5CJ3

Crystal structure of the zorbamycin binding protein (ZbmA) from Streptomyces flavoviridis with zorbamycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6499 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.2 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, B
135Streptomyces flavoviridisMutation(s): 0 
Gene Names: zbmA
Find proteins for B9UIZ4 (Streptomyces flavoviridis)
Go to UniProtKB:  B9UIZ4
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
52G
Query on 52G

Download SDF File 
Download CCD File 
A, B
Zorbamycin
(2R,3S,4S,5R,6R)-2-{[(2R,3S,4S,5S,6S)-2-{[(1R,2S)-2-[({6-amino-2-[(1S)-3-amino-1-{[(2S)-2,3-diamino-3-oxopropyl]amino}-3-oxopropyl]-5-methylpyrimidin-4-yl}carbonyl)amino]-3-{[(3R,4S,5S)-6-{[(2S)-1-({2-[(4'R)-4-{[(3E)-3-amino-3-iminopropyl]carbamoyl}-4',5'-dihydro-2,4'-bi-1,3-thiazol-2'-yl]ethyl}amino)-3-hydroxy-3-methyl-1-oxobutan-2-yl]amino}-1,4-dihydroxy-5-methyl-6-oxohexan-3-yl]amino}-1-(1H-imidazol-4-yl)-3-oxopropyl]oxy}-4,5-dihydroxy-6-methyltetrahydro-2H-pyran-3-yl]oxy}-3,5-dihydroxy-6-(hydroxymethyl)
C55 H85 N19 O21 S2
UJKRUPHWCPAJIL-CPLCKGKLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6499 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 40.737α = 90.00
b = 78.989β = 90.00
c = 79.542γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000phasing
SBC-Collectdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2015-07-22
    Type: Initial release
  • Version 1.1: 2015-11-11
    Type: Database references
  • Version 1.2: 2015-11-25
    Type: Database references