8ICA

DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DATP (1 MILLIMOLAR) AND CACL2 (5 MILLIMOLAR)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis.

Pelletier, H.Sawaya, M.R.

(1996) Biochemistry 35: 12778-12787

  • DOI: 10.1021/bi960790i
  • Primary Citation of Related Structures:  1NOM, 1ZQA, 1ZQB, 1ZQC, 1ZQD, 1ZQE, 1ZQF, 1ZQG, 1ZQH, 1ZQI, 1ZQJ, 1ZQK, 1ZQL, 1ZQM, 1ZQN, 1ZQO, 1ZQP, 1ZQQ, 1ZQR, 1ZQS, 1ZQU, 1ZQV, 1ZQW, 1ZQX, 1ZQY, 1ZQZ, 8ICB, 8ICC, 8ICF, 8ICE, 8ICG, 8ICH, 8ICI, 8ICZ, 9ICA, 9ICB, 9ICC, 9ICE, 9ICG, 9ICH, 9ICI, 9ICJ, 9ICL

  • PubMed Abstract: 
  • X-ray crystallographic studies have shown that DNA binding by human polymerase beta (pol beta) occurs primarily through two structurally and sequentially homologous helix-hairpin-helix (HhH) motifs, one in the fingers subdomain and the other in the 8 ...

    X-ray crystallographic studies have shown that DNA binding by human polymerase beta (pol beta) occurs primarily through two structurally and sequentially homologous helix-hairpin-helix (HhH) motifs, one in the fingers subdomain and the other in the 8-kDa domain [Pelletier, H., Sawaya, M. R., Wolfle, W., Wilson, S. H., & Kraut, J. (1996a) Biochemistry 35, 12742-12761]. In that DNA binding by each HhH motif is facilitated by a metal ion, we set out to determine the identity of the metal ion that most likely binds to the HhH motif in vivo. Crystal soaking experiments were performed on human pol beta-DNA cocrystals with Mg2+, Ca2+, Na+, and K+, the four most prevalent metal ions in the cell, and in each case a data set was collected and the resulting structure was refined. Under the conditions tested, the HhH motifs of pol beta have an affinity for these biologically prevalent metal ions in the order Mg2+ < Ca2+ < Na+ < K+, with K+ displaying the strongest binding. Crystals soaked in the presence of Tl+, a commonly used spectroscopic probe for K+, were too X-ray-sensitive to establish the binding behavior of Tl+, but soaking experiments with Ba2+ and Cs+ resulted in relatively stable crystals that gave evidence of metal ion binding in both HhH motifs, confirming that larger monovalent and divalent metal ions are capable of binding to the HhH metal sites. Although Mn2+, which has been categorized as a potent polymerase mutagen, binds to the HhH motifs with a greater affinity than Mg2+, Mn2+ does not bind to the HhH motifs in the presence of equimolar concentrations of Na+. These results suggest that in vivo, where Mn2+ is present only in trace amounts, Mn2+ probably does not have a large effect on DNA binding and may instead manifest a mutagenic effect on pol beta primarily by distorting nucleotide binding or by directly affecting the catalytic step [Pelletier, H., Sawaya, M. R., Wolfle, W., Wilson, S. H., & Kraut, J. (1996b) Biochemistry 35, 12762-12777]. Crystal soaking experiments with 31-kDa apoenzyme crystals show that, in the absence of DNA, the HhH motif in the fingers subdomain binds metal ions with either much lower occupancy or not at all, indicating that metal ion binding is dependent on the presence of the DNA substrate.


    Related Citations: 
    • A Structural Basis for Metal Ion Mutagenicity and Nucleotide Selectivity in Human DNA Polymerase Beta
      Pelletier, H.,Sawaya, M.R.,Wolfle, W.,Wilson, S.H.,Kraut, J.
      (1996) Biochemistry 35: 12762
    • Crystal Structures of Human DNA Polymerase Beta Complexed with Nicked and Gapped DNA Substrates
      Sawaya, M.R.,Rawson, T.,Wilson, S.H.,Kraut, J.,Pelletier, H.
      () TO BE PUBLISHED --: --
    • The Role of Thumb Movement and Template Bending in Polymerase Fidelity
      Pelletier, H.
      () TO BE PUBLISHED --: --
    • Polymerase Structures and Mechanism
      Pelletier, H.
      (1994) Science 266: 2025
    • Structures of Ternary Complexes of Rat DNA Polymerase Beta, a DNA Template- Primer, and ddCTP
      Pelletier, H.,Sawaya, M.R.,Kumar, A.,Wilson, S.H.,Kraut, J.
      (1994) Science 264: 1891
    • Crystal Structures of Human DNA Polymerase Beta Complexed with DNA; Implications for Catalytic Mechanism, Processivity, and Fidelity
      Pelletier, H.,Sawaya, M.R.,Wolfle, W.,Wilson, S.H.,Kraut, J.
      (1996) Biochemistry 35: 12742
    • Crystal Structure of Rat DNA Polymerase Beta: Evidence for a Common Polymerase Mechanism
      Sawaya, M.R.,Pelletier, H.,Kumar, A.,Wilson, S.H.,Kraut, J.
      (1994) Science 264: 1930


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla 92093-0506, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (DNA POLYMERASE BETA (E.C.2.7.7.7))
A
335Homo sapiensGene Names: POLB
EC: 2.7.7.7, 4.2.99.-
Find proteins for P06746 (Homo sapiens)
Go to Gene View: POLB
Go to UniProtKB:  P06746
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*AP*TP*TP*AP*GP*AP*A)-3')T8N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*CP*TP*AP*AP*TP*G)-3')P7N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DTP
Query on DTP

Download SDF File 
Download CCD File 
A
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
C10 H16 N5 O12 P3
SUYVUBYJARFZHO-RRKCRQDMSA-N
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 179.839α = 90.00
b = 57.719β = 90.00
c = 48.175γ = 90.00
Software Package:
Software NamePurpose
SDMSdata reduction
TNTphasing
TNTrefinement
SDMSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-11-15
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance