1EWJ

CRYSTAL STRUCTURE OF BLEOMYCIN-BINDING PROTEIN COMPLEXED WITH BLEOMYCIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.302 
  • R-Value Work: 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

  • 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 resolut ...

    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: 
    • 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.,Sect.D 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
    • 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 --: --


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BLEOMYCIN RESISTANCE DETERMINANT
A, B, C, D, E, F, G, H
126Klebsiella pneumoniaeGene Names: ble
Find proteins for P13081 (Klebsiella pneumoniae)
Go to UniProtKB:  P13081
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BLM
Query on BLM

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
BLEOMYCIN A2
N1-[3-(DIMETHYLSULFONIO)-PROPYL]BLEOMYCINAMIDE
C55 H85 N17 O21 S3
ZGCQRJQBETWECF-UAPAGMARSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BLMKd: 32 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 115.270α = 90.00
b = 117.000β = 90.00
c = 79.860γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORrefinement
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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