The 1.6-Å Crystal Structure of the Copper(II)-bound Bleomycin Complexed with the Bleomycin-binding Protein from Bleomycin-producing Streptomyces verticillus

Sugiyama, Masanori; Kumagai, Toru; Hayashida, Minoru; Maruyama, Masafumi; Matoba, Yasuyuki

doi:10.1074/jbc.m103278200

Cited by 60 publications

(91 citation statements)

References 42 publications

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“…Nonetheless, an important role for the disaccharide moiety in DNA-binding and cleavage by HOOFe(III)⅐bleomycin has been indicated by the reduced DNA cleavage activity of deglycobleomycin in vitro (35,36). One possibility is that the gulopyranose serves as a ''space-filling'' unit allowing the metal binding domain to adopt an optimized and stabilized orientation relative to the target C4Ј-H. We further note that the respective orientations and intramolecular hydrogen-bonding interactions of the metal-binding and disaccharide domains of Co⅐BLM bound to 1 are similar to those observed in the crystal structure of Cu(II)⅐bleomycin bound to a bleomycin resistance protein (37) (Fig. S1).…”

Section: Discussionsupporting

confidence: 51%

Crystal structure of DNA-bound Co(III)·bleomycin B ₂ : Insights on intercalation and minor groove binding

Goodwin

Lewis

Long

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

108

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Bleomycins constitute a widely studied class of complex DNA cleaving natural products that are used to treat various cancers. Since their first isolation, the bleomycins have provided a paradigm for the development and discovery of additional DNA-cleaving chemotherapeutic agents. The bleomycins consist of a disaccharide-modified metal-binding domain connected to a bithiazole/Cterminal tail via a methylvalerate-Thr linker and induce DNA damage after oxygen activation through site-selective cleavage of duplex DNA at 5-GT/C sites. Here, we present crystal structures of two different 5-GT containing oligonucleotides in both the presence and absence of bound Co(III)⅐bleomycin B 2. Several findings from our studies impact the current view of bleomycin binding to DNA. First, we report that the bithiazole intercalates in two distinct modes and can do so independently of well ordered minor groove binding of the metal binding/disaccharide domains. Second, the Co(III)-coordinating equatorial ligands in our structure include the imidazole, histidine amide, pyrimidine N1, and the secondary amine of the ␤ aminoalanine, whereas the primary amine acts as an axial ligand. Third, minor groove binding of Co(III)⅐bleomycin involves direct hydrogen bonding interactions of the metal binding domain and disaccharide with the DNA. Finally, modeling of a hydroperoxide ligand coordinated to Co(III) suggests that it is ideally positioned for initiation of C4-H abstraction.antitumor ͉ DNA-binding ͉ HOO-Co(III) bleomycin T he bleomycins are a family of glycopeptide-derived antitumor natural products first isolated from Streptomyces verticillus by Umezawa (1). Bleomycins are used to treat lymphomas (2, 3) and testicular cancers (4), most often in combination therapies. The clinical efficacy of the bleomycins is thought to derive from their ability to mediate single-and double-strand DNA cleavage (5, 6) resulting from Fe 2ϩ and O 2 -dependent (7) C4Ј-H abstraction from pyrimidine nucleotides (8) contained within 5Ј-GT/C dinucleotide sites (9). Of the DNA lesions formed, double-strand DNA cleavage is thought to be most relevant to the cytotoxicity of bleomycin. Although DNA is the generally accepted locus of drug activity, O 2 -activated Fe(II)⅐bleomycin also mediates the selective cleavage of RNA (10), and Cu(I)⅐bleomycin is capable of cleaving DNA (11); however, the in vivo relevance of this alternative nucleic acid target and metal ion remain to be fully determined.The metallobleomycins have served as an important paradigm for nucleic acid-targeted drug design (12,13); and yet, despite extensive study over the past 40 years, fundamental aspects of their activity have yet to be fully defined including the role of particular DNA-binding modes on drug activity and the mechanism of double-strand DNA cleavage (14). Facilitating structural studies, HOO-Co(III)⅐bleomycin ''green'' (Fig. 1) (15) constitutes a stable structural analogue of O 2 activated Fe(II)⅐bleomycin, HOO-Fe(III)⅐bleomycin, that interacts with the same DNA site-selectivity (16-20)...

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Section: Discussionsupporting

confidence: 51%

Crystal structure of DNA-bound Co(III)·bleomycin B ₂ : Insights on intercalation and minor groove binding

Goodwin

Lewis

Long

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

108

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“…BlmA has been shown to encode an acidic protein, designated BLMA, with a strong affinity to Bm (11). We have previously determined the crystal structures of BLMA both uncomplexed and complexed with Bm (12,13). A blmA-like gene is present in the tallysomycin producer (14) as well as in other bacteria that do not produce any Bm-related compounds (11,15).…”

mentioning

confidence: 99%

Catalytic Mechanism of Bleomycin N-Acetyltransferase Proposed on the Basis of Its Crystal Structure

