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: 1.60 Å
  • R-Value Free: 0.207 
  • R-Value Observed: 0.158 

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:  
    1JIF, 1JIE

  • 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 A, respectively, which are complexed with a Bm resistance determinant from Bm-producing S ...

    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 D Biol Crystallogr 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
bleomycin-binding proteinA, B122Streptomyces verticillusMutation(s): 0 
Gene Names: blmAble
Find proteins for Q53793 (Streptomyces verticillus)
Explore Q53793 
Go to UniProtKB:  Q53793
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BLM
Query on BLM

Download Ideal Coordinates CCD File 
G [auth B], H [auth B]BLEOMYCIN A2
C55 H85 N17 O21 S3
ZGCQRJQBETWECF-UAPAGMARSA-N
 Ligand Interaction
CU
Query on CU

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A], F [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BLMKd :  630   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.207 
  • R-Value Observed: 0.158 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.73α = 90
b = 83.47β = 106.2
c = 43.06γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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