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Crystal structure of the Bloom's syndrome helicase indicates a role for the HRDC domain in conformational changes.

Newman JA, Savitsky P, Allerston CK, Bizard AH, Özer Ö, Sarlós K, Liu Y, Pardon E, Steyaert J, Hickson ID, Gileadi O - Nucleic Acids Res. (2015)

Bottom Line: We show an unexpected nucleotide-dependent interaction of the core helicase domain with the conserved, poorly characterized HRDC domain.The BLM-DNA complex shows an unusual base-flipping mechanism with unique positioning of the DNA duplex relative to the helicase core domains.Comparison with other crystal structures of RecQ helicases permits the definition of structural transitions underlying ATP-driven helicase action, and the identification of a nucleotide-regulated tunnel that may play a role in interactions with complex DNA substrates.

View Article: PubMed Central - PubMed

Affiliation: Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, UK.

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Comparison of the BLM-DNA complex (4CGZ) with 4O3M. (A) Overall comparison of the BLM-DNA complex (pink with red DNA) and 4O3M (blue with dark blue DNA), with the same view as in Figure 3A. (B) Comparison of individual domains with key structural differences labelled. (C) Comparison of the DNA substrates aligned by superposition of the WH domain. The conserved motifs IV and V on 4CGZ contact phosphates p4 and p5, whereas in 4O3M they make similar contacts to p3 and p4, consistent with a conformation that represents pre- and post-translocation states, respectively.
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Figure 7: Comparison of the BLM-DNA complex (4CGZ) with 4O3M. (A) Overall comparison of the BLM-DNA complex (pink with red DNA) and 4O3M (blue with dark blue DNA), with the same view as in Figure 3A. (B) Comparison of individual domains with key structural differences labelled. (C) Comparison of the DNA substrates aligned by superposition of the WH domain. The conserved motifs IV and V on 4CGZ contact phosphates p4 and p5, whereas in 4O3M they make similar contacts to p3 and p4, consistent with a conformation that represents pre- and post-translocation states, respectively.

Mentions: During the late stages of preparation of this manuscript another study was published in which the authors describe a structure of BLM in complex with ADP and DNA (PDB: 4O3M; (67)). This structure, determined at 2.3-Å resolution obtained in the presence of a 16-bp DNA duplex with an 8-bp overhang, is very similar to our DNA complex, and can be aligned with a 1.5-Å RMSD over the entire structure (Figure 7A). Comparing the individual domains separately reveals an even higher degree of similarity, indicating a slight difference is present in their relative positioning (Figure 7B). Superposition on the basis of the D1 domain alone reveals a small difference in WH domain orientation (maximal displacements of ∼4.5 Å between equivalent residues), which is possibly a result of the different lengths of double-stranded DNA present.


Crystal structure of the Bloom's syndrome helicase indicates a role for the HRDC domain in conformational changes.

Newman JA, Savitsky P, Allerston CK, Bizard AH, Özer Ö, Sarlós K, Liu Y, Pardon E, Steyaert J, Hickson ID, Gileadi O - Nucleic Acids Res. (2015)

Comparison of the BLM-DNA complex (4CGZ) with 4O3M. (A) Overall comparison of the BLM-DNA complex (pink with red DNA) and 4O3M (blue with dark blue DNA), with the same view as in Figure 3A. (B) Comparison of individual domains with key structural differences labelled. (C) Comparison of the DNA substrates aligned by superposition of the WH domain. The conserved motifs IV and V on 4CGZ contact phosphates p4 and p5, whereas in 4O3M they make similar contacts to p3 and p4, consistent with a conformation that represents pre- and post-translocation states, respectively.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4446433&req=5

Figure 7: Comparison of the BLM-DNA complex (4CGZ) with 4O3M. (A) Overall comparison of the BLM-DNA complex (pink with red DNA) and 4O3M (blue with dark blue DNA), with the same view as in Figure 3A. (B) Comparison of individual domains with key structural differences labelled. (C) Comparison of the DNA substrates aligned by superposition of the WH domain. The conserved motifs IV and V on 4CGZ contact phosphates p4 and p5, whereas in 4O3M they make similar contacts to p3 and p4, consistent with a conformation that represents pre- and post-translocation states, respectively.
Mentions: During the late stages of preparation of this manuscript another study was published in which the authors describe a structure of BLM in complex with ADP and DNA (PDB: 4O3M; (67)). This structure, determined at 2.3-Å resolution obtained in the presence of a 16-bp DNA duplex with an 8-bp overhang, is very similar to our DNA complex, and can be aligned with a 1.5-Å RMSD over the entire structure (Figure 7A). Comparing the individual domains separately reveals an even higher degree of similarity, indicating a slight difference is present in their relative positioning (Figure 7B). Superposition on the basis of the D1 domain alone reveals a small difference in WH domain orientation (maximal displacements of ∼4.5 Å between equivalent residues), which is possibly a result of the different lengths of double-stranded DNA present.

Bottom Line: We show an unexpected nucleotide-dependent interaction of the core helicase domain with the conserved, poorly characterized HRDC domain.The BLM-DNA complex shows an unusual base-flipping mechanism with unique positioning of the DNA duplex relative to the helicase core domains.Comparison with other crystal structures of RecQ helicases permits the definition of structural transitions underlying ATP-driven helicase action, and the identification of a nucleotide-regulated tunnel that may play a role in interactions with complex DNA substrates.

View Article: PubMed Central - PubMed

Affiliation: Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, UK.

Show MeSH
Related in: MedlinePlus