4ESV

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.245 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

The Hexameric Helicase DnaB Adopts a Nonplanar Conformation during Translocation.

Itsathitphaisarn, O., Wing, R.A., Eliason, W.K., Wang, J., Steitz, T.A.

(2012) Cell 151: 267-277

  • DOI: 10.1016/j.cell.2012.09.014
  • Primary Citation of Related Structures:  
    4ESV

  • PubMed Abstract: 

    • 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 ...

    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.

    Organizational Affiliation: 

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.



Macromolecules

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(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Replicative helicase454Geobacillus stearothermophilusMutation(s): 0 
Gene Names: dnaB
EC: 3.6.4.12
UniProt
Find proteins for Q9X4C9 (Geobacillus stearothermophilus)
Explore Q9X4C9 
Go to UniProtKB:  Q9X4C9
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3'A [auth V]14synthetic construct
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3'B [auth W]13synthetic construct
      Protein Feature View
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      • Reference Sequence
      Small Molecules
      Ligands 4 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      GDP
      Query on GDP
      Download Ideal Coordinates CCD File 
      CA [auth D] , GA [auth E] , KA [auth F] , MA [auth G] , PA [auth I] , Q [auth A] , TA [auth J] , VA [auth K] , 
      CA [auth D],  GA [auth E],  KA [auth F],  MA [auth G],  PA [auth I],  Q [auth A],  TA [auth J],  VA [auth K],  X [auth C],  XA [auth L]
      		GUANOSINE-5'-DIPHOSPHATE
      C10 H15 N5 O11 P2
      QGWNDRXFNXRZMB-UUOKFMHZSA-N      		 Ligand Interaction
      MES
      Query on MES
      Download Ideal Coordinates CCD File 
      		 BA [auth C], JA [auth E], O [auth W], SA [auth I]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
      C6 H13 N O4 S
      SXGZJKUKBWWHRA-UHFFFAOYSA-N      		 Ligand Interaction
      ALF
      Query on ALF
      Download Ideal Coordinates CCD File 
      AA [auth C] , EA [auth D] , IA [auth E] , NA [auth G] , RA [auth I] , S [auth A] , UA [auth J] , WA [auth K] , 
      AA [auth C],  EA [auth D],  IA [auth E],  NA [auth G],  RA [auth I],  S [auth A],  UA [auth J],  WA [auth K],  YA [auth L],  Z [auth C]
      		TETRAFLUOROALUMINATE ION
      Al F4
      UYOMQIYKOOHAMK-UHFFFAOYSA-J      		 Ligand Interaction
      CA
      Query on CA
      Download Ideal Coordinates CCD File 
      DA [auth D] , FA [auth D] , HA [auth E] , LA [auth F] , OA [auth G] , P [auth A] , QA [auth I] , R [auth A] , 
      DA [auth D],  FA [auth D],  HA [auth E],  LA [auth F],  OA [auth G],  P [auth A],  QA [auth I],  R [auth A],  T [auth A],  U [auth A],  V [auth A],  W [auth B],  Y [auth C],  ZA [auth L]
      		CALCIUM ION
      Ca
      BHPQYMZQTOCNFJ-UHFFFAOYSA-N      		 Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 3.20 Å
      • R-Value Free: 0.289 
      • R-Value Work: 0.242 
      • R-Value Observed: 0.245 
      • Space Group: P 2 2 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 149.124α = 90
      b = 180.321β = 90
      c = 279.128γ = 90
      Software Package:
      Software NamePurpose
      DENZOdata reduction
      SCALEPACKdata scaling
      SHELXphasing
      SHELXmodel building
      REFMACrefinement
      PDB_EXTRACTdata extraction
      ADSCdata collection
      CBASSdata collection
      HKL-2000data reduction
      HKL-2000data scaling
      SHELXDphasing

      Structure Validation

      View Full Validation Report


      View more in-depth experimental data

      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2012-10-24
        Type: Initial release
      • Version 1.1: 2017-11-15
        Changes: Advisory, Refinement description
      • Version 1.2: 2018-06-06
        Changes: Data collection, Refinement description, Source and taxonomy