Crystal Structure of a DinB Homolog (DBH) Lesion Bypass DNA Polymerase Catalytic Fragment from Sulfolobus solfataricus

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 

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Crystal structure of a DinB lesion bypass DNA polymerase catalytic fragment reveals a classic polymerase catalytic domain.

Zhou, B.L.Pata, J.D.Steitz, T.A.

(2001) Mol Cell 8: 427-437

  • DOI: https://doi.org/10.1016/s1097-2765(01)00310-0
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The UmuC/DinB family of bypass polymerases is responsible for translesion DNA synthesis and includes the human polymerases eta, iota, and kappa. We determined the 2.3 A resolution crystal structure of a catalytic fragment of the DinB homolog (Dbh) polymerase from Sulfolobus solfataricus and show that it is nonprocessive and can bypass an abasic site. The structure of the catalytic domain is nearly identical to those of most other polymerase families. Homology modeling suggests that there is minimal contact between protein and DNA, that the nascent base pair binding pocket is quite accessible, and that the enzyme is already in a closed conformation characteristic of ternary polymerase complexes. These observations afford insights into the sources of low fidelity and low processivity of the UmuC/DinB polymerases.

  • Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DBH221Saccharolobus solfataricusMutation(s): 0 
Gene Names: DBH
Find proteins for P96022 (Saccharolobus solfataricus)
Explore P96022 
Go to UniProtKB:  P96022
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP96022
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.988α = 90
b = 87.542β = 90
c = 76.983γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-09-12
    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: 2024-02-07
    Changes: Data collection, Database references, Derived calculations