4YFU

Crystal structure of open Bacillus fragment DNA polymerase bound to DNA and dTTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

The Closing Mechanism of DNA Polymerase I at Atomic Resolution.

Miller, B.R.Beese, L.S.Parish, C.A.Wu, E.Y.

(2015) Structure 23: 1609-1620

  • DOI: 10.1016/j.str.2015.06.016
  • Primary Citation of Related Structures:  
    4YFU

  • PubMed Abstract: 
  • DNA polymerases must quickly and accurately distinguish between similar nucleic acids to form Watson-Crick base pairs and avoid DNA replication errors. Deoxynucleoside triphosphate (dNTP) binding to the DNA polymerase active site induces a large conformational change that is difficult to characterize experimentally on an atomic level ...

    DNA polymerases must quickly and accurately distinguish between similar nucleic acids to form Watson-Crick base pairs and avoid DNA replication errors. Deoxynucleoside triphosphate (dNTP) binding to the DNA polymerase active site induces a large conformational change that is difficult to characterize experimentally on an atomic level. Here, we report an X-ray crystal structure of DNA polymerase I bound to DNA in the open conformation with a dNTP present in the active site. We use this structure to computationally simulate the open to closed transition of DNA polymerase in the presence of a Watson-Crick base pair. Our microsecond simulations allowed us to characterize the key steps involved in active site assembly, and propose the sequence of events involved in the prechemistry steps of DNA polymerase catalysis. They also reveal new features of the polymerase mechanism, such as a conserved histidine as a potential proton acceptor from the primer 3'-hydroxyl.


    Organizational Affiliation

    Department of Biology, University of Richmond, 28 Westhampton Way, Richmond, VA 23173, USA; Department of Biochemistry, Duke University Medical Center, 255 Nanaline H. Duke Building, Durham, NC 27710, USA. Electronic address: ewu@richmond.edu.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymeraseA, B [auth D]580Geobacillus stearothermophilusMutation(s): 2 
Gene Names: polA
EC: 2.7.7.7
Find proteins for E1C9K5 (Geobacillus stearothermophilus)
Explore E1C9K5 
Go to UniProtKB:  E1C9K5
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    Primer DNAC [auth B], E9synthetic construct
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      Template DNAD [auth C], F14synthetic construct
      Oligosaccharides

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      Entity ID: 4
      MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
      beta-D-fructofuranose-(2-1)-alpha-D-glucopyranoseG, H2 N/A Oligosaccharides Interaction
      Small Molecules
      Ligands 3 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      TTP
      Query on TTP

      Download Ideal Coordinates CCD File 
      I [auth A]THYMIDINE-5'-TRIPHOSPHATE
      C10 H17 N2 O14 P3
      NHVNXKFIZYSCEB-XLPZGREQSA-N
       Ligand Interaction
      2DT
      Query on 2DT

      Download Ideal Coordinates CCD File 
      K [auth B], L [auth E]3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE
      C10 H15 N2 O7 P
      WVNRRNJFRREKAR-JGVFFNPUSA-N
       Ligand Interaction
      SO4
      Query on SO4

      Download Ideal Coordinates CCD File 
      J [auth D]SULFATE ION
      O4 S
      QAOWNCQODCNURD-UHFFFAOYSA-L
       Ligand Interaction
      Modified Residues  1 Unique
      IDChainsTypeFormula2D DiagramParent
      CME
      Query on CME
      A, B [auth D]L-PEPTIDE LINKINGC5 H11 N O3 S2CYS
      Biologically Interesting Molecules (External Reference) 1 Unique
      Entity ID: 4
      IDChainsNameType/Class2D Diagram3D Interactions
      PRD_900003
      Query on PRD_900003
      G, HsucroseOligosaccharide /  Nutrient

      --

      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 1.50 Å
      • R-Value Free: 0.230 
      • R-Value Work: 0.195 
      • R-Value Observed: 0.197 
      • Space Group: P 21 21 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 93.23α = 90
      b = 108.1β = 90
      c = 151.34γ = 90
      Software Package:
      Software NamePurpose
      REFMACrefinement
      DENZOdata reduction
      XSCALEdata scaling
      PDB_EXTRACTdata extraction
      REFMACphasing
      Cootmodel building

      Structure Validation

      View Full Validation Report



      Entry History & Funding Information

      Deposition Data

      • Deposited Date: 2015-02-25 
      • Released Date: 2015-07-22 
      • Deposition Author(s): Wu, E.Y.

      Funding OrganizationLocationGrant Number
      Jeffress TrustUnited States--

      Revision History  (Full details and data files)

      • Version 1.0: 2015-07-22
        Type: Initial release
      • Version 1.1: 2015-08-12
        Changes: Refinement description
      • Version 1.2: 2015-09-16
        Changes: Database references
      • Version 2.0: 2020-07-29
        Type: Remediation
        Reason: Carbohydrate remediation
        Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary