0.39 Å) and F2 (backbone rmsd 0.37 Å) shown in a cartoon representation, colored as for Fig. 1. Zinc ions are shown as blue spheres and zinc coordinating residues in stick representation with carbon atoms in magenta. The two zinc fingers are connected by a linker of 15 residues (shown as a dotted line) that is flexible, as judged by NMR measurements of PARP-1 F1 + F2. (b) Close-up of the zinc coordination of PARP-1 F1 [rotated about the vertical by 90° relative to the view in (a)]. The absolute chirality of the zinc binding configuration is S, as defined by Berg.38 (c) Schematic showing the zinc binding and secondary-structure topology of the two N-terminal PARP-1 zinc finger domains F1 and F2, colored as for Fig. 1.
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f0010: Solution structures of the N-terminal zinc fingers F1 and F2 of human PARP-1. (a) Ensemble views of the 30 accepted structures of F1 (backbone rmsd 0.39 Å) and F2 (backbone rmsd 0.37 Å) shown in a cartoon representation, colored as for Fig. 1. Zinc ions are shown as blue spheres and zinc coordinating residues in stick representation with carbon atoms in magenta. The two zinc fingers are connected by a linker of 15 residues (shown as a dotted line) that is flexible, as judged by NMR measurements of PARP-1 F1 + F2. (b) Close-up of the zinc coordination of PARP-1 F1 [rotated about the vertical by 90° relative to the view in (a)]. The absolute chirality of the zinc binding configuration is S, as defined by Berg.38 (c) Schematic showing the zinc binding and secondary-structure topology of the two N-terminal PARP-1 zinc finger domains F1 and F2, colored as for Fig. 1.

Mentions: Ensemble views of the structures of F1 and F2 are shown in Fig. 2. Both fingers share the same overall architecture with the previously determined structure of the PARP-like zinc finger from DL3 (1uw0), comprising a three-stranded antiparallel β-sheet that carries the first pair of zinc-binding residues on an extended hairpin between strands 1 and 2, followed by two helices that pack together in a parallel fashion, the first of which carries the second pair of zinc-binding residues on its first turn. In F1, the sheet comprises strand 1 (residues 8–12), strand 2 (residues 35–39) and strand 3 (residues 48–52); helix 1 comprises residues 54–60; helix 2 comprises residues 78–92 and the metal binding residues are Cys21, Cys24, His53 and Cys56. Correspondingly, in F2 the sheet comprises strand 1 (residues 112–116), strand 2 (residues 138–143) and strand 3 (residues 154–158); helix 1 comprises residues 160–166; helix 2 comprises residues 188–199 and the metal binding residues are Cys125, Cys128, His159 and Cys162. In both fingers, both helices and the interhelix linker (loop 4) make extensive hydrophobic contacts to residues of the β-sheet. In addition, between helices 1 and 2, one residue (Asp72 in F1, Lys182 in F2) makes one or two hydrogen bonds to the edge of strand 1 of the β-sheet. However, this feature is probably on the borderline of detectability by NMR, because its formation depends on the precise arrangement between large-scale elements of the structure whose relationship is not highly constrained. Similar to the DL3 finger, both F1 and F2 of PARP-1 have an S absolute chirality of the zinc-binding ligands, as defined by Berg38 (see also Kulczyk et al.31), and the loops between strands 2 and 3 of the β-sheets are relatively disordered. These structures are similar to those previously deposited by RSGI for F1 (2dmj) and F2 (2cs2) of human PARP-1; for the ordered regions of F1 (residues 7–40 and 46–93) the backbone rmsd between our structure and 2dmj is 1.31 Å, while for the ordered regions of F2 (residues 109–144 and 152–200) the rmsd between our structure and 2cs2 is 1.37 Å (in each case, the ensemble member closest to the mean is used for the fitting).


The DNA-binding domain of human PARP-1 interacts with DNA single-strand breaks as a monomer through its second zinc finger.

