Abstract
Aminoacyl-tRNA synthetases (aaRS) ensure the faithful transmission of genetic information in all living cells. The 24 known aaRS families are divided into 2 structurally distinct classes (class I and class II), each featuring a catalytic domain with a common fold that binds ATP, amino acid, and the 3′-terminus of tRNA. In a common two-step reaction, each aaRS first uses the energy stored in ATP to synthesize an activated aminoacyl adenylate intermediate. In the second step, either the 2′- or 3′-hydroxyl oxygen atom of the 3′-A76 tRNA nucleotide functions as a nucleophile in synthesis of aminoacyl-tRNA. Ten of the 24 aaRS families are unable to distinguish cognate from noncognate amino acids in the synthetic reactions alone. These enzymes possess additional editing activities for hydrolysis of misactivated amino acids and misacylated tRNAs, with clearance of the latter species accomplished in spatially separate post-transfer editing domains. A distinct class of trans-acting proteins that are homologous to class II editing domains also perform hydrolytic editing of some misacylated tRNAs. Here we review essential themes in catalysis with a view toward integrating the kinetic, stereochemical, and structural mechanisms of the enzymes. Although the aaRS have now been the subject of investigation for many decades, it will be seen that a significant number of questions regarding fundamental catalytic functioning still remain unresolved.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Abbreviations
- AA-AMP:
-
Aminoacyl-AMP
- aaRS:
-
Aminoacyl-tRNA synthetase
- LUCA:
-
Last universal common ancestor
- MARS:
-
Multi-tRNA synthetase complex
- UAA:
-
Unnatural amino acid
References
Perona JJ, Hadd A (2012) Structural diversity and protein engineering of the aminoacyl-tRNA synthetases. Biochemistry 51:8705–8729
Yadavalli SS, Ibba M (2012) Quality control in aminoacyl-tRNA synthesis its role in translational fidelity. Adv Protein Chem Struct Biol 86:1–43
Perona JJ, Hou YM (2007) Indirect readout of tRNA for aminoacylation. Biochemistry 46:10419–10432
Post CB, Ray WJ Jr (1995) Reexamination of induced fit as a determinant of substrate specificity in enzymatic reactions. Biochemistry 34:15881–15885
Bruice TC (2002) A view at the millennium: the efficiency of enzymatic catalysis. Acc Chem Res 35:139–148
Ibba M, Sever S, Praetorius-Ibba M, Soll D (1999) Transfer RNA identity contributes to transition state stabilization during aminoacyl-tRNA synthesis. Nucleic Acids Res 27:3631–3637
Ebel JP, Giege R, Bonnet J, Kern D, Befort N, Bollack C, Fasiolo F, Gangloff J, Dirheimer G (1973) Factors determining the specificity of the tRNA aminoacylation reaction. Non-absolute specificity of tRNA-aminoacyl-tRNA synthetase recognition and particular importance of the maximal velocity. Biochimie 55:547–557
Fersht AR (1977) Editing mechanisms in protein synthesis. Rejection of valine by the isoleucyl-tRNA synthetase. Biochemistry 16:1025–1030
Baldwin AN, Berg P (1966) Transfer ribonucleic acid-induced hydrolysis of valyladenylate bound to isoleucyl ribonucleic acid synthetase. J Biol Chem 241:839–845
Fersht AR, Kaethner MM (1976) Enzyme hyperspecificity. Rejection of threonine by the valyl-tRNA synthetase by misacylation and hydrolytic editing. Biochemistry 15:3342–3346
