4IAG image
Deposition Date 2012-12-06
Release Date 2013-02-20
Last Version Date 2025-03-26
Entry Detail
PDB ID:
4IAG
Title:
Crystal structure of ZbmA, the zorbamycin binding protein from Streptomyces flavoviridis
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.90 Å
R-Value Free:
0.23
R-Value Work:
0.18
R-Value Observed:
0.19
Space Group:
P 65 2 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Zbm binding protein
Gene (Uniprot):zbmA
Chain IDs:A
Chain Length:135
Number of Molecules:1
Biological Source:Streptomyces flavoviridis
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
ILY A LYS N~6~-PROPAN-2-YL-L-LYSINE
MSE A MET SELENOMETHIONINE
Primary Citation
Crystal Structure of the Zorbamycin-Binding Protein ZbmA, the Primary Self-Resistance Element in Streptomyces flavoviridis ATCC21892.
Biochemistry 54 6842 6851 (2015)
PMID: 26512730 DOI: 10.1021/acs.biochem.5b01008

Abstact

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.

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Primary Citation of related structures