Eustermann S, Videler H, Yang JC, Cole PT, Gruszka D, Veprintsev D, Neuhaus D - J. Mol. Biol. (2011)

Solution structures of the N-terminal zinc fingers F1 and F2 of human PARP-1. (a) Ensemble views of the 30 accepted structures of F1 (backbone rmsd 0.39 Å) and F2 (backbone rmsd 0.37 Å) shown in a cartoon representation, colored as for Fig. 1. Zinc ions are shown as blue spheres and zinc coordinating residues in stick representation with carbon atoms in magenta. The two zinc fingers are connected by a linker of 15 residues (shown as a dotted line) that is flexible, as judged by NMR measurements of PARP-1 F1 + F2. (b) Close-up of the zinc coordination of PARP-1 F1 [rotated about the vertical by 90° relative to the view in (a)]. The absolute chirality of the zinc binding configuration is S, as defined by Berg.38 (c) Schematic showing the zinc binding and secondary-structure topology of the two N-terminal PARP-1 zinc finger domains F1 and F2, colored as for Fig. 1.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3094755&req=5

f0010: Solution structures of the N-terminal zinc fingers F1 and F2 of human PARP-1. (a) Ensemble views of the 30 accepted structures of F1 (backbone rmsd 0.39 Å) and F2 (backbone rmsd 0.37 Å) shown in a cartoon representation, colored as for Fig. 1. Zinc ions are shown as blue spheres and zinc coordinating residues in stick representation with carbon atoms in magenta. The two zinc fingers are connected by a linker of 15 residues (shown as a dotted line) that is flexible, as judged by NMR measurements of PARP-1 F1 + F2. (b) Close-up of the zinc coordination of PARP-1 F1 [rotated about the vertical by 90° relative to the view in (a)]. The absolute chirality of the zinc binding configuration is S, as defined by Berg.38 (c) Schematic showing the zinc binding and secondary-structure topology of the two N-terminal PARP-1 zinc finger domains F1 and F2, colored as for Fig. 1.
Mentions: Ensemble views of the structures of F1 and F2 are shown in Fig. 2. Both fingers share the same overall architecture with the previously determined structure of the PARP-like zinc finger from DL3 (1uw0), comprising a three-stranded antiparallel β-sheet that carries the first pair of zinc-binding residues on an extended hairpin between strands 1 and 2, followed by two helices that pack together in a parallel fashion, the first of which carries the second pair of zinc-binding residues on its first turn. In F1, the sheet comprises strand 1 (residues 8–12), strand 2 (residues 35–39) and strand 3 (residues 48–52); helix 1 comprises residues 54–60; helix 2 comprises residues 78–92 and the metal binding residues are Cys21, Cys24, His53 and Cys56. Correspondingly, in F2 the sheet comprises strand 1 (residues 112–116), strand 2 (residues 138–143) and strand 3 (residues 154–158); helix 1 comprises residues 160–166; helix 2 comprises residues 188–199 and the metal binding residues are Cys125, Cys128, His159 and Cys162. In both fingers, both helices and the interhelix linker (loop 4) make extensive hydrophobic contacts to residues of the β-sheet. In addition, between helices 1 and 2, one residue (Asp72 in F1, Lys182 in F2) makes one or two hydrogen bonds to the edge of strand 1 of the β-sheet. However, this feature is probably on the borderline of detectability by NMR, because its formation depends on the precise arrangement between large-scale elements of the structure whose relationship is not highly constrained. Similar to the DL3 finger, both F1 and F2 of PARP-1 have an S absolute chirality of the zinc-binding ligands, as defined by Berg38 (see also Kulczyk et al.31), and the loops between strands 2 and 3 of the β-sheets are relatively disordered. These structures are similar to those previously deposited by RSGI for F1 (2dmj) and F2 (2cs2) of human PARP-1; for the ordered regions of F1 (residues 7–40 and 46–93) the backbone rmsd between our structure and 2dmj is 1.31 Å, while for the ordered regions of F2 (residues 109–144 and 152–200) the rmsd between our structure and 2cs2 is 1.37 Å (in each case, the ensemble member closest to the mean is used for the fitting).

Bottom Line: Poly(ADP-ribose)polymerase-1 (PARP-1) is a highly abundant chromatin-associated enzyme present in all higher eukaryotic cell nuclei, where it plays key roles in the maintenance of genomic integrity, chromatin remodeling and transcriptional control.F2 interacts much more strongly with nicked or gapped DNA ligands than does F1, and we present a mutational study that suggests origins of this difference.Our data suggest that different DNA lesions are recognized by the DNA-binding domain of PARP-1 in a highly similar conformation, helping to rationalize how the full-length protein participates in multiple steps of DNA single-strand breakage and base excision repair.

View Article: PubMed Central - PubMed

Affiliation: MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.

Show MeSH
Related in: MedlinePlus