Jakubowski H (1978) Valyl-tRNA synthetase from yellow lupin seeds. Instability of enzyme-bound noncognate adenylates versus cognate adenylate. FEBS Lett 95:235–238
Jakubowski H, Fersht AR (1981) Alternative pathways for editing non-cognate amino acids by aminoacyl-tRNA synthetases. Nucleic Acids Res 9:3105–3117
Fersht AR, Dingwall C (1979) An editing mechanism for the methionyl-tRNA synthetase in the selection of amino acids in protein synthesis. Biochemistry 18:1250–1256
Tsui WC, Fersht AR (1981) Probing the principles of amino acid selection using the alanyl-tRNA synthetase from Escherichia coli. Nucleic Acids Res 9:4627–4637
Ibba M, Kast P, Hennecke H (1994) Substrate specificity is determined by amino acid binding pocket size in Escherichia coli phenylalanyl-tRNA synthetase. Biochemistry 33:7107–7112
Palencia A, Crepin T, Vu MT, Lincecum TL Jr, Martinis SA, Cusack S (2012) Structural dynamics of the aminoacylation and proofreading functional cycle of bacterial leucyl-tRNA synthetase. Nat Struct Mol Biol 19:677–684
Gruic-Sovulj I, Landeka I, Soll D, Weygand-Durasevic I (2002) tRNA-dependent amino acid discrimination by yeast seryl-tRNA synthetase. Eur J Biochem 269:5271–5279
Ibba M, Hong KW, Sherman JM, Sever S, Soll D (1996) Interactions between tRNA identity nucleotides and their recognition sites in glutaminyl-tRNA synthetase determine the cognate amino acid affinity of the enzyme. Proc Natl Acad Sci USA 93:6953–6958
Uter NT, Gruic-Sovulj I, Perona JJ (2005) Amino acid-dependent transfer RNA affinity in a class I aminoacyl-tRNA synthetase. J Biol Chem 280:23966–23977
Bullock TL, Rodriguez-Hernandez A, Corigliano EM, Perona JJ (2008) A rationally engineered misacylating aminoacyl-tRNA synthetase. Proc Natl Acad Sci USA 105:7428–7433
Rodriguez-Hernandez A, Bhaskaran H, Hadd A, Perona JJ (2010) Synthesis of Glu-tRNA(Gln) by engineered and natural aminoacyl-tRNA synthetases. Biochemistry 49:6727–6736
de Duve C (1988) Transfer RNAs: the second genetic code. Nature 333:117–118
Park SG, Schimmel P, Kim S (2008) Aminoacyl tRNA synthetases and their connections to disease. Proc Natl Acad Sci USA 105:11043–11049
Guo M, Yang XL, Schimmel P (2010) New functions of aminoacyl-tRNA synthetases beyond translation. Nat Rev Mol Cell Biol 11:668–674
Irwin MJ, Nyborg J, Reid BR, Blow DM (1976) The crystal structure of tyrosyl-transfer RNA synthetase at 2–7 A resolution. J Mol Biol 105:577–586
Brick P, Bhat TN, Blow DM (1989) Structure of tyrosyl-tRNA synthetase refined at 2.3 A resolution. Interaction of the enzyme with the tyrosyl adenylate intermediate. J Mol Biol 208:83–98
Schmidt E, Schimmel P (1995) Residues in a class I tRNA synthetase which determine selectivity of amino acid recognition in the context of tRNA. Biochemistry 34:11204–11210
Rould MA, Perona JJ, Soll D, Steitz TA (1989) Structure of E. coli glutaminyl-tRNA synthetase complexed with tRNA(Gln) and ATP at 2.8 A resolution. Science 246:1135–1142
Yaremchuk A, Kriklivyi I, Tukalo M, Cusack S (2002) Class I tyrosyl-tRNA synthetase has a class II mode of cognate tRNA recognition. EMBO J 21:3829–3840
Ruff M, Krishnaswamy S, Boeglin M, Poterszman A, Mitschler A, Podjarny A, Rees B, Thierry JC, Moras D (1991) Class II aminoacyl transfer RNA synthetases: crystal structure of yeast aspartyl-tRNA synthetase complexed with tRNA(Asp). Science 252:1682–1689
