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: 3.2 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.242 

wwPDB Validation 3D Report Full Report


This is version 1.1 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

  • 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. ...

    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

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Replicative helicase
A, B, C, D, E, F, G, H, I, J, K, L
454Geobacillus stearothermophilusGene Names: dnaB
EC: 3.6.4.12
Find proteins for Q9X4C9 (Geobacillus stearothermophilus)
Go to UniProtKB:  Q9X4C9
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3'V14N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3'W13N/A
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
A, C, D, E, F, G, I, J, K, L
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, B, C, D, E, F, G, I, L
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
ALF
Query on ALF

Download SDF File 
Download CCD File 
A, C, D, E, G, I, J, K, L
TETRAFLUOROALUMINATE ION
Al F4
UYOMQIYKOOHAMK-UHFFFAOYSA-J
 Ligand Interaction
MES
Query on MES

Download SDF File 
Download CCD File 
C, E, I, W
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.242 
  • Space Group: P 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 149.124α = 90.00
b = 180.321β = 90.00
c = 279.128γ = 90.00
Software Package:
Software NamePurpose
CBASSdata collection
HKL-2000data reduction
DENZOdata reduction
SHELXDphasing
SCALEPACKdata scaling
ADSCdata collection
SHELXphasing
PDB_EXTRACTdata extraction
SHELXdensity modification
HKL-2000data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-24
    Type: Initial release
  • Version 1.1: 2017-11-15
    Type: Advisory, Refinement description