Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Review
. 2010 Jun;20(3):283-94.
doi: 10.1016/j.sbi.2010.03.012. Epub 2010 May 1.

Structural dynamics in DNA damage signaling and repair

J Jefferson P Perry  1 , Elizabeth Cotner-Gohara, Tom Ellenberger, John A Tainer
Affiliations
Review

Structural dynamics in DNA damage signaling and repair

J Jefferson P Perry et al. Curr Opin Struct Biol. 2010 Jun.

Abstract

Changing macromolecular conformations and complexes are critical features of cellular networks, typified by DNA damage response pathways that are essential to life. These fluctuations enhance the specificity of macromolecular recognition and catalysis, and enable an integrated functioning of pathway components, ensuring efficiency while reducing off pathway reactions. Such dynamic complexes challenge classical detailed structural analyses, so their characterizations demand combining methods that provide detail with those that inform dynamics in solution. Small-angle X-ray scattering, electron microscopy, hydrogen-deuterium exchange and computation are complementing detailed structures from crystallography and NMR to provide comprehensive models for DNA damage searching, specificity, signaling, and repair. Here, we review new approaches and results on DNA damage responses that advance structural biology in the fourth dimension, connecting proteins to pathways.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Differential interactions and crystal structure of the 9-1-1 heterotrimeric complex. 9-1-1 has a PCNA-like trimeric ring structure with asymmetry in the IDCL (PDB ID 3G65). Rad9 (green), Rad1 (magenta) and Hus1 (cyan) are shown with hydrophobic pocket region that binds PIP-box motifs (dotted circles), as noted for Rad1 and Rad9 interactions with FEN-1. The flexible connection to the Rad9 120 KDa region with role in DNA binding (dashed green line, lower left) was removed for crystallization.
Figure 2
Figure 2
Architecture and conformational change in the DNA-PK holo-enzyme, as defined by protein crystallography and in solution SAXS analyses. (A) The DNA-PK structure (PDB ID 3KGV) forms a ring-like shape (left) built from α-helical heat repeats, with a head/crown at the top. A side view reveals that the head domain and ends of the arms arch towards each other (right) creating a cradle-like architecture. Head/Crown Kinase domain (yellow) and FAT and FAT-C domains (magenta) have extended HEAT domain arms forming a ring-like structure (green) with a putative DNA binding domain (blue) and a ‘forehead’ region (dark green). (B) The averaged SAXS volumes for DNA-PKcs (gray) and phosphorylated DNA-PKcs (yellow) each with the crystal structure superimposed, plus representative single SAXS envelope for DNA-PKcs (gray) and phosphorylated DNA-PKcs (yellow) revealing the large conformational change resulting from phosphorylation. The enclosed cavity in the head region, observed in the crystal structure, is seen visible in the SAXS data as highlighted by darker shading. The bottom panel depicts a carton describing proposed conformational changes during autophosphorylation of DNA-PKcs, as revealed by SAXS.
Figure 3
Figure 3
Nbs1 domain structures and flexibly connected interaction interfaces characterized by combined crystallographic and SAXS analyses. (A) Cancer-causing Mre11 mutations in ataxia telangiectasia-like disorder (ATLD missense mutations W120C and N117S), which result in a loss of Nbs1 binding, suggest that Nbs1 binds across the back face of the Mre11 dimer, opposite the DNA-binding cleft (PDB ID 3DSC). (B) Crystal structure of the N-terminal Nbs1 folded regions (PDB ID 3HUF), revealing FHA domain, (blue), BRCT1 (yellow) and BRCT2 (brown) domains in complex with a phosphorylated Ctp1 peptide (orange) that binds Nbs1 in a surface groove at the distal N-terminal FHA domain. (C) FHA-bound Ctp1 is linked to the Mre11-Rad50 hetero-tetrameric Mre-Rad50 core (labeled M and R, center) that is bridging a DNA double strand-break through the flexible Nbs1 C-terminus defined by SAXS.
Figure 4
Figure 4
Proposed mechanism of DNA ligase IV-XRCC4, based on the crystal structure (PDB ID 3II6) and electron micrographs of the complex. DNA ligase IV binds to XRCC4 (pink) through its tandem C-terminal BRCT domains. EM studies indicate that the catalytic domains (DBD, NTase, and OBD) extend away from XRCC4. This flexible connection may allow ligase IV to catalyze both enzyme self-adenylation (A) and DNA end-joining (B) without dissociating from the XRCC4-associated repair complex. Abbreviations: B1 – BRCT domain 1, B2 – BRCT domain 2, HLH – helix-loop-helix.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Jackson SP, Bartek J. The DNA-damage response in human biology and disease. Nature. 2009;461:1071–1078. - PMC - PubMed
    1. Hitomi K, Iwai S, Tainer JA. The intricate structural chemistry of base excision repair machinery: implications for DNA damage recognition, removal, and repair. DNA Repair (Amst) 2007;6:410–428. - PubMed
    1. Garcin ED, Hosfield DJ, Desai SA, Haas BJ, Bjoras M, Cunningham RP, Tainer JA. DNA apurinic-apyrimidinic site binding and excision by endonuclease IV. Nat Struct Mol Biol. 2008;15:515–522. The endonuclease IV structures and mutational analyses provide experimental evidence for strain in BER backbone incision and for stable product complexes that aid handoffs without the release of toxic DNA repair intermediates. - PubMed
    1. Chapados BR, Hosfield DJ, Han S, Qiu J, Yelent B, Shen B, Tainer JA. Structural basis for FEN-1 substrate specificity and PCNA-mediated activation in DNA replication and repair. Cell. 2004;116:39–50. - PubMed
    1. Pascal JM, Tsodikov OV, Hura GL, Song W, Cotner EA, Classen S, Tomkinson AE, Tainer JA, Ellenberger T. A flexible interface between DNA ligase and PCNA supports conformational switching and efficient ligation of DNA. Mol Cell. 2006;24:279–291. - PubMed

Publication types

LinkOut - more resources