Cusack S, Berthet-Colominas C, Hartlein M, Nassar N, Leberman R (1990) A second class of synthetase structure revealed by X-ray analysis of Escherichia coli seryl-tRNA synthetase at 2.5 A. Nature 347:249–255
First EA (2005) Catalysis of the tRNA aminoacylation reaction. In: Michael Ibba CFaSC (ed) The aminoacyl-tRNA synthetases. Georgetown: Landes Bioscience/Eurekah.com, pp 328–352
Ibba M, Soll D (2000) Aminoacyl-tRNA synthesis. Annu Rev Biochem 69:617–650
Arnez JG, Moras D (1997) Structural and functional considerations of the aminoacylation reaction. Trends Biochem Sci 22:211–216
Cusack S (1995) Eleven down and nine to go. Nat Struct Biol 2:824–831
Cusack S (1997) Aminoacyl-tRNA synthetases. Curr Opin Struct Biol 7:881–889
Guo M, Schimmel P (2012) Structural analyses clarify the complex control of mistranslation by tRNA synthetases. Curr Opin Struct Biol 22:119–126
Tang SN, Huang JF (2005) Evolution of different oligomeric glycyl-tRNA synthetases. FEBS Lett 579:1441–1445
Dock-Bregeon A, Sankaranarayanan R, Romby P, Caillet J, Springer M, Rees B, Francklyn CS, Ehresmann C, Moras D (2000) Transfer RNA-mediated editing in threonyl-tRNA synthetase. The class II solution to the double discrimination problem. Cell 103:877–884
Cusack S, Yaremchuk A, Krikliviy I, Tukalo M (1998) tRNA(Pro) anticodon recognition by Thermus thermophilus prolyl-tRNA synthetase. Structure 6:101–108
Wong FC, Beuning PJ, Nagan M, Shiba K, Musier-Forsyth K (2002) Functional role of the prokaryotic proline-tRNA synthetase insertion domain in amino acid editing. Biochemistry 41:7108–7115
Goldgur Y, Mosyak L, Reshetnikova L, Ankilova V, Lavrik O, Khodyreva S, Safro M (1997) The crystal structure of phenylalanyl-tRNA synthetase from Thermus thermophilus complexed with cognate tRNAPhe. Structure 5:59–68
Crepin T, Yaremchuk A, Tukalo M, Cusack S (2006) Structures of two bacterial prolyl-tRNA synthetases with and without a cis-editing domain. Structure 14:1511–1525
Naganuma M, Sekine S, Fukunaga R, Yokoyama S (2009) Unique protein architecture of alanyl-tRNA synthetase for aminoacylation, editing, and dimerization. Proc Natl Acad Sci USA 106:8489–8494
Sokabe M, Ose T, Nakamura A, Tokunaga K, Nureki O, Yao M, Tanaka I (2009) The structure of alanyl-tRNA synthetase with editing domain. Proc Natl Acad Sci USA 106:11028–11033
Zhang CM, Perona JJ, Ryu K, Francklyn C, Hou YM (2006) Distinct kinetic mechanisms of the two classes of aminoacyl-tRNA synthetases. J Mol Biol 361:300–311
Dulic M, Cvetesic N, Perona JJ, Gruic-Sovulj I (2010) Partitioning of tRNA-dependent editing between pre- and post-transfer pathways in class I aminoacyl-tRNA synthetases. J Biol Chem 285:23799–23809
Bhaskaran H, Perona JJ (2011) Two-step aminoacylation of tRNA without channeling in archaea. J Mol Biol 411:854–869
Fersht AR, Kaethner MM (1976) Mechanism of aminoacylation of tRNA. Proof of the aminoacyl adenylate pathway for the isoleucyl- and tyrosyl-tRNA synthetases from Escherichia coli K12. Biochemistry 15:818–823
Guth E, Connolly SH, Bovee M, Francklyn CS (2005) A substrate-assisted concerted mechanism for aminoacylation by a class II aminoacyl-tRNA synthetase. Biochemistry 44:3785–3794
