1EWJ

CRYSTAL STRUCTURE OF BLEOMYCIN-BINDING PROTEIN COMPLEXED WITH BLEOMYCIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structures of the transposon Tn5-carried bleomycin resistance determinant uncomplexed and complexed with bleomycin.

Maruyama, M.Kumagai, T.Matoba, Y.Hayashida, M.Fujii, T.Hata, Y.Sugiyama, M.

(2001) J Biol Chem 276: 9992-9999

  • DOI: 10.1074/jbc.M009874200
  • Primary Citation of Related Structures:  
    1ECS, 1EWJ

  • PubMed Abstract: 
  • The transposon Tn5 carries a gene designated ble that confers resistance to bleomycin (Bm). In this study, we determined the x-ray crystal structures of the ble gene product, designated BLMT, uncomplexed and complexed with Bm at 1.7 and 2.5 A resolution, respectively ...

    The transposon Tn5 carries a gene designated ble that confers resistance to bleomycin (Bm). In this study, we determined the x-ray crystal structures of the ble gene product, designated BLMT, uncomplexed and complexed with Bm at 1.7 and 2.5 A resolution, respectively. The structure of BLMT is a dimer with two Bm-binding pockets composed of two large concavities and two long grooves. This crystal structure of BLMT complexed with Bm gives a precise mode for binding of the antibiotic to BLMT. The conformational change of BLMT generated by binding to Bm occurs at a beta-turn composed of the residues from Gln(97) to Thr(102). Crystallographic analysis of Bm bound to BLMT shows that two thiazolium rings of the bithiazole moiety are in the trans conformation. The axial ligand, which binds a metal ion, seems to be the primary amine in the beta-aminoalanine moiety. This report, which is the first with regard to the x-ray crystal structure of Bm, shows that the bithiazole moiety of Bm is far from the metal-binding domain. That is, Bm complexed with BLMT takes a more extended form than the drug complexed with DNA.


    Related Citations: 
    • The 1.7 A Crystal structure of a bleomycin resistance protein encoded on the transposon Tn5
      Maruyama, M., Matoba, Y., Kumagai, T., Sugiyama, M.
      () To be published --: --
    • Crystallization and preliminary X-ray diffraction studies of bleomycin-binding protein encoded on the transposon Tn5
      Kumagai, T., Maruyama, M., Matoba, Y., Kawano, Y., Sugiyama, M.
      (1999) Acta Crystallogr D Biol Crystallogr 55: 1095
    • The 1.5 A crystal structure of a bleomycin resistance determinant from bleomycin-producing Streptomyces verticillus
      Kawano, Y., Kumagai, T., Muta, K., Matoba, Y., Sugiyama, M.
      (2000) J Mol Biol 295: 915

    Organizational Affiliation

    Institute of Pharmaceutical Sciences, Faculty of Medicine, Hiroshima University, Kasumi 1-2-3, Minami-ku, Hiroshima, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BLEOMYCIN RESISTANCE DETERMINANT
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H
126Klebsiella pneumoniaeMutation(s): 0 
Gene Names: TRANSPOSON TN5ble
UniProt
Find proteins for P13081 (Klebsiella pneumoniae)
Explore P13081 
Go to UniProtKB:  P13081
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13081
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
BLM PDBBind:  1EWJ Kd: 32 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.27α = 90
b = 117β = 90
c = 79.86γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-04-26
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description