1JX4

Crystal Structure of a Y-family DNA Polymerase in a Ternary Complex with DNA Substrates and an Incoming Nucleotide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Crystal structure of a Y-family DNA polymerase in action: a mechanism for error-prone and lesion-bypass replication.

Ling, H., Boudsocq, F., Woodgate, R., Yang, W.

(2001) Cell 107: 91-102

  • DOI: 10.1016/s0092-8674(01)00515-3
  • Primary Citation of Related Structures:  
    1JX4, 1JXL

  • PubMed Abstract: 

    • Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) is a DinB homolog that belongs to the recently described Y-family of DNA polymerases, which are best characterized by their low-fidelity synthesis on undamaged DNA templates and propensity to traverse normally replication-blocking lesions ...

    Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) is a DinB homolog that belongs to the recently described Y-family of DNA polymerases, which are best characterized by their low-fidelity synthesis on undamaged DNA templates and propensity to traverse normally replication-blocking lesions. Crystal structures of Dpo4 in ternary complexes with DNA and an incoming nucleotide, either correct or incorrect, have been solved at 1.7 A and 2.1 A resolution, respectively. Despite a conserved active site and a hand-like configuration similar to all known polymerases, Dpo4 makes limited and nonspecific contacts with the replicating base pair, thus relaxing base selection. Dpo4 is also captured in the crystal translocating two template bases to the active site at once, suggesting a possible mechanism for bypassing thymine dimers.

    Organizational Affiliation: 

    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.



Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase IV (family Y) A352Saccharolobus solfataricusMutation(s): 6 
Gene Names: dpo4
EC: 2.7.7.7
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: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*A)-3'P13N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      5'-D(*T*TP*CP*AP*TP*TP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'T18N/A
      Small Molecules
      Ligands 3 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      ADI
      Query on ADI
      Download Ideal Coordinates CCD File 
      A
      		2',3'-DIDEOXYADENOSINE-5'-DIPHOSPHATE
      C10 H15 N5 O8 P2
      QYFSANXOEHYVFG-NKWVEPMBSA-N      		 Ligand Interaction
      CA
      Query on CA
      Download Ideal Coordinates CCD File 
      A
      		CALCIUM ION
      Ca
      BHPQYMZQTOCNFJ-UHFFFAOYSA-N      		 Ligand Interaction
      MG
      Query on MG
      Download Ideal Coordinates CCD File 
      A
      		MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N      		 Ligand Interaction
      Modified Residues  1 Unique
      IDChainsTypeFormula2D DiagramParent
      MSE
      Query on MSE      		AL-PEPTIDE LINKINGC5 H11 N O2 SeMET
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 1.70 Å
      • R-Value Free: 0.228 
      • R-Value Work: 0.213 
      • R-Value Observed: 0.213 
      • Space Group: P 21 21 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 97.09α = 90
      b = 102.82β = 90
      c = 52.3γ = 90
      Software Package:
      Software NamePurpose
      SOLVEphasing
      CNSrefinement
      DENZOdata reduction
      SCALEPACKdata scaling

      Structure Validation

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      View more in-depth experimental data

      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2001-10-05
        Type: Initial release
      • Version 1.1: 2008-04-27
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance
      • Version 1.3: 2011-11-16
        Changes: Atomic model