6CTO

Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CF2, beta, gamma dTTP analogue


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs.

Batra, V.K.Oertell, K.Beard, W.A.Kashemirov, B.A.McKenna, C.E.Goodman, M.F.Wilson, S.H.

(2018) Biochemistry 57: 3934-3944

  • DOI: 10.1021/acs.biochem.8b00418
  • Primary Citation of Related Structures:  
    6G2Q, 6CRB, 6CRC, 6CR6, 6CR5, 6CR8, 6CR7, 6CR9, 6CR4, 6CR3

  • PubMed Abstract: 
  • We report high-resolution crystal structures of DNA polymerase (pol) β in ternary complex with a panel of incoming dNTPs carrying acidity-modified 5'-triphosphate groups. These novel dNTP analogues have a variety of halomethylene substitutions replac ...

    We report high-resolution crystal structures of DNA polymerase (pol) β in ternary complex with a panel of incoming dNTPs carrying acidity-modified 5'-triphosphate groups. These novel dNTP analogues have a variety of halomethylene substitutions replacing the bridging oxygen between Pβ and Pγ of the incoming dNTP, whereas other analogues have alkaline substitutions at the bridging oxygen. Use of these analogues allows the first systematic comparison of effects of 5'-triphosphate acidity modification on active site structures and the rate constant of DNA synthesis. These ternary complex structures with incoming dATP, dTTP, and dCTP analogues reveal the enzyme's active site is not grossly altered by the acidity modifications of the triphosphate group, yet with analogues of all three incoming dNTP bases, subtle structural differences are apparent in interactions around the nascent base pair and at the guanidinium groups of active site arginine residues. These results are important for understanding how acidity modification of the incoming dNTP's 5'-triphosphate can influence DNA polymerase activity and the significance of interactions at arginines 183 and 149 in the active site.


    Organizational Affiliation

    Genome Integrity and Structural Biology Laboratory , National Institute of Environmental Health Sciences, National Institutes of Health , 111 T. W. Alexander Drive , Research Triangle Park , North Carolina 27709 , United States.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase betaA335Homo sapiensMutation(s): 0 
Gene Names: POLB
EC: 2.7.7.7 (PDB Primary Data), 4.2.99 (PDB Primary Data)
Find proteins for P06746 (Homo sapiens)
Explore P06746 
Go to UniProtKB:  P06746
NIH Common Fund Data Resources
PHAROS  P06746
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')T16Homo sapiens
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(DOC))-3')P10Homo sapiens
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 3
        MoleculeChainsLengthOrganismImage
        DNA (5'-D(P*GP*TP*CP*GP*G)-3')D5Homo sapiens
        Small Molecules
        Ligands 4 Unique
        IDChainsName / Formula / InChI Key2D Diagram3D Interactions
        VT7
        Query on VT7

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        A
        5'-O-[(R)-{[(R)-[difluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]thymidine
        C11 H17 F2 N2 O13 P3
        PZJVGXNXDJKXPK-XLPZGREQSA-N
         Ligand Interaction
        CL
        Query on CL

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        A
        CHLORIDE ION
        Cl
        VEXZGXHMUGYJMC-UHFFFAOYSA-M
         Ligand Interaction
        MG
        Query on MG

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        A
        MAGNESIUM ION
        Mg
        JLVVSXFLKOJNIY-UHFFFAOYSA-N
         Ligand Interaction
        NA
        Query on NA

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        A, D, P
        SODIUM ION
        Na
        FKNQFGJONOIPTF-UHFFFAOYSA-N
         Ligand Interaction
        Experimental Data & Validation

        Experimental Data

        • Method: X-RAY DIFFRACTION
        • Resolution: 2.04 Å
        • R-Value Free: 0.232 
        • R-Value Work: 0.179 
        • R-Value Observed: 0.183 
        • Space Group: P 1 21 1
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 50.784α = 90
        b = 79.168β = 107.1
        c = 55.494γ = 90
        Software Package:
        Software NamePurpose
        HKL-2000data reduction
        HKL-2000data scaling
        PHENIXrefinement
        PDB_EXTRACTdata extraction
        PHENIXphasing

        Structure Validation

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        Entry History 

        Deposition Data

        Revision History 

        • Version 1.0: 2018-06-20
          Type: Initial release
        • Version 1.1: 2018-07-11
          Changes: Data collection, Database references