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Pathway Description
tRNA Charging 2
Escherichia coli
Category:
Metabolite Pathway
Sub-Category:
Metabolic
Created: 2015-03-14
Last Updated: 2019-08-13
This pathway is a compilation of Escherichia coli tRNA charging reactions involving biosynthesized amino acids. The aminoacyl-tRNA synthetase is an enzyme that attaches the appropriate amino acid onto its tRNA by catalyzing the esterification of a specific cognate amino acid or its precursor to one of all its compatible cognate tRNAs to form an aminoacyl-tRNA, which plays an important role in RNA translation. 20 different Aminoacyl-tRNA synthetases can make 20 different types of aa-tRNA for each amino acid according to the genetic code. This process is called "charging" or "loading" the tRNA with amino acid. Ribosome can transfer the amino acid from tRNA to a growing peptide after the tRNA is charged.
References
tRNA Charging 2 References
Abdeljabbar DM, Klein TJ, Zhang S, Link AJ: A single genomic copy of an engineered methionyl-tRNA synthetase enables robust incorporation of azidonorleucine into recombinant proteins in E. coli. J Am Chem Soc. 2009 Dec 2;131(47):17078-9. doi: 10.1021/ja907969m.
Pubmed: 19894713
Abibi A, Ferguson AD, Fleming PR, Gao N, Hajec LI, Hu J, Laganas VA, McKinney DC, McLeod SM, Prince DB, Shapiro AB, Buurman ET: The role of a novel auxiliary pocket in bacterial phenylalanyl-tRNA synthetase druggability. J Biol Chem. 2014 Aug 1;289(31):21651-62. doi: 10.1074/jbc.M114.574061. Epub 2014 Jun 16.
Pubmed: 24936059
Ahel I, Stathopoulos C, Ambrogelly A, Sauerwald A, Toogood H, Hartsch T, Soll D: Cysteine activation is an inherent in vitro property of prolyl-tRNA synthetases. J Biol Chem. 2002 Sep 20;277(38):34743-8. doi: 10.1074/jbc.M206928200. Epub 2002 Jul 18.
Pubmed: 12130657
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Pubmed: 16054140
Airas RK: Analysis of the kinetic mechanism of arginyl-tRNA synthetase. Biochim Biophys Acta. 2006 Feb;1764(2):307-19. doi: 10.1016/j.bbapap.2005.11.020. Epub 2005 Dec 22.
Pubmed: 16427818
Airas RK: Magnesium dependence of the measured equilibrium constants of aminoacyl-tRNA synthetases. Biophys Chem. 2007 Dec;131(1-3):29-35. doi: 10.1016/j.bpc.2007.08.006. Epub 2007 Sep 4.
Pubmed: 17889423
Airas RK: Differences in the magnesium dependences of the class I and class II aminoacyl-tRNA synthetases from Escherichia coli. Eur J Biochem. 1996 Aug 15;240(1):223-31.
Pubmed: 8797857
Airas RK: Chloride affects the interaction between tyrosyl-tRNA synthetase and tRNA. Biochim Biophys Acta. 1999 Oct 18;1472(1-2):51-61.
Pubmed: 10572925
Akesson B, Lundvik L: Simultaneous purification and some properties of aspartate: tRNA ligase and seven other amino-acid:tRNA ligases from Escherichia coli. Eur J Biochem. 1978 Feb 1;83(1):29-36.
Pubmed: 342244
Aldinger CA, Leisinger AK, Igloi GL: The influence of identity elements on the aminoacylation of tRNA(Arg) by plant and Escherichia coli arginyl-tRNA synthetases. FEBS J. 2012 Oct;279(19):3622-3638. doi: 10.1111/j.1742-4658.2012.08722.x. Epub 2012 Sep 3.
Pubmed: 22831759
Alexander RW, Schimmel P: Evidence for breaking domain-domain functional communication in a synthetase-tRNA complex. Biochemistry. 1999 Dec 7;38(49):16359-65.
Pubmed: 10587461
Andrews D, Trezeguet V, Merle M, Graves PV, Muench KH, Labouesse B: Tryptophanamide formation by Escherichia coli tryptophanyl-tRNA synthetase. Eur J Biochem. 1985 Jan 2;146(1):201-9.
