2ALZ

Ternary Complex of hPoli with DNA and dCTP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.228 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Human DNA Polymerase iota Incorporates dCTP Opposite Template G via a G.C+ Hoogsteen Base Pair.

Nair, D.T., Johnson, R.E., Prakash, L., Prakash, S., Aggarwal, A.K.

(2005) Structure 13: 1569-1577

  • DOI: 10.1016/j.str.2005.08.010
  • Primary Citation of Related Structures:  
    2ALZ

  • PubMed Abstract: 

    • Human DNA polymerase iota (hPoliota), a member of the Y family of DNA polymerases, differs in remarkable ways from other DNA polymerases, incorporating correct nucleotides opposite template purines with a much higher efficiency and fidelity than opposite template pyrimidines ...

    Human DNA polymerase iota (hPoliota), a member of the Y family of DNA polymerases, differs in remarkable ways from other DNA polymerases, incorporating correct nucleotides opposite template purines with a much higher efficiency and fidelity than opposite template pyrimidines. We present here the crystal structure of hPoliota bound to template G and incoming dCTP, which reveals a G.C + Hoogsteen base pair in a DNA polymerase active site. We show that the hPoliota active site has evolved to favor Hoogsteen base pairing, wherein the template sugar is fixed in a cavity that reduces the C1'-C1' distance across the nascent base pair from approximately 10.5 A in other DNA polymerases to 8.6 A in hPoliota. The rotation of G from anti to syn is then largely in response to this curtailed C1'-C1' distance. A G.C+ Hoogsteen base pair suggests a specific mechanism for hPoliota's ability to bypass N(2)-adducted guanines that obstruct replication.

    Organizational Affiliation: 

    Structural Biology Program, Department of Physiology and Biophysics, Mount Sinai School of Medicine, Box 1677, 1425 Madison Avenue, New York, New York 10029, USA.



Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase iota A390Homo sapiensMutation(s): 0 
Gene Names: POLI, RAD30B
EC: 2.7.7.7
Find proteins for Q9UNA4 (Homo sapiens)
Explore Q9UNA4 
Go to UniProtKB:  Q9UNA4
NIH Common Fund Data Resources
PHAROS:  Q9UNA4
GTEx:  ENSG00000101751
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*TP*GP*GP*GP*GP*TP*CP*CP*T)-3'T9N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      5'-D(*AP*GP*GP*AP*CP*CP*(DOC))-3'P7N/A
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      DCP
      Query on DCP
      Download Ideal Coordinates CCD File 
      A
      		2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
      C9 H16 N3 O13 P3
      RGWHQCVHVJXOKC-SHYZEUOFSA-N      		 Ligand Interaction
      MG
      Query on MG
      Download Ideal Coordinates CCD File 
      A
      		MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N      		 Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.50 Å
      • R-Value Free: 0.272 
      • R-Value Work: 0.228 
      • Space Group: P 65 2 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 98.114α = 90
      b = 98.114β = 90
      c = 202.823γ = 120
      Software Package:
      Software NamePurpose
      REFMACrefinement
      PDB_EXTRACTdata extraction
      HKL-2000data reduction
      SCALEPACKdata scaling
      AMoREphasing

      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: 2005-10-25
        Type: Initial release
      • Version 1.1: 2008-04-30
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Advisory, Version format compliance