6IG1

DNA polymerase IV - DNA ternary complex 10

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

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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: https://doi.org/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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase IVA [auth F],
B [auth A]		352Escherichia coli K-12Mutation(s): 0 
Gene Names: dinB, dinP, b0231, JW0221
EC: 2.7.7.7
UniProt
Find proteins for Q47155 (Escherichia coli (strain K12))
Explore Q47155 
Go to UniProtKB:  Q47155
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ47155
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DTN3C [auth G],
D [auth H],
E [auth B],
F [auth C]		19Escherichia coli K-12
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.38α = 90
b = 57.16β = 94.49
c = 110.58γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
India--

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-28
    Type: Initial release