Publications

• Phylogenetic analyses of the ATP-binding constituents of bacterial extracytoplasmic receptor-dependent ABC-type nutrient uptake permeases.

  Kuan G., Dassa E., Saurin W., Hofnung M., Saier M.H. Jr.

  Thirty-eight ATP-binding cassette (ABC) protein constituents of bacterial extracytoplasmic receptor-dependent nutrient uptake systems, including one homologous chloroplast protein were analysed for sequence conservation and phylogenetic relatedness. The proteins were generally found to cluster in ... >> More

  Thirty-eight ATP-binding cassette (ABC) protein constituents of bacterial extracytoplasmic receptor-dependent nutrient uptake systems, including one homologous chloroplast protein were analysed for sequence conservation and phylogenetic relatedness. The proteins were generally found to cluster in accordance with the clustering patterns previously observed for the extracytoplasmic receptors and the transmembrane channel-forming constituents of these permeases. The results suggest that these transport systems evolved from a single primordial system with minimal shuffling of the three dissimilar protein constituents of the systems. << Less

  Res Microbiol 146:271-278(1995) [PubMed] [EuropePMC]

  This publication is cited by 2 other entries.

• Molecular phylogeny as a basis for the classification of transport proteins from bacteria, archaea and eukarya.

  Saier M.H. Jr.

  Although enzymes catalyzing chemical reactions have long been classified according to the system developed by the Enzyme Commission (EC), no comparable system has been developed or proposed for transport proteins catalyzing transmembrane vectorial reactions. We here propose a comprehensive system, ... >> More

  Although enzymes catalyzing chemical reactions have long been classified according to the system developed by the Enzyme Commission (EC), no comparable system has been developed or proposed for transport proteins catalyzing transmembrane vectorial reactions. We here propose a comprehensive system, designated the Transport Commission (TC) system, based both on function and phylogeny. The TC system initially categorizes permeases according to mode of transport and energy coupling mechanism, and each category is assigned a one-component TC number (W). The secondary level of classification corresponds to the phylogenetic family (or superfamily) to which a particular permease is assigned, and each family is assigned a two-component TC number (W.X). The third level of classification refers to the phylogenetic cluster within a family (or the family within a superfamily) to which the permease belongs, and each cluster receives a three-component TC number (W.X.Y). Finally, the last level of categorization is based on substrate specificity and polarity of transport, and each entry is assigned a four component TC number (W.X.Y.Z). This system is based on the observation that mode of transport and energy coupling mechanism are fundamental properties of transport systems that very seldom transcend familial lines, but substrate specificity, being readily alterable by point mutations, is a superficial characteristic that often transcends familial lines. The proposed system has the potential to include all known permeases for which sequence data are available and has the flexibility to accommodate the multitude of permeases likely to be revealed by future genome sequencing and biochemical analysis. Major conclusions resulting from our classification efforts are described. The classification system, which will be continuously updated, is available on our World Wide Web site (http:/(/)www-biology.ucsd.edu/ approximately msaier/transport/titlepage.html). << Less

  Adv Microb Physiol 40:81-136(1998) [PubMed] [EuropePMC]

  This publication is cited by 4 other entries.

• Membrane topology of the integral membrane components, OppB and OppC, of the oligopeptide permease of Salmonella typhimurium.

  Pearce S.R., Mimmack M.L., Gallagher M.P., Gileadi U., Hyde S.C., Higgins C.F.

  The oligopeptide permease of Salmonella typhimurium is a periplasmic binding protein-dependent transport system. Five gene products, OppABCDF, are required for the functioning of this transporter, two of which (OppB and OppC) are highly hydrophobic, integral membrane proteins and are responsible f ... >> More

  The oligopeptide permease of Salmonella typhimurium is a periplasmic binding protein-dependent transport system. Five gene products, OppABCDF, are required for the functioning of this transporter, two of which (OppB and OppC) are highly hydrophobic, integral membrane proteins and are responsible for mediating passage of peptides across the cytoplasmic membrane. OppB and OppC are each predicted, from their sequences, to span the membrane many times. In this paper we describe experimental evidence confirming these predictions using a combination of biochemical, immunological and genetic procedures. Each of these two proteins is shown to span the membrane six times, with the N- and C-termini both being located at the cytoplasmic face of the membrane. Opp is apparently a typical member of the ABC (ATP-binding cassette) superfamily of transporters. These findings, therefore, have general implications for the organization and function of other ABC transporters, including the human multidrug resistance protein and the product of the cystic fibrosis gene. << Less

  Mol. Microbiol. 6:47-57(1992) [PubMed] [EuropePMC]