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 

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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)  |  3D 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X4C9
Protein Feature View
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  • Reference Sequence

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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

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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],
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],
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],
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

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Ligand Structure Quality Assessment 


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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