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 4IAG | pdb_00004iag

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.231 (Depositor), 0.218 (DCC) 
  • R-Value Work: 
    0.189 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 
    0.191 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4IAG

This is version 1.5 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: https://doi.org/10.1021/acs.biochem.5b01008
  • Primary Citation Related Structures: 
    4IAG, 5CJ3

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 15.6 kDa 
  • Atom Count: 1,059 
  • Modeled Residue Count: 121 
  • Deposited Residue Count: 135 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Zbm binding protein135Streptomyces pilosusMutation(s): 0 
Gene Names: zbmA
UniProt
Find proteins for B9UIZ4 (Streptomyces pilosus)
Explore B9UIZ4 
Go to UniProtKB:  B9UIZ4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB9UIZ4
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL

Query on GOL



Download:Ideal Coordinates CCD File
D [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
B [auth A]
C [auth A]
E [auth A]
F [auth A]
G [auth A]
B [auth A],
C [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.231 (Depositor), 0.218 (DCC) 
  • R-Value Work:  0.189 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 0.191 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.787α = 90
b = 38.787β = 90
c = 268.524γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DMphasing
REFMACrefinement
PDB_EXTRACTdata extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-20
    Type: Initial release
  • Version 1.1: 2013-12-25
    Changes: Structure summary
  • Version 1.2: 2015-11-11
    Changes: Database references
  • Version 1.3: 2015-12-02
    Changes: Database references
  • Version 1.4: 2017-11-15
    Changes: Refinement description
  • Version 1.5: 2025-03-26
    Changes: Data collection, Database references, Derived calculations, Structure summary