Pubmed: 3881255
Ankilova VN, Vlassov VV, Knorre DG, Melamed NV, Nuzdihna NA: Involvement of the D-stem of tRNAPhe (E. coli) in interaction with phenylalanyl-tRNA synthetase as shown by chemical modification. FEBS Lett. 1975 Dec 1;60(1):168-71.
Pubmed: 776674
Anselme J, Hartlein M: Asparaginyl-tRNA synthetase from Escherichia coli has significant sequence homologies with yeast aspartyl-tRNA synthetase. Gene. 1989 Dec 14;84(2):481-5.
Pubmed: 2693216
Anselme J, Hartlein M: Tyr-426 of the Escherichia coli asparaginyl-tRNA synthetase, an amino acid in a C-terminal conserved motif, is involved in ATP binding. FEBS Lett. 1991 Mar 11;280(1):163-6.
Pubmed: 2009959
Aoki H, Yaworsky PJ, Patel SD, Margolin-Brzezinski D, Park KS, Ganoza MC: The asparaginyl-tRNA synthetase gene encodes one of the complementing factors for thermosensitive translation in the Escherichia coli mutant strain, N4316. Eur J Biochem. 1992 Oct 15;209(2):511-21.
Pubmed: 1425658
Archibold ER, Williams LS: Regulation of synthesis of methionyl-, prolyl-, and threonyl-transfer ribonucleic acid synthetases of Escherichia coli. J Bacteriol. 1972 Mar;109(3):1020-6.
Pubmed: 4551738
Archibold ER, Williams LS: Regulation of methionyl-transfer ribonucleic acid synthetase formation in Escherichia coli and Salmonella typhimurium. J Bacteriol. 1973 Jun;114(3):1007-13.
Pubmed: 4576394
Archontis G, Simonson T, Karplus M: Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase. J Mol Biol. 2001 Feb 16;306(2):307-27. doi: 10.1006/jmbi.2000.4285.
Pubmed: 11237602
Archontis G, Simonson T: Dielectric relaxation in an enzyme active site: molecular dynamics simulations interpreted with a macroscopic continuum model. J Am Chem Soc. 2001 Nov 7;123(44):11047-56.
Pubmed: 11686711
Eriani G, Dirheimer G, Gangloff J: Isolation and characterization of the gene coding for Escherichia coli arginyl-tRNA synthetase. Nucleic Acids Res. 1989 Jul 25;17(14):5725-36. doi: 10.1093/nar/17.14.5725.
Pubmed: 2668891
Itoh T, Aiba H, Baba T, Hayashi K, Inada T, Isono K, Kasai H, Kimura S, Kitakawa M, Kitagawa M, Makino K, Miki T, Mizobuchi K, Mori H, Mori T, Motomura K, Nakade S, Nakamura Y, Nashimoto H, Nishio Y, Oshima T, Saito N, Sampei G, Seki Y, Horiuchi T, et al.: A 460-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 40.1-50.0 min region on the linkage map. DNA Res. 1996 Dec 31;3(6):379-92. doi: 10.1093/dnares/3.6.379.
Pubmed: 9097040
Blattner FR, Plunkett G 3rd, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y: The complete genome sequence of Escherichia coli K-12. Science. 1997 Sep 5;277(5331):1453-62. doi: 10.1126/science.277.5331.1453.
Pubmed: 9278503
Avalos J, Corrochano LM, Brenner S: Cysteinyl-tRNA synthetase is a direct descendant of the first aminoacyl-tRNA synthetase. FEBS Lett. 1991 Jul 29;286(1-2):176-80. doi: 10.1016/0014-5793(91)80968-9.
Pubmed: 1864365
Eriani G, Dirheimer G, Gangloff J: Cysteinyl-tRNA synthetase: determination of the last E. coli aminoacyl-tRNA synthetase primary structure. Nucleic Acids Res. 1991 Jan 25;19(2):265-9. doi: 10.1093/nar/19.2.265.
Pubmed: 2014166
Hou YM, Shiba K, Mottes C, Schimmel P: Sequence determination and modeling of structural motifs for the smallest monomeric aminoacyl-tRNA synthetase. Proc Natl Acad Sci U S A. 1991 Feb 1;88(3):976-80. doi: 10.1073/pnas.88.3.976.
Pubmed: 1992490
Breton R, Sanfacon H, Papayannopoulos I, Biemann K, Lapointe J: Glutamyl-tRNA synthetase of Escherichia coli. Isolation and primary structure of the gltX gene and homology with other aminoacyl-tRNA synthetases. J Biol Chem. 1986 Aug 15;261(23):10610-7.
