2P6R

Crystal structure of superfamily 2 helicase Hel308 in complex with unwound DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.232 

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This is version 1.2 of the entry. See complete history


Literature

Structural basis for DNA duplex separation by a superfamily-2 helicase.

Buttner, K.Nehring, S.Hopfner, K.P.

(2007) Nat Struct Mol Biol 14: 647-652

  • DOI: 10.1038/nsmb1246
  • Primary Citation of Related Structures:  
    2P6R, 2P6U

  • PubMed Abstract: 
  • To reveal the mechanism of processive strand separation by superfamily-2 (SF2) 3'-->5' helicases, we determined apo and DNA-bound crystal structures of archaeal Hel308, a helicase that unwinds lagging strands and is related to human DNA polymerase theta. Our structure captures the duplex-unwinding reaction, shows that initial strand separation does not require ATP and identifies a prominent beta-hairpin loop as the unwinding element ...

    To reveal the mechanism of processive strand separation by superfamily-2 (SF2) 3'-->5' helicases, we determined apo and DNA-bound crystal structures of archaeal Hel308, a helicase that unwinds lagging strands and is related to human DNA polymerase theta. Our structure captures the duplex-unwinding reaction, shows that initial strand separation does not require ATP and identifies a prominent beta-hairpin loop as the unwinding element. Similar loops in hepatitis C virus NS3 helicase and RNA-decay factors support the idea that this duplex-unwinding mechanism is applicable to a broad subset of SF2 helicases. Comparison with ATP-bound SF2 enzymes suggests that ATP promotes processive unwinding of 1 base pair by ratchet-like transport of the 3' product strand. Our results provide a first structural framework for strand separation by processive SF2 3'-->5' helicases and reveal important mechanistic differences from SF1 helicases.


    Organizational Affiliation

    Center for Integrated Protein Science, Gene Center and Department of Chemistry and Biochemistry, Ludwig-Maximilians-University Munich, Feodor-Lynen-Str. 25, 81377 Munich, Germany.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
afUHEL308 HELICASEC [auth A]702Archaeoglobus fulgidusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
25-MERA [auth X]25N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-D(*CP*TP*AP*GP*AP*GP*AP*CP*TP*AP*TP*CP*GP*AP*T)-3'B [auth Y]15N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.232 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.379α = 90
b = 138.379β = 90
c = 252.973γ = 120
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-06-12
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance