Database accession: MF7000846
Name: Bleomycin-binding protein with metal-free bleomycin (Streptomyces verticillus)
PDB ID: 1jie
Experimental method: X-ray (1.80 Å)
Assembly: Homodimer
Source organism: Streptomyces verticillus
Primary publication of the structure:
Sugiyama M, Kumagai T, Hayashida M, Maruyama M, Matoba Y
The 1.6-A crystal structure of the copper(II)-bound bleomycin complexed with the bleomycin-binding protein from bleomycin-producing Streptomyces verticillus.
(2002) J. Biol. Chem. 277: 2311-20
PMID: 11706014
Abstract:
Bleomycin (Bm) in the culture broth of Streptomyces verticillus is complexed with Cu(2+) (Cu(II)). In the present study, we determined the x-ray crystal structures of the Cu(II)-bound and the metal-free types of Bm at a high resolution of 1.6 and 1.8 A, respectively, which are complexed with a Bm resistance determinant from Bm-producing S. verticillus, designated BLMA. In the current model of Cu(II).Bm complexed with BLMA, two Cu(II).Bm molecules bind to the BLMA dimer. The electron density map shows that the copper ion is clearly defined in the metal-binding domain of the Bm molecule. The metal ion is penta-coordinated by a tetragonal monopyramidal cage of nitrogens and binds to the primary amine of the beta-aminoalanine moiety of Bm. The binding experiment between Bm and BLMA showed that each of the two Bm-binding pockets has a different dissociation constant (K(d)(1) and K(d)(2)). The K(d)(1) value of 630 nm for the first Bm binding is larger than the K(d)(2) value of 120 nm, indicating that the first Bm binding gives rise to a cooperative binding of the second Bm to the other pocket.
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, B
Notes: All chains according to the most probable oligomerization state stored in PDBe were considered.
Number of unique protein segments: 1
Name: Bleomycin resistance protein
Source organism: Streptomyces verticillus
Length: 122 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMVKFLGAVPVLTAVDVPANVSFWVDTLGFEKDFGDRDFAGVRRGDIRLHISRTEHQIVADNTSAWIEVTDPDALHEEWARAVSTDYADTSGPAMTPVGESPAGREFAVRDPAGNCVHFTAGE
UniProtKB AC: Q53793 (positions: 1-122)
Coverage: 100%
Name: Bleomycin resistance protein
Source organism: Streptomyces verticillus
Length: 122 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMVKFLGAVPVLTAVDVPANVSFWVDTLGFEKDFGDRDFAGVRRGDIRLHISRTEHQIVADNTSAWIEVTDPDALHEEWARAVSTDYADTSGPAMTPVGESPAGREFAVRDPAGNCVHFTAGE
UniProtKB AC: Q53793 (positions: 1-122)
Coverage: 100%
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 B:
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)
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