Substrate binding, deprotonation, and selectivity at the periplasmic entrance of the Escherichia coli ammonia channel AmtB

Proceedings of the National Academy of Sciences of the United States of America

Volumn 105, Issue 13, 2008, Pages 5040-5045

  Javelle, Arnaud ^a   Lupo, Domenico ^a   Ripoche, Pierre ^b   Fulford, Tim ^c   Merrick, Mike ^c   Winkler, Fritz K ^a  

^a PAUL SCHERRER INSTITUTE   (Switzerland)

^b INSTITUT NATIONAL DE LA TRANSFUSION SANGUINE   (France)

^c JOHN INNES CENTRE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

AMMONIA; BACTERIAL PROTEIN; BENZENE DERIVATIVE; PERIPLASMIC PROTEIN; PHENYLALANINE; PROTEIN AMTB; WATER; AMTB PROTEIN, E COLI; CATION TRANSPORT PROTEIN; ESCHERICHIA COLI PROTEIN; PROTON; UNCLASSIFIED DRUG;

ARTICLE; BINDING SITE; CHANNEL GATING; CONCENTRATION (PARAMETERS); ESCHERICHIA COLI; HYDROPHOBICITY; MEMBRANE CHANNEL; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN FAMILY; PROTON TRANSPORT; SITE DIRECTED MUTAGENESIS; CELL MEMBRANE; CHEMICAL STRUCTURE; CHEMISTRY; GENETICS; METABOLISM; MUTATION; PROTEIN TERTIARY STRUCTURE; SENSITIVITY AND SPECIFICITY;

ESCHERICHIA COLI;

AMMONIA; BINDING SITES; CATION TRANSPORT PROTEINS; CELL MEMBRANE; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; MODELS, MOLECULAR; MUTATION; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; PROTONS; SENSITIVITY AND SPECIFICITY;

EID: 42449099887     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0711742105     Document Type: Article

References (40)

