Database accession: MF7000849
Name: Zorbamycin-binding protein (ZbmA) (Streptomyces flavoviridis)
PDB ID: 4iag
Experimental method: X-ray (1.90 Å)
Assembly: Homodimer
Source organism: Streptomyces pilosus
Primary publication of the structure:
Rudolf JD, Bigelow L, Chang C, Cuff ME, Lohman JR, Chang CY, Ma M, Yang D, Clancy S, Babnigg G, Joachimiak A, Phillips GN, Shen B
Crystal Structure of the Zorbamycin-Binding Protein ZbmA, the Primary Self-Resistance Element in Streptomyces flavoviridis ATCC21892.
(2015) Biochemistry 54: 6842-51
PMID: 26512730
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.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown.Molecular function: not assigned
Biological process:
response to antibiotic response to antibiotic
Cellular component: not assigned
Structural annotations of the participating protein chains.Entry contents: 2 distinct polypeptide molecules
Chains: A, A-2
Notes: All chains according to the most probable oligomerization state stored in PDBe were considered.
Number of unique protein segments: 1
Name: Zbm binding protein
Source organism: Streptomyces pilosus
Length: 132 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMAVLLSGVPVLAALDVSTTQKFWIEVLGFTEEFLTEDFGGVSRDGVELFICSVEDQVVPDNTQAWLRVRDIDALHAEWSARVSSDYADASHPAMTAIREVPWGREFGLRDPAGNLVHFSELSEAAETTRTVR
UniProtKB AC: B9UIZ4 (positions: 2-122)
Coverage: 91%
Name: Zbm binding protein
Source organism: Streptomyces pilosus
Length: 132 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMAVLLSGVPVLAALDVSTTQKFWIEVLGFTEEFLTEDFGGVSRDGVELFICSVEDQVVPDNTQAWLRVRDIDALHAEWSARVSSDYADASHPAMTAIREVPWGREFGLRDPAGNLVHFSELSEAAETTRTVR
UniProtKB AC: B9UIZ4 (positions: 2-122)
Coverage: 91%
Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding. Representative domain in related structures: Glyoxalase superfamily
Evidence level: Indirect evidence
Evidence coverage: The full structure participates in mutual synergistic folding.
Complex Evidence:
The bleomycin resistance protein forms a tight dimer with a large hydrophobic interface and domain-swapping involving the N-terminal end of both monomers. Only dimeric form could be detected in solution by several dedicated methods. The antibiotic binds to he dimer interface contacting both monomers (PMID:7516875). Temperature-induced equilibrium unfolding experiments on the Shble protein and its engineered variants suggested a two-state model of unfolding (although unfolding was largely irreversible with only 40% of the native folded signal regained during the refolding phase) and the strong stabilizing effect of bleomycin on the dimer based on largely increased thermostability of the protein in the presence of the antibiotic (PMID:15640151).
Chain A:
N/A
Chain A-2:
N/A
Surface and contacts features:
Structures from the PDB that contain the same number of proteins, and the proteins from the two structures show a sufficient degree of pairwise similarity, i.e. they belong to the same UniRef90 cluster (the full proteins exhibit at least 90% sequence identity) and convey roughly the same region to their respective interactions (the two regions from the two proteins share a minimum of 70% overlap). Download the CIF file (.cif)
Download this entry's XML file (.xml)
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