5HHH

Structure of human DNA polymerase beta Host-Guest complexed with the control G for N7-CBZ-platination


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Synthesis, structure, and biological evaluation of a platinum-carbazole conjugate.

Cheun, Y.Koag, M.C.Naguib, Y.W.Ouzon-Shubeita, H.Cui, Z.Pakotiprapha, D.Lee, S.

(2018) Chem Biol Drug Des 91: 116-125

  • DOI: 10.1111/cbdd.13062
  • Primary Citation of Related Structures:  
    5HHH, 5HHI

  • PubMed Abstract: 
  • Cisplatin resistance is caused, in part, by the efficient removal of the helix-distorting cisplatin 1,2-intrastrand cross-links by nucleotide excision repair (NER) machinery. To make a platinum-DNA adduct that causes less helical distortion than the cisplatin 1,2-intrastrand adduct, we designed and synthesized a monofunctional platinum-carbazole conjugate (carbazoplatin) ...

    Cisplatin resistance is caused, in part, by the efficient removal of the helix-distorting cisplatin 1,2-intrastrand cross-links by nucleotide excision repair (NER) machinery. To make a platinum-DNA adduct that causes less helical distortion than the cisplatin 1,2-intrastrand adduct, we designed and synthesized a monofunctional platinum-carbazole conjugate (carbazoplatin). The 2.5 Å crystal structure of carbazoplatin-DNA adduct revealed both the monoplatination of the N7 of a guanine (G) base and the intercalation into two G:C base pairs, while causing a minor distortion of the DNA helix. A 50-mer dsDNA containing a single carbazoplatin lesion was poorly processed by UvrABC endonuclease, the prokaryotic NER machinery that detects helical distortion and performs dual incision around the lesion. Our cell viability assay indicated that the cytotoxic pathways of carbazoplatin might be different from those of cisplatin; carbazoplatin was 5-8 times more cytotoxic than cisplatin against PANC-1 and MDA-MB-231 cancer cell lines.


    Organizational Affiliation

    Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase betaA327Homo 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
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*AP*GP*GP*AP*GP*CP*AP*GP*G)-3')B [auth T]16synthetic construct
    Protein Feature View
    Expand
    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(P*CP*CP*TP*GP*CP*TP*CP*CP*TP*C)-3')C [auth P]10synthetic construct
      Protein Feature View
      Expand
      • Reference Sequence
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 4
        MoleculeChainsLengthOrganismImage
        DNA (5'-D(P*GP*TP*CP*GP*G)-3')D5synthetic construct
        Protein Feature View
        Expand
        • Reference Sequence
        Small Molecules
        Ligands 1 Unique
        IDChainsName / Formula / InChI Key2D Diagram3D Interactions
        NA
        Query on NA

        Download Ideal Coordinates CCD File 
        E [auth A], F [auth A]SODIUM ION
        Na
        FKNQFGJONOIPTF-UHFFFAOYSA-N
         Ligand Interaction
        Experimental Data & Validation

        Experimental Data

        • Method: X-RAY DIFFRACTION
        • Resolution: 2.36 Å
        • R-Value Free: 0.265 
        • R-Value Work: 0.213 
        • R-Value Observed: 0.216 
        • Space Group: P 1 21 1
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 51.334α = 90
        b = 84.595β = 107.49
        c = 55.523γ = 90
        Software Package:
        Software NamePurpose
        PHENIXrefinement
        DENZOdata reduction
        HKL-2000data scaling
        MOLREPphasing

        Structure Validation

        View Full Validation Report




        Entry History 

        Deposition Data

        • Deposited Date: 2016-01-11 
        • Released Date: 2017-01-18 
        • Deposition Author(s): Koag, M.-C., Lee, S.

        Revision History  (Full details and data files)

        • Version 1.0: 2017-01-18
          Type: Initial release
        • Version 1.1: 2018-07-25
          Changes: Data collection, Database references