4F50

Y-family DNA polymerase chimera Dbh-Dbh-Dpo4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Y-family polymerase conformation is a major determinant of fidelity and translesion specificity.

Wilson, R.C.Jackson, M.A.Pata, J.D.

(2013) Structure 21: 20-31

  • DOI: 10.1016/j.str.2012.11.005
  • Primary Citation of Related Structures:  
    4HYK, 4F4Z, 4F4W, 4F4X, 4F4Y, 4F50

  • PubMed Abstract: 
  • Y-family polymerases help cells tolerate DNA damage by performing translesion synthesis opposite damaged DNA bases, yet they also have a high intrinsic error rate. We constructed chimeras of two closely related Y-family polymerases that display distinctly different activity profiles and found that the polypeptide linker that tethers the catalytic polymerase domain to the C-terminal DNA-binding domain is a major determinant of overall polymerase activity, nucleotide incorporation fidelity, and abasic site-bypass ability ...

    Y-family polymerases help cells tolerate DNA damage by performing translesion synthesis opposite damaged DNA bases, yet they also have a high intrinsic error rate. We constructed chimeras of two closely related Y-family polymerases that display distinctly different activity profiles and found that the polypeptide linker that tethers the catalytic polymerase domain to the C-terminal DNA-binding domain is a major determinant of overall polymerase activity, nucleotide incorporation fidelity, and abasic site-bypass ability. Exchanging just 3 out of the 15 linker residues is sufficient to interconvert the polymerase activities tested. Crystal structures of four chimeras show that the conformation of the protein correlates with the identity of the interdomain linker sequence. Thus, residues that are more than 15 Å away from the active site are able to influence many aspects of polymerase activity by altering the relative orientations of the catalytic and DNA-binding domains.


    Organizational Affiliation

    Wadsworth Center, New York State Department of Health, Albany, NY 12201-0509, USA; Department of Biomedical Sciences, University at Albany, Albany, NY 12201-0509, USA. Electronic address: jpata@wadsworth.org.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase IVA361Sulfolobus acidocaldarius DSM 639Saccharolobus solfataricus P2
This entity is chimeric
Mutation(s): 0 
Gene Names: dbhdpo4Dpo4 (S. solfataricus) and Dbh (S. acidocaldarius)Saci_0554SSO24 48
EC: 2.7.7.7
Find proteins for Q4JB80 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
Explore Q4JB80 
Go to UniProtKB:  Q4JB80
Find proteins for Q97W02 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Explore Q97W02 
Go to UniProtKB:  Q97W02
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*GP*GP*GP*AP*AP*GP*CP*CP*GP*GP*C)-3')P11N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*CP*CP*GP*CP*CP*T*GP*GP*CP*TP*TP*CP*CP*C)-3')T14N/A
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      CA
      Query on CA

      Download CCD File 
      A
      CALCIUM ION
      Ca
      BHPQYMZQTOCNFJ-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.21 Å
      • R-Value Free: 0.269 
      • R-Value Work: 0.212 
      • R-Value Observed: 0.214 
      • Space Group: P 41 21 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 124.482α = 90
      b = 124.482β = 90
      c = 70.474γ = 90
      Software Package:
      Software NamePurpose
      CBASSdata collection
      PHASERphasing
      PHENIXrefinement
      HKL-2000data reduction
      HKL-2000data scaling

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 2013-01-02
        Type: Initial release
      • Version 1.1: 2013-02-13
        Changes: Database references
      • Version 1.2: 2014-01-29
        Changes: Source and taxonomy
      • Version 1.3: 2014-02-12
        Changes: Source and taxonomy
      • Version 1.4: 2017-08-16
        Changes: Refinement description, Source and taxonomy