2R2T

d(ATTTAGTTAACTAAAT) complexed with MMLV RT catalytic fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of DNA-bound Co(III) bleomycin B2: Insights on intercalation and minor groove binding.

Goodwin, K.D.Lewis, M.A.Long, E.C.Georgiadis, M.M.

(2008) Proc.Natl.Acad.Sci.Usa 105: 5052-5056

  • DOI: 10.1073/pnas.0708143105
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bleomycins constitute a widely studied class of complex DNA cleaving natural products that are used to treat various cancers. Since their first isolation, the bleomycins have provided a paradigm for the development and discovery of additional DNA-cle ...

    Bleomycins constitute a widely studied class of complex DNA cleaving natural products that are used to treat various cancers. Since their first isolation, the bleomycins have provided a paradigm for the development and discovery of additional DNA-cleaving chemotherapeutic agents. The bleomycins consist of a disaccharide-modified metal-binding domain connected to a bithiazole/C-terminal tail via a methylvalerate-Thr linker and induce DNA damage after oxygen activation through site-selective cleavage of duplex DNA at 5'-GT/C sites. Here, we present crystal structures of two different 5'-GT containing oligonucleotides in both the presence and absence of bound Co(III).bleomycin B(2). Several findings from our studies impact the current view of bleomycin binding to DNA. First, we report that the bithiazole intercalates in two distinct modes and can do so independently of well ordered minor groove binding of the metal binding/disaccharide domains. Second, the Co(III)-coordinating equatorial ligands in our structure include the imidazole, histidine amide, pyrimidine N1, and the secondary amine of the beta aminoalanine, whereas the primary amine acts as an axial ligand. Third, minor groove binding of Co(III).bleomycin involves direct hydrogen bonding interactions of the metal binding domain and disaccharide with the DNA. Finally, modeling of a hydroperoxide ligand coordinated to Co(III) suggests that it is ideally positioned for initiation of C4'-H abstraction.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Purdue School of Science, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Reverse transcriptase
A
255Moloney murine leukemia virusMutation(s): 0 
Gene Names: gag-pol
Find proteins for P03355 (Moloney murine leukemia virus)
Go to UniProtKB:  P03355
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*DAP*DTP*DTP*DTP*DAP*DGP*DTP*DT)-3')B8N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(P*DAP*DAP*DCP*DTP*DAP*DAP*DAP*DT)-3')G8N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.224 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 54.641α = 90.00
b = 145.801β = 90.00
c = 46.881γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
CNSrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-07-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description