Database accession: MF7000845
Name: Bleomycin-binding protein (Streptomyces verticillus)
PDB ID: 1qto
Experimental method: X-ray (1.50 Å)
Assembly: Homodimer
Source organism: Streptomyces verticillus
Primary publication of the structure:
Kawano Y, Kumagai T, Muta K, Matoba Y, Davies J, Sugiyama M
The 1.5 A crystal structure of a bleomycin resistance determinant from bleomycin-producing Streptomyces verticillus.
(2000) J. Mol. Biol. 295: 915-25
PMID: 10656800
Abstract:
Bleomycin (Bm)-binding protein, designated BLMA, which is a Bm resistance determinant from Bm-producing Streptomyces verticillus, was crystallized in a form suitable for X-ray diffraction analysis. The diffraction intensity data were collected up to a resolution of 1.5 A with a merging R-value of 0.054 at a completeness of 94 %. The BLMA structure, determined by the single isomorphous replacement method including the anomalous scattering effect (SIR-AS) at a resolution of 2.0 A, was refined at 1.5 A resolution. The final R-factor was 19.0 % and R(free) was 22.1 % including 91 water molecules. The crystal packing showed a dimer form, which was generated by arm exchange. The 1.5 A high-resolution experiment allowed an analysis of the side-chain disorder of BLMA. The structural comparison of BLMA with a homologous protein from Streptoalloteichus hindustanus, designated Shble protein, showed that a Ser100-Gly103 loop was farther from the groove, which is a Bm-binding site, in BLMA than in the Shble protein. Furthermore the hydrophobicity of the groove in BLMA is much lower than that in the Shble protein. The structural differences between these proteins may be responsible for the observation that a half-saturating concentration (K(1/2)) of Bm is higher for BLMA than for the Shble protein.
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: 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 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)
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