106
views
0
recommends
+1 Recommend
0 collections
    16
    shares
      • Record: found
      • Abstract: found
      • Article: not found

      Structure-based mechanism for Na +/melibiose symport by MelB

      research-article

      Read this article at

      ScienceOpenPublisherPMC
      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          The bacterial melibiose permease (MelB) belongs to the glycoside- pentoside- hexuronide:cation symporter family (GPH), a part of the major facilitator superfamily (MFS). Structural information regarding GPH transporters and other Na +-coupled permeases within MFS has been lacking, although a wealth of biochemical and biophysical data are available. Here we present the 3D crystal structures of Salmonella typhimurium MelB St in two conformations, representing an outward partially occluded and an outward inactive state of MelB St. MelB adopts a typical MFS fold, and contains a previously unidentified cation-binding motif. Three conserved acidic residues form a pyramidal-shaped cation-binding site for Na +, Li +, or H +, which is in close proximity to the sugar-binding site. Both co-substrate-binding sites are mainly contributed by the residues from the N-terminal domain. These two structures and the functional data presented here provide mechanistic insights into Na +/melibiose symport. We also postulate a structural foundation for the conformational cycling necessary for transport catalyzed by MFS permeases in general.

          Related collections

          Most cited references62

          • Record: found
          • Abstract: found
          • Article: not found

          Crystal structure of a bacterial homologue of Na+/Cl--dependent neurotransmitter transporters.

          Na+/Cl--dependent transporters terminate synaptic transmission by using electrochemical gradients to drive the uptake of neurotransmitters, including the biogenic amines, from the synapse to the cytoplasm of neurons and glia. These transporters are the targets of therapeutic and illicit compounds, and their dysfunction has been implicated in multiple diseases of the nervous system. Here we present the crystal structure of a bacterial homologue of these transporters from Aquifex aeolicus, in complex with its substrate, leucine, and two sodium ions. The protein core consists of the first ten of twelve transmembrane segments, with segments 1-5 related to 6-10 by a pseudo-two-fold axis in the membrane plane. Leucine and the sodium ions are bound within the protein core, halfway across the membrane bilayer, in an occluded site devoid of water. The leucine and ion binding sites are defined by partially unwound transmembrane helices, with main-chain atoms and helix dipoles having key roles in substrate and ion binding. The structure reveals the architecture of this important class of transporter, illuminates the determinants of substrate binding and ion selectivity, and defines the external and internal gates.
            Bookmark
            • Record: found
            • Abstract: found
            • Article: not found

            Very fast prediction and rationalization of pKa values for protein-ligand complexes.

            The PROPKA method for the prediction of the pK(a) values of ionizable residues in proteins is extended to include the effect of non-proteinaceous ligands on protein pK(a) values as well as predict the change in pK(a) values of ionizable groups on the ligand itself. This new version of PROPKA (PROPKA 2.0) is, as much as possible, developed by adapting the empirical rules underlying PROPKA 1.0 to ligand functional groups. Thus, the speed of PROPKA is retained, so that the pK(a) values of all ionizable groups are computed in a matter of seconds for most proteins. This adaptation is validated by comparing PROPKA 2.0 predictions to experimental data for 26 protein-ligand complexes including trypsin, thrombin, three pepsins, HIV-1 protease, chymotrypsin, xylanase, hydroxynitrile lyase, and dihydrofolate reductase. For trypsin and thrombin, large protonation state changes (|n| > 0.5) have been observed experimentally for 4 out of 14 ligand complexes. PROPKA 2.0 and Klebe's PEOE approach (Czodrowski P et al. J Mol Biol 2007;367:1347-1356) both identify three of the four large protonation state changes. The protonation state changes due to plasmepsin II, cathepsin D and endothiapepsin binding to pepstatin are predicted to within 0.4 proton units at pH 6.5 and 7.0, respectively. The PROPKA 2.0 results indicate that structural changes due to ligand binding contribute significantly to the proton uptake/release, as do residues far away from the binding site, primarily due to the change in the local environment of a particular residue and hence the change in the local hydrogen bonding network. Overall the results suggest that PROPKA 2.0 provides a good description of the protein-ligand interactions that have an important effect on the pK(a) values of titratable groups, thereby permitting fast and accurate determination of the protonation states of key residues and ligand functional groups within the binding or active site of a protein.
              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              Structure and mechanism of the glycerol-3-phosphate transporter from Escherichia coli.

              The major facilitator superfamily represents the largest group of secondary membrane transporters in the cell. Here we report the 3.3 angstrom resolution structure of a member of this superfamily, GlpT, which transports glycerol-3-phosphate into the cytoplasm and inorganic phosphate into the periplasm. The amino- and carboxyl-terminal halves of the protein exhibit a pseudo two-fold symmetry. Closed off to the periplasm, a centrally located substrate-translocation pore contains two arginines at its closed end, which comprise the substrate-binding site. Upon substrate binding, the protein adopts a more compact conformation. We propose that GlpT operates by a single-binding site, alternating-access mechanism through a rocker-switch type of movement.
                Bookmark

                Author and article information

                Journal
                101528555
                37539
                Nat Commun
                Nat Commun
                Nature communications
                2041-1723
                25 February 2014
                2014
                01 July 2014
                : 5
                : 3009
                Affiliations
                [1 ]Department of Cell Physiology & Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX, 79430, USA.
                [2 ]Department of Physiology, University of California, Los Angeles, CA 90095, USA.
                Author notes
                [* ]Corresponding author. Lan.Guan@ 123456ttuhsc.edu
                [†]

                Current address: Department of Physics, College of Arts & Sciences, Southern Illinois University, Edwardsville, IL 62026-1654 (On leave from: Biophysics Department, Faculty of Science, Cairo University, Egypt).

                [‡]

                Current address: CEA-DSV- Fontenay aux Roses, Cross Division of Toxicology, 92 265 Fontenay aux Roses BP 6 France.

                Author Contributions

                ASE, MSY, and LG performed protein production, crystallization, X-ray diffraction, data collection and processing. ASE and LG performed collection and processing of data for the PDB accessing 4M64 and structure interpretation. LG, ASE, and AA designed and AA performed all transport assays and FRET measurements. LG interpreted functional data. LG directed the research. HRK and GL provided advice and research reagents. All authors contributed to manuscript preparation. LG and ASE wrote the manuscript with help from HRK.

                Article
                NIHMS560147
                10.1038/ncomms4009
                4026327
                24389923
                6cf24522-9c2b-42fe-af4b-8b5d59f4ede5
                History
                Categories
                Article

                Uncategorized
                Uncategorized

                Comments

                Comment on this article