4esv | pdb_00004esv

A New Twist on the Translocation Mechanism of Helicases from the Structure of DnaB with its Substrates

spinqualitylabelsall models 4esv, resolution 3.20Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 4esv is a 14 chain structure with sequence from Geobacillus stearothermophilus and Synthetic construct. The December 2013 RCSB PDB Molecule of the Month feature on DNA Helicase by David Goodsell is 10.2210/rcsb_pdb/mom_2013_12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 3.2Å Ligands: ALF, CA, GDP, MES Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function DNAB_GEOSE The main replicative DNA helicase, it participates in initiation and elongation during chromosome replication. Travels ahead of the DNA replisome, separating double-stranded (ds)DNA into templates for DNA synthesis. Binding of single-stranded (ss)DNA to the hexamer suggests a 2-nucleotide step size for the helicase and a hand-over-hand mechanism of DNA unwinding (Probable) (PubMed:23022319). Has ssDNA-stimulated ATPase activity (PubMed:10625492). DnaG primase stimulates the helicase activity (the helicase direction was not determine but is probably 5'-3') (PubMed:10625492, PubMed:12235389, PubMed:23022319). Loaded onto DNA by helicase loader DnaI (shown with DnaI of B.subtilis); ATP-binding enhances loading and subsequent ATP hydrolysis dissociates the complex, leaving helicase on the DNA (PubMed:17003052). Binds ssDNA and less well dsDNA, in the presence of ADPNP (probably 5'-adenylyl beta, gamma-imidodiphosphate, but not ATP) binding to both DNAs is improved (PubMed:12235389, PubMed:17003052). Publication Abstract from PubMed 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. The Hexameric Helicase DnaB Adopts a Nonplanar Conformation during Translocation.,Itsathitphaisarn O, Wing RA, Eliason WK, Wang J, Steitz TA Cell. 2012 Oct 12;151(2):267-77. doi: 10.1016/j.cell.2012.09.014. Epub 2012 Sep, 27. PMID:23022319 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Helicase 3D structures

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