Oda

Matoba

Noda

et al. 2010

Journal of Biological Chemistry

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Bleomycin (Bm) N-acetyltransferase, BAT, is a self-resistance determinant in Bm-producing Streptomyces verticillus ATCC15003. In our present study, we crystallized BAT under both a terrestrial and a microgravity environment in the International Space Station. In addition to substrate-free BAT, the crystal structures of BAT in a binary complex with CoA and in a ternary complex with Bm and CoA were determined. BAT forms a dimer structure via interaction of its C-terminal domains in the monomers. However, each N-terminal domain in the dimer is positioned without mutual interaction. The tunnel observed in the N-terminal domain of BAT has two entrances: one that adopts a wide funnel-like structure necessary to accommodate the metal-binding domain of Bm, and another narrow entrance that accommodates acetyl-CoA (AcCoA). A groove formed on the dimer interface of two BAT C-terminal domains accommodates the DNA-binding domain of Bm. In a ternary complex of BAT, BmA 2 , and CoA, a thiol group of CoA is positioned near the primary amine of Bm at the midpoint of the tunnel. This proximity ensures efficient transfer of an acetyl group from AcCoA to the primary amine of Bm. Based on the BAT crystal structure and the enzymatic kinetic study, we propose that the catalytic mode of BAT takes an ordered-like mechanism.

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“…Resistance to bleomycin can be mediated by three different types of proteins or mechanisms: (i) bleomycin hydrolases; (ii) bleomycin N-acetylating enzymes that inactivate bleomycin-like molecules; and (iii) bleomycin-binding proteins (BMLA and BMLT) that act by trapping the bleomycin-like molecules (2,3). Bleomycin hydrolase from rabbit lungs is an aminopeptidase B-like enzyme that is inhibited by N-ethylmaleimide, leupeptin, puromycin, and divalent cations but is unaffected by chelating agents (4).…”

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confidence: 99%

Characterization of BRP _MBL , the Bleomycin Resistance Protein Associated with the Carbapenemase NDM

Dortet

Girlich

Virlouvet

et al. 2017

Antimicrob Agents Chemother

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The metallo-␤-lactamase NDM-1 is among the most worrisome resistance determinants and is spreading worldwide among Gram-negative bacilli. A bleomycin resistance gene, ble MBL , downstream of the bla NDM-1 gene has been associated with resistance almost systematically. Here, we characterized the corresponding protein, BRP MBL , conferring resistance to bleomycin, an antitumoral glycopeptide molecule. We have determined whether the expression of the bla NDM-1 -ble MBL operon is inducible in the presence of carbapenems and/or bleomycin-like molecules using quantitative reverse transcription-PCR (qRT-PCR), determination of imipenem and zeocin MICs, and carbapenemase-specific activity assays. We showed that the bla NDM-1 -ble MBL operon is constitutively expressed. Using electrophoretic mobility shift and DNA protection assays performed with purified glutathione S-transferase (GST)-BRP MBL , we demonstrated that BRP MBL is able to bind and sequester bleomycin-like molecules, thus preventing bleomycin-dependent DNA degradation. In silico modeling confirmed that the mechanism of action required the dimerization of the BRP MBL protein in order to sequester bleomycin and prevent DNA damage. BRP MBL acts specifically on bleomycinlike molecules since cloning and expression of ble MBL in Staphyloccoccus aureus did not confer cross-resistance to any other antimicrobial glycopeptides such as vancomycin and teicoplanin.

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The 1.6-Å Crystal Structure of the Copper(II)-bound Bleomycin Complexed with the Bleomycin-binding Protein from Bleomycin-producing Streptomyces verticillus

Cited by 60 publications

References 42 publications

Crystal structure of DNA-bound Co(III)·bleomycin B ₂ : Insights on intercalation and minor groove binding

Crystal structure of DNA-bound Co(III)·bleomycin B ₂ : Insights on intercalation and minor groove binding

Catalytic Mechanism of Bleomycin N-Acetyltransferase Proposed on the Basis of Its Crystal Structure

Characterization of BRP _MBL , the Bleomycin Resistance Protein Associated with the Carbapenemase NDM

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The 1.6-Å Crystal Structure of the Copper(II)-bound Bleomycin Complexed with the Bleomycin-binding Protein from Bleomycin-producing Streptomyces verticillus

Cited by 60 publications

References 42 publications

Crystal structure of DNA-bound Co(III)·bleomycin B 2 : Insights on intercalation and minor groove binding

Crystal structure of DNA-bound Co(III)·bleomycin B 2 : Insights on intercalation and minor groove binding

Catalytic Mechanism of Bleomycin N-Acetyltransferase Proposed on the Basis of Its Crystal Structure

Characterization of BRP MBL , the Bleomycin Resistance Protein Associated with the Carbapenemase NDM

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Crystal structure of DNA-bound Co(III)·bleomycin B ₂ : Insights on intercalation and minor groove binding

Crystal structure of DNA-bound Co(III)·bleomycin B ₂ : Insights on intercalation and minor groove binding

Characterization of BRP _MBL , the Bleomycin Resistance Protein Associated with the Carbapenemase NDM