4ESV image
Deposition Date 2012-04-23
Release Date 2012-10-24
Last Version Date 2024-02-28
Entry Detail
PDB ID:
4ESV
Keywords:
Title:
A New Twist on the Translocation Mechanism of Helicases from the Structure of DnaB with its Substrates
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
3.20 Å
R-Value Free:
0.28
R-Value Work:
0.24
R-Value Observed:
0.24
Space Group:
P 2 2 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Replicative helicase
Gene (Uniprot):dnaB
Chain IDs:C (auth: A), D (auth: B), E (auth: C), F (auth: D), G (auth: E), H (auth: F), I (auth: G), J (auth: H), K (auth: I), L (auth: J), M (auth: K), N (auth: L)
Chain Length:454
Number of Molecules:12
Biological Source:Geobacillus stearothermophilus
Polymer Type:polydeoxyribonucleotide
Molecule:5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3'
Chain IDs:A (auth: V)
Chain Length:14
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Molecule:5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3'
Chain IDs:B (auth: W)
Chain Length:13
Number of Molecules:1
Biological Source:synthetic construct
Primary Citation
The Hexameric Helicase DnaB Adopts a Nonplanar Conformation during Translocation.
Cell(Cambridge,Mass.) 151 267 277 (2012)
PMID: 23022319 DOI: 10.1016/j.cell.2012.09.014

Abstact

DNA polymerases can only synthesize nascent DNA from single-stranded DNA (ssDNA) templates. In bacteria, the unwinding of parental duplex DNA is carried out by the replicative DNA helicase (DnaB) that couples NTP hydrolysis to 5' to 3' translocation. The crystal structure of the DnaB hexamer in complex with GDP-AlF(4) and ssDNA reported here reveals that DnaB adopts a closed spiral staircase quaternary structure around an A-form ssDNA with each C-terminal domain coordinating two nucleotides of ssDNA. The structure not only provides structural insights into the translocation mechanism of superfamily IV helicases but also suggests that members of this superfamily employ a translocation mechanism that is distinct from other helicase superfamilies. We propose a hand-over-hand mechanism in which sequential hydrolysis of NTP causes a sequential 5' to 3' movement of the subunits along the helical axis of the staircase, resulting in the unwinding of two nucleotides per subunit.

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Primary Citation of related structures