Pubmed: 3015933
Brun YV, Sanfacon H, Breton R, Lapointe J: Closely spaced and divergent promoters for an aminoacyl-tRNA synthetase gene and a tRNA operon in Escherichia coli. Transcriptional and post-transcriptional regulation of gltX, valU and alaW. J Mol Biol. 1990 Aug 20;214(4):845-64. doi: 10.1016/0022-2836(90)90340-R.
Pubmed: 2201777
Yamamoto Y, Aiba H, Baba T, Hayashi K, Inada T, Isono K, Itoh T, Kimura S, Kitagawa M, Makino K, Miki T, Mitsuhashi N, Mizobuchi K, Mori H, Nakade S, Nakamura Y, Nashimoto H, Oshima T, Oyama S, Saito N, Sampei G, Satoh Y, Sivasundaram S, Tagami H, Horiuchi T, et al.: Construction of a contiguous 874-kb sequence of the Escherichia coli -K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features. DNA Res. 1997 Apr 28;4(2):91-113. doi: 10.1093/dnares/4.2.91.
Pubmed: 9205837
Hayashi K, Morooka N, Yamamoto Y, Fujita K, Isono K, Choi S, Ohtsubo E, Baba T, Wanner BL, Mori H, Horiuchi T: Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110. Mol Syst Biol. 2006;2:2006.0007. doi: 10.1038/msb4100049. Epub 2006 Feb 21.
Pubmed: 16738553
Webster TA, Gibson BW, Keng T, Biemann K, Schimmel P: Primary structures of both subunits of Escherichia coli glycyl-tRNA synthetase. J Biol Chem. 1983 Sep 10;258(17):10637-41.
Pubmed: 6309809
Sofia HJ, Burland V, Daniels DL, Plunkett G 3rd, Blattner FR: Analysis of the Escherichia coli genome. V. DNA sequence of the region from 76.0 to 81.5 minutes. Nucleic Acids Res. 1994 Jul 11;22(13):2576-86. doi: 10.1093/nar/22.13.2576.
Pubmed: 8041620
Borel F, Vincent C, Leberman R, Hartlein M: Seryl-tRNA synthetase from Escherichia coli: implication of its N-terminal domain in aminoacylation activity and specificity. Nucleic Acids Res. 1994 Aug 11;22(15):2963-9. doi: 10.1093/nar/22.15.2963.
Pubmed: 8065908
Vincent C, Borel F, Willison JC, Leberman R, Hartlein M: Seryl-tRNA synthetase from Escherichia coli: functional evidence for cross-dimer tRNA binding during aminoacylation. Nucleic Acids Res. 1995 Apr 11;23(7):1113-8. doi: 10.1093/nar/23.7.1113.
Pubmed: 7537870
Hartlein M, Madern D, Leberman R: Cloning and characterization of the gene for Escherichia coli seryl-tRNA synthetase. Nucleic Acids Res. 1987 Feb 11;15(3):1005-17. doi: 10.1093/nar/15.3.1005.
Pubmed: 3029694
Durfee T, Nelson R, Baldwin S, Plunkett G 3rd, Burland V, Mau B, Petrosino JF, Qin X, Muzny DM, Ayele M, Gibbs RA, Csorgo B, Posfai G, Weinstock GM, Blattner FR: The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse. J Bacteriol. 2008 Apr;190(7):2597-606. doi: 10.1128/JB.01695-07. Epub 2008 Feb 1.
Pubmed: 18245285
Hartlein M, Madern D: Molecular cloning and nucleotide sequence of the gene for Escherichia coli leucyl-tRNA synthetase. Nucleic Acids Res. 1987 Dec 23;15(24):10199-210. doi: 10.1093/nar/15.24.10199.
Pubmed: 3320963
Oshima T, Aiba H, Baba T, Fujita K, Hayashi K, Honjo A, Ikemoto K, Inada T, Itoh T, Kajihara M, Kanai K, Kashimoto K, Kimura S, Kitagawa M, Makino K, Masuda S, Miki T, Mizobuchi K, Mori H, Motomura K, Nakamura Y, Nashimoto H, Nishio Y, Saito N, Horiuchi T, et al.: A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 12.7-28.0 min region on the linkage map. DNA Res. 1996 Jun 30;3(3):137-55. doi: 10.1093/dnares/3.3.137.
Pubmed: 8905232
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