5U2T

Pre-catalytic ternary complex of Human DNA Polymerase Beta With Gapped DNA substrate incoming (-)FTC-TP and Ca2+.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structural basis for the D-stereoselectivity of human DNA polymerase beta.

Vyas, R.Reed, A.J.Raper, A.T.Zahurancik, W.J.Wallenmeyer, P.C.Suo, Z.

(2017) Nucleic Acids Res 45: 6228-6237

  • DOI: 10.1093/nar/gkx252
  • Primary Citation of Related Structures:  
    5U2R, 5U2S, 5U2T

  • PubMed Abstract: 
  • Nucleoside reverse transcriptase inhibitors (NRTIs) with L-stereochemistry have long been an effective treatment for viral infections because of the strong D-stereoselectivity exhibited by human DNA polymerases relative to viral reverse transcriptases. The D-stereoselectivity of DNA polymerases has only recently been explored structurally and all three DNA polymerases studied to date have demonstrated unique stereochemical selection mechanisms ...

    Nucleoside reverse transcriptase inhibitors (NRTIs) with L-stereochemistry have long been an effective treatment for viral infections because of the strong D-stereoselectivity exhibited by human DNA polymerases relative to viral reverse transcriptases. The D-stereoselectivity of DNA polymerases has only recently been explored structurally and all three DNA polymerases studied to date have demonstrated unique stereochemical selection mechanisms. Here, we have solved structures of human DNA polymerase β (hPolβ), in complex with single-nucleotide gapped DNA and L-nucleotides and performed pre-steady-state kinetic analysis to determine the D-stereoselectivity mechanism of hPolβ. Beyond a similar 180° rotation of the L-nucleotide ribose ring seen in other studies, the pre-catalytic ternary crystal structures of hPolβ, DNA and L-dCTP or the triphosphate forms of antiviral drugs lamivudine ((-)3TC-TP) and emtricitabine ((-)FTC-TP) provide little structural evidence to suggest that hPolβ follows the previously characterized mechanisms of D-stereoselectivity. Instead, hPolβ discriminates against L-stereochemistry through accumulation of several active site rearrangements that lead to a decreased nucleotide binding affinity and incorporation rate. The two NRTIs escape some of the active site selection through the base and sugar modifications but are selected against through the inability of hPolβ to complete thumb domain closure.


    Organizational Affiliation

    The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase betaA343Homo sapiensMutation(s): 0 
Gene Names: POLB
EC: 2.7.7.7 (PDB Primary Data), 4.2.99 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P06746 (Homo sapiens)
Explore P06746 
Go to UniProtKB:  P06746
PHAROS:  P06746
Protein Feature View
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  • Reference Sequence
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  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5-MER PHOSPHORYLATED DOWNSTREAM PRIMERB [auth D]5synthetic construct
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      10- MER PRIMERC [auth P]10synthetic construct
      Protein Feature View
      Expand
      • Reference Sequence
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 4
        MoleculeChainsLengthOrganismImage
        16- MER TEMPLATED [auth T]16synthetic construct
        Protein Feature View
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        • Reference Sequence
        Small Molecules
        Ligands 4 Unique
        IDChainsName / Formula / InChI Key2D Diagram3D Interactions
        1RY (Subject of Investigation/LOI)
        Query on 1RY

        Download Ideal Coordinates CCD File 
        E [auth A][[(2R,5S)-5-(4-azanyl-5-fluoranyl-2-oxidanylidene-pyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
        C8 H13 F N3 O12 P3 S
        WIEOLFZNMKSGEX-NTSWFWBYSA-N
         Ligand Interaction
        ACT
        Query on ACT

        Download Ideal Coordinates CCD File 
        J [auth A], K [auth A], L [auth A]ACETATE ION
        C2 H3 O2
        QTBSBXVTEAMEQO-UHFFFAOYSA-M
         Ligand Interaction
        CA
        Query on CA

        Download Ideal Coordinates CCD File 
        F [auth A]CALCIUM ION
        Ca
        BHPQYMZQTOCNFJ-UHFFFAOYSA-N
         Ligand Interaction
        NA
        Query on NA

        Download Ideal Coordinates CCD File 
        G [auth A], H [auth A], I [auth A], M [auth P], N [auth P]SODIUM ION
        Na
        FKNQFGJONOIPTF-UHFFFAOYSA-N
         Ligand Interaction
        Experimental Data & Validation

        Experimental Data

        • Method: X-RAY DIFFRACTION
        • Resolution: 1.79 Å
        • R-Value Free: 0.247 
        • R-Value Work: 0.200 
        • R-Value Observed: 0.202 
        • Space Group: P 1 21 1
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 54.615α = 90
        b = 79.395β = 107.6
        c = 54.795γ = 90
        Software Package:
        Software NamePurpose
        HKL-2000data reduction
        SCALAdata scaling
        PHASERphasing
        REFMACrefinement

        Structure Validation

        View Full Validation Report



        Ligand Structure Quality Assessment  



        Entry History & Funding Information

        Deposition Data

        • Deposited Date: 2016-11-30 
        • Released Date: 2017-05-24 
        • Deposition Author(s): Vyas, R., Suo, Z.

        Funding OrganizationLocationGrant Number
        National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United StatesES024585 and ES026821
        National Science Foundation (NSF, United States)United StatesMCB-0960961

        Revision History  (Full details and data files)

        • Version 1.0: 2017-05-24
          Type: Initial release
        • Version 1.1: 2017-06-14
          Changes: Database references
        • Version 1.2: 2017-09-13
          Changes: Author supporting evidence
        • Version 1.3: 2019-11-27
          Changes: Author supporting evidence