1S5J

Insight in DNA Replication: The crystal structure of DNA Polymerase B1 from the archaeon Sulfolobus solfataricus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Insights into DNA replication: the crystal structure of DNA polymerase B1 from the archaeon Sulfolobus solfataricus

Savino, C.Federici, L.Johnson, K.A.Vallone, B.Nastopoulos, V.Rossi, M.Pisani, F.M.Tsernoglou, D.

(2004) Structure 12: 2001-2008

  • DOI: 10.1016/j.str.2004.09.007

  • PubMed Abstract: 
  • To minimize the large number of mispairs during genome duplication owing to the large amount of DNA to be synthesized, many replicative polymerases have accessory domains with complementary functions. We describe the crystal structure of replicative ...

    To minimize the large number of mispairs during genome duplication owing to the large amount of DNA to be synthesized, many replicative polymerases have accessory domains with complementary functions. We describe the crystal structure of replicative DNA polymerase B1 from the archaeon Sulfolobus solfataricus. Comparison between other known structures indicates that although the protein is folded into the typical N-terminal, editing 3'-5'exonuclease, and C-terminal right-handed polymerase domains, it is characterized by the unusual presence of two extra alpha helices in the N-terminal domain interacting with the fingers helices to form an extended fingers subdomain, a structural feature that can account for some functional features of the protein. We explore the structural basis of specific lesion recognition, the initial step in DNA repair, describing how the N-terminal subdomain pocket of archaeal DNA polymerases could allow specific recognition of deaminated bases such as uracil and hypoxanthine in addition to the typical DNA bases.


    Related Citations: 
    • Crystallization and preliminary X-ray diffraction studies of DNA polymerase from the thermophilic archaeon Sulfolobus solfataricus
      Nastopoulos, V.,Pisani, F.M.,Savino, C.,Federici, L.,Rossi, M.,Tsernoglou, D.
      (1998) Acta Crystallogr.,Sect.D 54: 1002


    Organizational Affiliation

    Department of Biochemical Sciences and Consiglio Nazionale delle Ricerche, Institute of Molecular Biology and Pathology, University of Rome La Sapienza, P.le A. Moro 5, 00185 Roma, Italy. linda.savino@uniroma1.it




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase I
A
847Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)Mutation(s): 0 
Gene Names: dpo1 (polS)
EC: 2.7.7.7
Find proteins for P26811 (Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Go to UniProtKB:  P26811
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.232 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 187.470α = 90.00
b = 68.800β = 107.94
c = 125.850γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
CCP4data scaling
DENZOdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-11-09
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance