1L3T

Crystal Structure of Bacillus DNA Polymerase I Fragment product complex with 10 base pairs of duplex DNA following addition of a single dTTP residue


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations

Johnson, S.J.Taylor, J.S.Beese, L.S.

(2003) Proc Natl Acad Sci U S A 100: 3895-3900

  • DOI: 10.1073/pnas.0630532100
  • Primary Citation of Related Structures:  
    1L3S, 1L3T, 1L3U, 1L3V, 1L5U, 1LV5

  • PubMed Abstract: 
  • DNA polymerases replicate DNA by adding nucleotides to a growing primer strand while avoiding frameshift and point mutations. Here we present a series of up to six successive replication events that were obtained by extension of a primed template directly in a crystal of the thermostable Bacillus DNA polymerase I ...

    DNA polymerases replicate DNA by adding nucleotides to a growing primer strand while avoiding frameshift and point mutations. Here we present a series of up to six successive replication events that were obtained by extension of a primed template directly in a crystal of the thermostable Bacillus DNA polymerase I. The 6-bp extension involves a 20-A translocation of the DNA duplex, representing the largest molecular movement observed in a protein crystal. In addition, we obtained the structure of a "closed" conformation of the enzyme with a bound triphosphate juxtaposed to a template and a dideoxy-terminated primer by constructing a point mutant that destroys a crystal lattice contact stabilizing the wild-type polymerase in an "open" conformation. Together, these observations allow many of the steps involved in DNA replication to be observed in the same enzyme at near atomic detail. The successive replication events observed directly by catalysis in the crystal confirm the general reaction sequence deduced from observations obtained by using several other polymerases and further refine critical aspects of the known reaction mechanism, and also allow us to propose new features that concern the regulated transfer of the template strand between a preinsertion site and an insertion site. We propose that such regulated transfer is an important element in the prevention of frameshift mutations in high-fidelity DNA polymerases. The ability to observe processive, high-fidelity replication directly in a crystal establishes this polymerase as a powerful model system for mechanistic studies in which the structural consequences of mismatches and DNA adducts are observed.


    Related Citations: 
    • Visualizing DNA Replication in a Catalytically Active Bacillus DNA Polymerase Crystal
      Kiefer, J.R., Mao, C., Braman, J.C., Beese, L.S.
      (1998) Nature 391: 304
    • Crystal structure of a thermostable Bacillus DNA polymerase I large fragment at 2.1 A resolution
      Kiefer, J.R., Mao, C., Hansen, C.J., Basehore, S.L., Hogrefe, H.H., Braman, J.C., Beese, L.S.
      (1997) Structure 5: 95

    Organizational Affiliation

    Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA Polymerase IC [auth A]580Geobacillus stearothermophilusMutation(s): 0 
Gene Names: polApol
EC: 2.7.7.7
UniProt
Find proteins for P52026 (Geobacillus stearothermophilus)
Explore P52026 
Go to UniProtKB:  P52026
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*GP*T)-3'A [auth B]10N/A
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-D(*GP*AP*CP*G*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3'B [auth C]16N/A
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranoseD2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G05551OP
GlyCosmos:  G05551OP
Small Molecules
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 4
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900003
Query on PRD_900003
DsucroseOligosaccharide / Nutrient Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.53α = 90
b = 93.356β = 90
c = 106.229γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-03-25
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary