3BQ1

Insertion ternary complex of Dbh DNA polymerase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural insights into the generation of single-base deletions by the Y family DNA polymerase dbh.

Wilson, R.C.Pata, J.D.

(2008) Mol Cell 29: 767-779

  • DOI: 10.1016/j.molcel.2008.01.014
  • Primary Citation of Related Structures:  
    3BQ0, 3BQ1, 3BQ2

  • PubMed Abstract: 
  • Dbh is a Y family translesion DNA polymerase that accurately bypasses some damaged forms of deoxyguanosine, but also generates single-base deletion errors at frequencies of up to 50%, in specific hot spot sequences. We describe preinsertion binary, insertion ternary, and postinsertion binary crystal structures of Dbh synthesizing DNA after making a single-base deletion ...

    Dbh is a Y family translesion DNA polymerase that accurately bypasses some damaged forms of deoxyguanosine, but also generates single-base deletion errors at frequencies of up to 50%, in specific hot spot sequences. We describe preinsertion binary, insertion ternary, and postinsertion binary crystal structures of Dbh synthesizing DNA after making a single-base deletion. The skipped template base adopts an extrahelical conformation stabilized by interactions with the C-terminal domain of the enzyme. DNA translocation and positioning of the next templating base at the active site, with space opposite to accommodate incoming nucleotide, occur independently of nucleotide binding, incorporation, and pyrophosphate release. We also show that Dbh creates single-base deletions more rapidly when the skipped base is located two or three bases upstream of the nascent base pair than when it is directly adjacent to the templating base, indicating that Dbh predominantly creates single-base deletions by template slippage rather than by dNTP-stabilized misalignment.


    Organizational Affiliation

    Division of Molecular Medicine, Wadsworth Center, New York State Department of Health, The State University of New York at Albany, Albany, NY 12201-0509, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase IVC [auth A]354Sulfolobus acidocaldariusMutation(s): 0 
Gene Names: dbh
EC: 2.7.7.7
UniProt
Find proteins for Q4JB80 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
Explore Q4JB80 
Go to UniProtKB:  Q4JB80
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*DGP*DAP*DAP*DGP*DCP*DCP*DGP*DGP*DCP*DG)-3')A [auth P]10N/A
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*DT*DTP*DCP*DCP*DGP*DCP*DCP*DCP*DGP*DGP*DCP*DTP*DTP*DCP*DC)-3')B [auth T]15N/A
      Protein Feature View
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      • Reference Sequence
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      DG3 (Subject of Investigation/LOI)
      Query on DG3

      Download Ideal Coordinates CCD File 
      D [auth P]2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE
      C10 H16 N5 O12 P3
      HDRRAMINWIWTNU-NTSWFWBYSA-N
       Ligand Interaction
      CA
      Query on CA

      Download Ideal Coordinates CCD File 
      E [auth A]CALCIUM ION
      Ca
      BHPQYMZQTOCNFJ-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.70 Å
      • R-Value Free: 0.267 
      • R-Value Work: 0.204 
      • R-Value Observed: 0.207 
      • Space Group: P 41 21 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 124.96α = 90
      b = 124.96β = 90
      c = 70.21γ = 90
      Software Package:
      Software NamePurpose
      REFMACrefinement
      PDB_EXTRACTdata extraction
      CBASSdata collection
      HKL-2000data reduction
      HKL-2000data scaling
      PHASERphasing

      Structure Validation

      View Full Validation Report



      Ligand Structure Quality Assessment  



      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2008-04-08
        Type: Initial release
      • Version 1.1: 2011-07-13
        Changes: Advisory, Version format compliance