1JIF

Crystal structure of bleomycin-binding protein from bleomycin-producing Streptomyces verticillus complexed with copper(II)-bleomycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The 1.6-A crystal structure of the copper(II)-bound bleomycin complexed with the bleomycin-binding protein from bleomycin-producing Streptomyces verticillus.

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

(2002) J.Biol.Chem. 277: 2311-2320

  • DOI: 10.1074/jbc.M103278200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bleomycin (Bm) in the culture broth of Streptomyces verticillus is complexed with Cu(2+) (Cu(II)). In the present study, we determined the x-ray crystal structures of the Cu(II)-bound and the metal-free types of Bm at a high resolution of 1.6 and 1.8 ...

    Bleomycin (Bm) in the culture broth of Streptomyces verticillus is complexed with Cu(2+) (Cu(II)). In the present study, we determined the x-ray crystal structures of the Cu(II)-bound and the metal-free types of Bm at a high resolution of 1.6 and 1.8 A, respectively, which are complexed with a Bm resistance determinant from Bm-producing S. verticillus, designated BLMA. In the current model of Cu(II).Bm complexed with BLMA, two Cu(II).Bm molecules bind to the BLMA dimer. The electron density map shows that the copper ion is clearly defined in the metal-binding domain of the Bm molecule. The metal ion is penta-coordinated by a tetragonal monopyramidal cage of nitrogens and binds to the primary amine of the beta-aminoalanine moiety of Bm. The binding experiment between Bm and BLMA showed that each of the two Bm-binding pockets has a different dissociation constant (K(d)(1) and K(d)(2)). The K(d)(1) value of 630 nm for the first Bm binding is larger than the K(d)(2) value of 120 nm, indicating that the first Bm binding gives rise to a cooperative binding of the second Bm to the other pocket.


    Related Citations: 
    • The 1.5 A crystal structure of a bleomycin resistance determinant from bleomycin-producing Streptomyces verticillus
      Kawano, Y.,Kumagai, T.,Muta, K.,Matoba, Y.,Davies, J.,Sugiyama, M.
      (2000) J.Mol.Biol. 295: 915
    • 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
    • Crystallization and preliminary X-ray diffraction studies of bleomycin-binding protein from bleomycin-producing Streptomyces verticillus
      Kumagai, T.,Muta, K.,Matoba, Y.,Kawano, Y.,Kamiya, N.,Davies, J.,Sugiyama, M.
      (1998) Acta Crystallogr.,Sect.D 54: 127


    Organizational Affiliation

    Institute of Pharmaceutical Sciences, Faculty of Medicine, Hiroshima University, Kasumi 1-2-3, Minami-ku, Hiroshima 734-8551, Japan. sugi@hiroshima-u.ac.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
bleomycin-binding protein
A, B
122Streptomyces verticillusMutation(s): 0 
Gene Names: ble
Find proteins for Q53793 (Streptomyces verticillus)
Go to UniProtKB:  Q53793
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CU
Query on CU

Download SDF File 
Download CCD File 
A, B
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
BLM
Query on BLM

Download SDF File 
Download CCD File 
B
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: 630 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.207 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 35.730α = 90.00
b = 83.470β = 106.20
c = 43.060γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
SHELXL-97refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-02-06
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance