A new subfamily of bacterial ABC‐type transport systems catalyzing export of drugs and carbohydrates

Reizer, Jonathan; Reizer, Aiala; Saier, Milton H.

doi:10.1002/pro.5560011012

Cited by 209 publications

(100 citation statements)

References 21 publications

(29 reference statements)

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“…Group 7, as well as probably, group 11, corresponds to the ABC-2 type transporters that include the capsular polysaccharide export system in Gramnegative bacteria (Reizer et al 1992) and NatB for sodium export in Bacillus subtilis (Cheng et al 1997). There is no substrate-binding protein in this group.…”

Section: Substrate Specificity In Known Groupsmentioning

confidence: 99%

A Comparative Analysis of ABC Transporters in Complete Microbial Genomes

Tomii

Kanehisa²

1998

Genome Res.

122

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The ABC transporter is a major class of cellular translocation machinery in all bacterial species encoded in the largest set of paralogous genes. The operon structure is frequently found for the genes of three molecular components: the ATP-binding protein, the membrane protein, and the substrate-binding protein. Here, we developed an ''ortholog group table'' by comparison and classification of known and putative ABC transporters in the complete genomes of seven microorganisms. Our procedure was to first search and classify the most conserved ATP-binding protein components by the sequence similarity and then to classify the entire transporter units by examining the similarity of the other components and the conservation of the operon structure. The resulting 25 ortholog groups of ABC transporters were well correlated with known functions. Through the analysis, we could assign substrate specificity to hypothetical transporters, predict additional transporter operons, and identify novel types of putative transporters. The ortholog group table was also used as a reference data set for functional assignment in four additional genomes. In general, the ABC transporter operons were strongly conserved despite the extensive shuffling of gene locations in bacterial evolution. In Synechocystis, however, the tendency of forming operons was clearly diminished. Our result suggests that the ancestral ABC transporter operons may have arisen early in evolution before the speciation of bacteria and archaea.

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Section: Substrate Specificity In Known Groupsmentioning

confidence: 99%

A Comparative Analysis of ABC Transporters in Complete Microbial Genomes

Tomii

Kanehisa²

1998

Genome Res.

122

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“…Self-resistance in S. peucetius to its own antibiotics results from the action of two proteins, DrrA and DrrB. The DrrA protein belongs to the ATP-binding cassette (ABC) 1 family of proteins (1), whereas DrrB bears homology to the membrane components of some bacterial ABC transporters (2). Together, DrrA and DrrB are proposed to form an ATP-dependent efflux pump for the export of these antibiotics (3)(4)(5).…”

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confidence: 99%

“…Together, DrrA and DrrB are proposed to form an ATP-dependent efflux pump for the export of these antibiotics (3)(4)(5). Based on the nucleotide sequence analysis, it has been proposed that DrrB belongs to a novel subfamily of ABC transporters (2). This subfamily has been termed ABC-2, and it includes four other members, namely NodJ, KpsM, BexB, and CtrC.…”

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confidence: 99%

“…This subfamily has been termed ABC-2, and it includes four other members, namely NodJ, KpsM, BexB, and CtrC. The membrane components of members of this subfamily (ABC-2) show significant sequence homology to each other but not to other ABC transporters (2). Within this subfamily, DrrB and NodJ are more closely related to each other than to the other three members.…”

mentioning

confidence: 99%

“…Although DrrAB is a drug export system, the other four transporters form the polysaccharide export systems in Gram-negative bacteria (6 -10). DrrA, the ABC component, shows homology to the ATP binding components of these four systems, however, DrrA also shows homology to other members of the ABC family, including the P-glycoproteins (Pgps) from mammalian tumor cells (2,3). Therefore, it has been proposed that DrrAB and the other four systems, mentioned above, comprise a novel subfamily of permeases that utilize an ABC-type ATPase to provide energy for export.…”

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confidence: 99%

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Membrane Topology of the DrrB Protein of the Doxorubicin Transporter of Streptomyces peucetius

Gandlur

Wei

Levine

et al. 2004

Journal of Biological Chemistry

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Daunorubicin and doxorubicin, two commonly used anticancer agents, are produced by the soil bacterium Streptomyces peucetius. Self-resistance to these antibiotics in S. peucetius is conferred by the drrAB locus that codes for two proteins, DrrA and DrrB. DrrA is an ATPbinding protein. It belongs to the ABC family of transporters and shares sequence and functional similarities with P-glycoprotein of cancer cells. DrrB is an integral membrane protein that might function as a transporter for the efflux of daunorubicin and doxorubicin. Together, DrrA and DrrB are believed to form an ATPdriven pump for the efflux of these drugs. The drrAB locus has been cloned, and the two proteins have been expressed in a functional form in Escherichia coli. A topological analysis of the DrrB protein was performed using gene fusion methodology. Random and site-directed fusions of the drrB gene to lacZ, phoA, or gfp reporter genes were created. Based on the fusion data, a topological model of the DrrB protein is proposed in which the protein has eight membrane-spanning domains with both the N terminus and the C terminus in the cytoplasm.

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Comparative Protein Structure Modeling Using MODELLER

Webb

Šali

2014

CP in Bioinformatics

905

474

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Functional characterization of a protein sequence is one of the most frequent problems in biology. This task is usually facilitated by accurate three-dimensional (3-D) structure of the studied protein. In the absence of an experimentally determined structure, comparative or homology modeling can sometimes provide a useful 3-D model for a protein that is related to at least one known protein structure. Comparative modeling predicts the 3-D structure of a given protein sequence (target) based primarily on its alignment to one or more proteins of known structure (templates). The prediction process consists of fold assignment, target-template alignment, model building, and model evaluation. This unit describes how to calculate comparative models using the program MODELLER and discusses all four steps of comparative modeling, frequently observed errors, and some applications. Modeling lactate dehydrogenase from Trichomonas vaginalis (TvLDH) is described as an example. The download and installation of the MODELLER software is also described.

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A new subfamily of bacterial ABC‐type transport systems catalyzing export of drugs and carbohydrates

Cited by 209 publications

References 21 publications

A Comparative Analysis of ABC Transporters in Complete Microbial Genomes

A Comparative Analysis of ABC Transporters in Complete Microbial Genomes

Membrane Topology of the DrrB Protein of the Doxorubicin Transporter of Streptomyces peucetius

Comparative Protein Structure Modeling Using MODELLER

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