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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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Structural details of the nucleotide binding site and the HRDC. (A) Comparison between BLM (green), human RECQ1 (blue) and E. coli RecQ (red) structures superposed on the basis of the D1 domain reveals conformational differences in the relative positioning of the D1-D2 domains, which affect the distance between D2 and the nucleotide bound to D1. (B) Close-up view of the nucleotide binding site with the ADP moiety in the ball and stick format and key interacting residues and motifs labelled. (C) Close-up view of the interface between the HRDC domain and the two RecA domains, with polar contacts highlighted. Residues highlighted with an asterisk were mutated to test their effect on BLM activity.
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Figure 2: Structural details of the nucleotide binding site and the HRDC. (A) Comparison between BLM (green), human RECQ1 (blue) and E. coli RecQ (red) structures superposed on the basis of the D1 domain reveals conformational differences in the relative positioning of the D1-D2 domains, which affect the distance between D2 and the nucleotide bound to D1. (B) Close-up view of the nucleotide binding site with the ADP moiety in the ball and stick format and key interacting residues and motifs labelled. (C) Close-up view of the interface between the HRDC domain and the two RecA domains, with polar contacts highlighted. Residues highlighted with an asterisk were mutated to test their effect on BLM activity.

Mentions: The individual fold of the two RecA domains is very similar to the HsRECQ1 and E. coli RecQ (EcRecQ) structures (22,54), with RMSD's between equivalent Cα atoms of 1.5 Å. However, the relative positioning of these two domains differs significantly in all three structures, with the BLM and HsRECQ1 being the most different and EcRecQ being somewhat intermediate (Figure 2A). The inter-domain movement can be described as a rigid body shift of up to 20°, with the loop connecting the two domains (residues 855–858) acting as a hinge, resulting in maximal displacements of equivalent regions of up to 15 Å. The cleft between the two RecA domains is considerably narrower in BLM than in either EcRecQ or HsRECQ1, with the D1-D2 conformation in BLM crystals appearing to be quite distinct amongst the SF2 family helicase structures solved to date.


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)

Structural details of the nucleotide binding site and the HRDC. (A) Comparison between BLM (green), human RECQ1 (blue) and E. coli RecQ (red) structures superposed on the basis of the D1 domain reveals conformational differences in the relative positioning of the D1-D2 domains, which affect the distance between D2 and the nucleotide bound to D1. (B) Close-up view of the nucleotide binding site with the ADP moiety in the ball and stick format and key interacting residues and motifs labelled. (C) Close-up view of the interface between the HRDC domain and the two RecA domains, with polar contacts highlighted. Residues highlighted with an asterisk were mutated to test their effect on BLM activity.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 2: Structural details of the nucleotide binding site and the HRDC. (A) Comparison between BLM (green), human RECQ1 (blue) and E. coli RecQ (red) structures superposed on the basis of the D1 domain reveals conformational differences in the relative positioning of the D1-D2 domains, which affect the distance between D2 and the nucleotide bound to D1. (B) Close-up view of the nucleotide binding site with the ADP moiety in the ball and stick format and key interacting residues and motifs labelled. (C) Close-up view of the interface between the HRDC domain and the two RecA domains, with polar contacts highlighted. Residues highlighted with an asterisk were mutated to test their effect on BLM activity.
Mentions: The individual fold of the two RecA domains is very similar to the HsRECQ1 and E. coli RecQ (EcRecQ) structures (22,54), with RMSD's between equivalent Cα atoms of 1.5 Å. However, the relative positioning of these two domains differs significantly in all three structures, with the BLM and HsRECQ1 being the most different and EcRecQ being somewhat intermediate (Figure 2A). The inter-domain movement can be described as a rigid body shift of up to 20°, with the loop connecting the two domains (residues 855–858) acting as a hinge, resulting in maximal displacements of equivalent regions of up to 15 Å. The cleft between the two RecA domains is considerably narrower in BLM than in either EcRecQ or HsRECQ1, with the D1-D2 conformation in BLM crystals appearing to be quite distinct amongst the SF2 family helicase structures solved to date.

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