Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 25.12 kDa 
• Atom Count: 1737 
• Modelled Residue Count: 205 
• Deposited Residue Count: 221 
• Unique protein chains: 1

1IM4

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

• PDB DOI: 10.2210/pdb1IM4/pdb

• Classification: TRANSFERASE
• Organism(s): Saccharolobus solfataricus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-05-09 Released: 2001-09-12 
• Deposition Author(s): Pata, J.D., Zhou, B.L., Steitz, T.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.261 
• R-Value Work: 0.227 
• R-Value Observed: 0.227 

Literature

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

• PubMed: 11545744 
• DOI: 10.1016/s1097-2765(01)00310-0
• Primary Citation of Related Structures:  
  1IM4


• 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.

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Related Citations: 

• Identification of a DinB/UmuC Homolog in the Archeon Sulfolobus solfataricus
  Kulaeva, O.I., Koonin, E.V., McDonald, J.P., Randall, S.K., Rabinovich, N., Connaughton, J.F., Levine, A.S., Woodgate, R.
  (1996) Mutat Res 357: 245

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DBH	A	221	Saccharolobus solfataricus	Mutation(s): 0  Gene Names: dbh EC: 2.7.7.7
UniProt
Find proteins for P96022 (Saccharolobus solfataricus) Explore P96022  Go to UniProtKB:  P96022

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 85.988	α = 90
b = 87.542	β = 90
c = 76.983	γ = 90

Software Package:

Software Name	Purpose
SOLVE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-05-09 
• Released Date: 2001-09-12 
Deposition Author(s): Pata, J.D., Zhou, B.L., Steitz, T.A.

Revision History  

• 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