4IAG

Crystal structure of ZbmA, the zorbamycin binding protein from Streptomyces flavoviridis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Crystal Structure of the Zorbamycin-Binding Protein ZbmA, the Primary Self-Resistance Element in Streptomyces flavoviridis ATCC21892.

Rudolf, J.D.Bigelow, L.Chang, C.Cuff, M.E.Lohman, J.R.Chang, C.Y.Ma, M.Yang, D.Clancy, S.Babnigg, G.Joachimiak, A.Phillips, G.N.Shen, B.

(2015) Biochemistry 54: 6842-6851

  • DOI: 10.1021/acs.biochem.5b01008
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The bleomycins (BLMs), tallysomycins (TLMs), phleomycin, and zorbamycin (ZBM) are members of the BLM family of glycopeptide-derived antitumor antibiotics. The BLM-producing Streptomyces verticillus ATCC15003 and the TLM-producing Streptoalloteichus h ...

    The bleomycins (BLMs), tallysomycins (TLMs), phleomycin, and zorbamycin (ZBM) are members of the BLM family of glycopeptide-derived antitumor antibiotics. The BLM-producing Streptomyces verticillus ATCC15003 and the TLM-producing Streptoalloteichus hindustanus E465-94 ATCC31158 both possess at least two self-resistance elements, an N-acetyltransferase and a binding protein. The N-acetyltransferase provides resistance by disrupting the metal-binding domain of the antibiotic that is required for activity, while the binding protein confers resistance by sequestering the metal-bound antibiotic and preventing drug activation via molecular oxygen. We recently established that the ZBM producer, Streptomyces flavoviridis ATCC21892, lacks the N-acetyltransferase resistance gene and that the ZBM-binding protein, ZbmA, is sufficient to confer resistance in the producing strain. To investigate the resistance mechanism attributed to ZbmA, we determined the crystal structures of apo and Cu(II)-ZBM-bound ZbmA at high resolutions of 1.90 and 1.65 Å, respectively. A comparison and contrast with other structurally characterized members of the BLM-binding protein family revealed key differences in the protein-ligand binding environment that fine-tunes the ability of ZbmA to sequester metal-bound ZBM and supports drug sequestration as the primary resistance mechanism in the producing organisms of the BLM family of antitumor antibiotics.


    Organizational Affiliation

    Department of Chemistry, The Scripps Research Institute , Jupiter, Florida 33458, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Zbm binding protein
A
135Streptomyces flavoviridisMutation(s): 0 
Gene Names: zbmA
Find proteins for B9UIZ4 (Streptomyces flavoviridis)
Go to UniProtKB:  B9UIZ4
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
ILY
Query on ILY
A
NON-POLYMERC9 H20 N2 O2LYS
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.189 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 38.787α = 90.00
b = 38.787β = 90.00
c = 268.524γ = 120.00
Software Package:
Software NamePurpose
SOLVEphasing
DENZOdata reduction
Cootmodel building
HKL-3000data scaling
SBC-Collectdata collection
HKL-3000phasing
PDB_EXTRACTdata extraction
CCP4phasing
SCALEPACKdata scaling
SHELXEmodel building
DMphasing
RESOLVEphasing
REFMACrefinement
ARP/wARPmodel building
MLPHAREphasing
Omodel building
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2013-02-20
    Type: Initial release
  • Version 1.1: 2013-12-25
    Type: Structure summary
  • Version 1.2: 2015-11-11
    Type: Database references
  • Version 1.3: 2015-12-02
    Type: Database references
  • Version 1.4: 2017-11-15
    Type: Refinement description