1BPY

HUMAN DNA POLYMERASE BETA COMPLEXED WITH GAPPED DNA AND DDCTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.330 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.227 

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This is version 1.3 of the entry. See complete history


Literature

Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: evidence for an induced fit mechanism.

Sawaya, M.R.Prasad, R.Wilson, S.H.Kraut, J.Pelletier, H.

(1997) Biochemistry 36: 11205-11215

  • DOI: 10.1021/bi9703812
  • Primary Citation of Related Structures:  
    1BPX, 1BPY, 1BPZ

  • PubMed Abstract: 
  • DNA polymerase beta (pol beta) fills single nucleotide (nt) gaps in DNA produced by the base excision repair pathway of mammalian cells. Crystal structures have been determined representing intermediates in the 1 nt gap-filling reaction of pol beta: the binary complex with a gapped DNA substrate (2 ...

    DNA polymerase beta (pol beta) fills single nucleotide (nt) gaps in DNA produced by the base excision repair pathway of mammalian cells. Crystal structures have been determined representing intermediates in the 1 nt gap-filling reaction of pol beta: the binary complex with a gapped DNA substrate (2.4 A resolution), the ternary complex including ddCTP (2.2 A), and the binary product complex containing only nicked DNA (2.6 A). Upon binding ddCTP to the binary gap complex, the thumb subdomain rotates into the closed conformation to contact the otherwise solvent-exposed ddCTP-template base pair. Thumb movement triggers further conformational changes which poise catalytic residue Asp192, dNTP, and template for nucleotidyl transfer, effectively assembling the active site. In the product nicked DNA complex, the thumb returns to the open conformation as in the gapped binary DNA complex, facilitating dissociation of the product. These findings suggest that pol beta may enhance fidelity by an induced fit mechanism in which correct base pairing between template and incoming dNTP induces alignment of catalytic groups for catalysis (via thumb closure), but incorrect base pairing will not. The structures also reveal that pol beta binds both gapped and nicked DNA with a 90 degrees kink occurring precisely at the 5'-phosphodiester linkage of the templating residue. If the DNA were not kinked in this way, contact between the thumb and dNTP-template base pair, presumably important for the checking mechanism, would be impossible, especially when the gap is but a single nucleotide. Such a 90 degrees kink may be a mechanistic feature employed by any polymerase involved in filling gaps to completion.


    Related Citations: 
    • 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
    • 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 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
    • 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

    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0506, USA. mrs@heckle.med.harvard.edu



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (DNA POLYMERASE BETA)D [auth A]335Homo sapiensMutation(s): 0 
Gene Names: POLB
EC: 2.7.7.7 (PDB Primary Data), 4.2.99 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P06746 (Homo sapiens)
Explore P06746 
Go to UniProtKB:  P06746
PHAROS:  P06746
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06746
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')A [auth T]16synthetic construct
Protein Feature View
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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*DOC)-3')B [auth P]10synthetic construct
Protein Feature View
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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (5'-D(*GP*TP*CP*GP*G)-3')C [auth D]5synthetic construct
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DCT
Query on DCT

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I [auth A]2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE
C9 H16 N3 O12 P3
ARLKCWCREKRROD-POYBYMJQSA-N
 Ligand Interaction
MG
Query on MG

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E [auth A],
F [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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G [auth A],
H [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.330 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.227 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.543α = 90
b = 79.817β = 107.11
c = 54.942γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MERLOTphasing
TNTrefinement

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-06-16
    Type: Initial release
  • Version 1.1: 2008-05-22
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-02-15
    Changes: Source and taxonomy, Structure summary