1. 2. Proc Natl Acad Sci USA 101:7787-7792.
2. Huang CH, Peng J (2005) Evolutionary conservation and diversification of Rh family genes and proteins. Proc Natl Acad Sci USA 102:15512-15517.
3. Javelle A, et al. (2007) Structural and mechanistic aspects of Amt/Rh proteins. J Struct Biol 158:472-481.
4. Zheng L, Kostrewa D, Bernèche S, Winkler FK, Li X-D (2004) The mechanism of ammonia transport based on the crystal structure of AmtB of E. coli. Proc Natl Acad Sci USA 101:17090-17095.
5. Khademi S, et al. (2004) Mechanism of ammonia transport by Amt/MEP/Rh: Structure of AmtB at 1.35 Å. Science 305:1587-1594.
6. Ludewig U (2006) Ion transport versus gas conduction: function of AMT/Rh-type proteins. Transfus Clin Biol 13:111-116.
7. Fong RN, Kim KS, Yoshihara C, Inwood WB, Kustu S (2007) The W148L substitution in the Escherichia coli ammonium channel AmtB increases flux and indicates that the substrate is an ion. Proc Natl Acad Sci USA 104:18706-18711.
8. Winkler FK (2006) Amt/MEP/Rh proteins conduct ammonia. Pflugers Arch 451:701-707.
9. Westhoff CM, Ferreri-Jacobia M, Mak DO, Foskett JK (2002) Identification of the erythrocyte Rh-blood group glycoprotein as a mammalian ammonium transporter. J Biol Chem 277:12499-12502.
10. Bakouh N, et al. (2004) NH3 is involved in the NH4 transport induced by the functional expression of the human Rh C glycoprotein. J Biol Chem 279:15975-15983.
11. Marini A-M, Soussi-Boudekou S, Vissers S, Andre B (1997) A family of ammonium transporters in Saccharomyces cerevisiae. Mol Cell Biol 17:4282-4293.
12. Bostick DL, Brooks CL, III (2007) On the equivalence point for ammonium (de)protonation during its transport through the AmtB channel. Biophys J 92:L103-L105.
13. Bostick DL, Brooks CL, III (2007) Deprotonation by dehydration: The origin of ammonium sensing in the AmtB channel. PLoS Comput Biol 3:e22.
14. Liu Y, Hu X (2006) Molecular determinants for binding of ammonium ion in the ammonia transporter AmtB-A quantum chemical analysis. J Phys Chem A 110:1375-1381.
15. Luzhkov VB, Almlof M, Nervall M, Aqvist J (2006) Computational study of the binding affinity and selectivity of the bacterial ammonium transporter AmtB. Biochemistry 45:10807-10814.
16. Lin Y, Cao Z, Mo Y (2006) Molecular dynamics simulations on the Escherichia coli ammonia channel protein AmtB: Mechanism of ammonia/ammonium transport. J Am Chem Soc 128:10876-10884.
17. Nygaard TP, Rovira C, Peters GH, Jensen MO (2006) Ammonium recruitment and ammonia transport by E. coli ammonia channel AmtB. Biophys J 91:4401-4412.
18. Lamoureux G, Klein ML, Berneche S (2007) A stable water chain in the hydrophobic pore of the AmtB ammonium transporter. Biophys J 92:L82-L84.
19. + in the Escherichia coli ammonium transporter AmtB: Insight from QM and QM/MM calculations. Angew Chem Int Ed Engl 46:6811-6815.
20. Javelle A, et al. (2006) An unusual twin-his arrangement in the pore of ammonia channels is essential for substrate conductance. J Biol Chem 281:39492-39498.
21. Javelle A, Thomas G, Marini AM, Kramer R, Merrick M (2005) In vivo functional characterisation of the E coli ammonium channel AmtB: Evidence for metabolic coupling of AmtB to glutamine synthetase. Biochem J 390:215-222.
22. Liaw SH, Kuo I, Eisenberg D (1995) Discovery of the ammonium substrate site on glutamine synthetase, a third cation binding site. Protein Sci 4:2358-2365.
23. von Wirén N, Merrick M (2004) Regulation and function of ammonium carriers in bacteria, fungi and plants. Trends Curr Genet 9:95-120.
24. Andrade SL, Dickmanns A, Ficner R, Einsle O (2005) Crystal structure of the archaeal ammonium transporter Amt-1 from Archaeoglobus fulgidus. Proc Natl Acad Sci USA 102:14994-14999.
25. Conroy MJ, et al. (2007) The crystal structure of the Escherichia coli AmtB-GlnK complex reveals how GlnK regulates the ammonia channel. Proc Natl Acad Sci USA 104:1213-1218.
26. 3: Molecular dynamics simulations. Biophys J 92:877-885.
27. Borgnia MJ, Agre P (2001) Reconstitution and functional comparison of purified GlpF and AqpZ, the glycerol and water channels from Escherichia coli. Proc Natl Acad Sci USA 98:2888-2893.
28. Kleiner D (1985) Bacterial ammonium transport. FEMS Microbiol Rev 32:87-100.
29. Soupene E, He L, Yan D, Kustu S (1998) Ammonia acquisition in enteric bacteria: Physiological role of the ammonium/methylammonium transport B (AmtB) protein. Proc Natl Acad Sci USA 95:7030-7034.
30. 3 bidirectionally. Proc Natl Acad Sci USA 99:3926-3931.
31. + by the root hair plasma membrane ammonium transporter LeAMT1;1. J Biol Chem 277:13548-13555.
32. 14C]- methylammonium as the substrate. J Biol Chem 245:4241-4250.
33. Booth IR, Edwards MD, Miller S (2003) Bacterial ion channels. Biochemistry 42:10045-10053.
34. +. Angew Chem Int Ed Engl 38:2756-2759.
35. Chin J, et al. (2002) Tuning and dissecting electronic and steric effects in ammonium receptors: Nonactin vs artificial receptors. J Am Chem Soc 124:5374-5379.
36. Ishikita H, Knapp EW (2007) Protonation states of ammonia/ammonium in the hydrophobic pore of ammonia transporter protein AmtB. J Am Chem Soc 129:1210-1215.
37. 3 transport by Rhesus family proteins. Proc Natl Acad Sci USA 104:19303-19308.
38. Zheng L, Baumann U, Reymond JL (2004) An efficient one-step site-directed and site-saturation mutagenesis protocol. Nucleic Acids Res 32:e115.
39. Javelle A, Severi E, Thornton J, Merrick M (2004) Ammonium sensing in E. coli: The role of the ammonium transporter AmtB and AmtB-GlnK complex formation. J Biol Chem 279:8530-8538.
40. Paula S, Volkov AG, Van Hoek AN, Haines TH, Deamer DW (1996) Permeation of protons, potassium ions, and small polar molecules through phospholipid bilayers as a function of membrane thickness. Biophys J 70:339-348.