Database accession: MF7000084
Name: Mitomycin C-Binding Protein/Metal-Free Bleomycin A2 complex
PDB ID: 2a4x
Experimental method: X-ray (1.40 Å)
Assembly: Homodimer
Source organism: Streptomyces lavendulae
Primary publication of the structure:
Danshiitsoodol N, de Pinho CA, Matoba Y, Kumagai T, Sugiyama M
The mitomycin C (MMC)-binding protein from MMC-producing microorganisms protects from the lethal effect of bleomycin: crystallographic analysis to elucidate the binding mode of the antibiotic to the protein.
(2006) J. Mol. Biol. 360: 398-408
PMID: 16756991
Abstract:
Antibiotic-producing microorganisms must be protected from the lethal effect of their own antibiotic. We have previously determined the X-ray crystal structure of the bleomycin (Bm)-binding protein, designated BLMA, as a self-resistance determinant from Bm-producing Streptomyces verticillus, which suggests that the binding of the first Bm to one of two pockets formed in the BLMA homodimer induces the cooperative binding of the second Bm to the other pocket. In the present study, we noticed that the X-ray crystallographic structure of a self-resistance determinant from a mitomycin C-producing microorganism, designated MRDP, reveals similarity to the folding pattern on the BLMA, although no sequence homology exists. To clarify the hypothesis that MRDP may function as a resistance determinant to Bm, we characterized and determined the crystal structure of MRDP complexed with the Cu(II)-bound form of BmA(2) grouped into the Bm family of antibiotics. The biochemical and structural studies for Bm binding provide evidence that the first Bm binds anti-cooperatively to a pocket of MRDP with binding affinity of the nanomolar order, whereas the second Bm binds to the other pocket, which has binding affinity of the micromolar order. The invisibility of the second Bm in the structure agrees with the observation that Escherichia coli-expressing MRDP displays lower resistance to Bm than that expressing BLMA. The structure of MRDP, which is complexed with the Cu(II)-bound BmA(2), revealed that the gamma-aminopropyldimethylsulphonium moiety of the antibiotic is sandwiched between the peripheral residues of the binding pocket and that its positively charged sulphonium head is accommodated completely in the negatively charged region of the MRDP pocket. Furthermore, the Cu(II)-bound BmA(2) has a very compact structure, in which the bithiazole ring of BmA(2) is folded back to the metal-binding domain.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown.Molecular function: not assigned
Biological process: not assigned
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: Mitomycin-binding protein
Source organism: Streptomyces lavendulae
Length: 130 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMSARISLFAVVVEDMAKSLEFYRKLGVEIPAEADSAPHTEAVLDGGIRLAWDTVETVRSYDPEWQAPTGGHRFAIAFEFPDTASVDKKYAELVDAGYEGHLKPWNAVWGQRYAIVKDPDGNVVDLFAPLP
UniProtKB AC: O05205 (positions: 2-130)
Coverage: 99%
Name: Mitomycin-binding protein
Source organism: Streptomyces lavendulae
Length: 130 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMSARISLFAVVVEDMAKSLEFYRKLGVEIPAEADSAPHTEAVLDGGIRLAWDTVETVRSYDPEWQAPTGGHRFAIAFEFPDTASVDKKYAELVDAGYEGHLKPWNAVWGQRYAIVKDPDGNVVDLFAPLP
UniProtKB AC: O05205 (positions: 2-129)
Coverage: 98%
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/Bleomycin resistance protein/Dioxygenase superfamily
Evidence level: Indirect evidence
Evidence coverage: The full structure participates in mutual synergistic folding.
Complex Evidence:
The VOC superfamily of metalloenzymes is characterized by a three-dimensional domain-swapped arrangement of tandem βαβββ-motifs (PMID:24447055). The original gene duplication event led to the βαβββ tandem structure, which appears to require dimerization for stability. Two different forms of domain-swapped dimers may coexist in solution (PMID:12121648) in which both subunits of the homodimer participate in coordination of each metal ion and formation of the U-shaped active sites in the enzyme (PMID:24004181). The complex is predominantly dimeric in solution (gel filtration) (PMID:12121648).
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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