5YUX

DNA polymerase IV - DNA ternary complex 8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 

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Literature

Pyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction

Kottur, J.Nair, D.T.

(2018) Nucleic Acids Res 46: 5875-5885

  • DOI: 10.1093/nar/gky402
  • Primary Citation of Related Structures:  
    5YUR, 5YUS, 5YUT, 5YUU, 5YUV, 5YUW, 5YUX, 5YUY, 5YUZ, 5YV0, 5YV1, 5YV2, 5YV3, 5YYD, 5YYE, 5ZLV, 6IG1

  • PubMed Abstract: 
  • DNA synthesis by DNA polymerases (dPols) is central to duplication and maintenance of the genome in all living organisms. dPols catalyze the formation of a phosphodiester bond between the incoming deoxynucleoside triphosphate and the terminal primer nucleotide with the release of a pyrophosphate (PPi) group ...

    DNA synthesis by DNA polymerases (dPols) is central to duplication and maintenance of the genome in all living organisms. dPols catalyze the formation of a phosphodiester bond between the incoming deoxynucleoside triphosphate and the terminal primer nucleotide with the release of a pyrophosphate (PPi) group. It is believed that formation of the phosphodiester bond is an endergonic reaction and PPi has to be hydrolyzed by accompanying pyrophosphatase enzymes to ensure that the free energy change of the DNA synthesis reaction is negative and it can proceed in the forward direction. The fact that DNA synthesis proceeds in vitro in the absence of pyrophosphatases represents a long-standing conundrum regarding the thermodynamics of the DNA synthesis reaction. Using time-resolved crystallography, we show that hydrolysis of PPi is an intrinsic and critical step of the DNA synthesis reaction catalyzed by dPols. The hydrolysis of PPi occurs after the formation of the phosphodiester bond and ensures that the DNA synthesis reaction is energetically favorable without the need for additional enzymes. Also, we observe that DNA synthesis is a two Mg2+ ion assisted stepwise associative SN2 reaction. Overall, this study provides deep temporal insight regarding the primary enzymatic reaction responsible for genome duplication.


    Organizational Affiliation

    Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad 121 001, India.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase IVB [auth A], A [auth F]352Escherichia coli K-12Mutation(s): 0 
Gene Names: dinBdinPb0231JW0221
EC: 2.7.7.7
UniProt
Find proteins for Q47155 (Escherichia coli (strain K12))
Explore Q47155 
Go to UniProtKB:  Q47155
Protein Feature View
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  • Reference Sequence
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  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DTN1E [auth B], F [auth C], C [auth G]19Escherichia coli K-12
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DTN2D [auth H]18Escherichia coli K-12
      Protein Feature View
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      • Reference Sequence
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.04 Å
      • R-Value Free: 0.237 
      • R-Value Work: 0.185 
      • R-Value Observed: 0.188 
      • Space Group: P 1 21 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 86.07α = 90
      b = 57.09β = 94.5
      c = 109.99γ = 90
      Software Package:
      Software NamePurpose
      PHENIXrefinement
      iMOSFLMdata reduction
      SCALAdata scaling
      PHASERphasing

      Structure Validation

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      Ligand Structure Quality Assessment  



      Entry History 

      Deposition Data

      • Deposited Date: 2017-11-23 
      • Released Date: 2018-12-19 
      • Deposition Author(s): Kottur, J., Nair, D.T.

      Revision History  (Full details and data files)

      • Version 1.0: 2018-12-19
        Type: Initial release
      • Version 1.1: 2018-12-26
        Changes: Data collection, Derived calculations