Banik SD, Nandi N (2012) Mechanism of the activation step of the aminoacylation reaction: a significant difference between class I and class II synthetases. J Biomol Struct Dyn 30:701–715
Ibba M, Losey HC, Kawarabayasi Y, Kikuchi H, Bunjun S, Soll D (1999) Substrate recognition by class I lysyl-tRNA synthetases: a molecular basis for gene displacement. Proc Natl Acad Sci USA 96:418–423
Kern D, Lapointe J (1979) Glutamyl transfer ribonucleic acid synthetase of Escherichia coli. Study of the interactions with its substrates. Biochemistry 18:5809–5818
Mehler AH, Mitra SK (1967) The activation of arginyl transfer ribonucleic acid synthetase by transfer ribonucleic acid. J Biol Chem 242:5495–5499
Ravel JM, Wang SF, Heinemeyer C, Shive W (1965) Glutamyl and glutaminyl ribonucleic acid synthetases of Escherichia coli W. Separation, properties, and stimulation of adenosine triphosphate-pyrophosphate exchange by acceptor ribonucleic acid. J Biol Chem 240:432–438
Sekine S, Nureki O, Dubois DY, Bernier S, Chenevert R, Lapointe J, Vassylyev DG, Yokoyama S (2003) ATP binding by glutamyl-tRNA synthetase is switched to the productive mode by tRNA binding. EMBO J 22:676–688
Gruic-Sovulj I, Uter N, Bullock T, Perona JJ (2005) tRNA-dependent aminoacyl-adenylate hydrolysis by a nonediting class I aminoacyl-tRNA synthetase. J Biol Chem 280:23978–23986
Perona JJ, Rould MA, Steitz TA (1993) Structural basis for transfer RNA aminoacylation by Escherichia coli glutaminyl-tRNA synthetase. Biochemistry 32:8758–8771
Desogus G, Todone F, Brick P, Onesti S (2000) Active site of lysyl-tRNA synthetase: structural studies of the adenylation reaction. Biochemistry 39:8418–8425
Avis JM, Fersht AR (1993) Use of binding energy in catalysis: optimization of rate in a multistep reaction. Biochemistry 32:5321–5326
Avis JM, Day AG, Garcia GA, Fersht AR (1993) Reaction of modified and unmodified tRNA(Tyr) substrates with tyrosyl-tRNA synthetase (Bacillus stearothermophilus). Biochemistry 32:5312–5320
Xin Y, Li W, Dwyer DS, First EA (2000) Correlating amino acid conservation with function in tyrosyl-tRNA synthetase. J Mol Biol 303:287–298
Minajigi A, Francklyn CS (2008) RNA-assisted catalysis in a protein enzyme: the 2′-hydroxyl of tRNA(Thr) A76 promotes aminoacylation by threonyl-tRNA synthetase. Proc Natl Acad Sci USA 105:17748–17753
Li L, Weinreb V, Francklyn C, Carter CW Jr (2011) Histidyl-tRNA synthetase urzymes: class I and II aminoacyl tRNA synthetase urzymes have comparable catalytic activities for cognate amino acid activation. J Biol Chem 286:10387–10395
Pham Y, Kuhlman B, Butterfoss GL, Hu H, Weinreb V, Carter CW Jr (2010) Tryptophanyl-tRNA synthetase urzyme: a model to recapitulate molecular evolution and investigate intramolecular complementation. J Biol Chem 285:38590–38601
Pham Y, Li L, Kim A, Erdogan O, Weinreb V, Butterfoss GL, Kuhlman B, Carter CW Jr (2007) A minimal TrpRS catalytic domain supports sense/antisense ancestry of class I and II aminoacyl-tRNA synthetases. Mol Cell 25:851–862
Sekine S, Shichiri M, Bernier S, Chenevert R, Lapointe J, Yokoyama S (2006) Structural bases of transfer RNA-dependent amino acid recognition and activation by glutamyl-tRNA synthetase. Structure 14:1791–1799
Retailleau P, Huang X, Yin Y, Hu M, Weinreb V, Vachette P, Vonrhein C, Bricogne G, Roversi P, Ilyin V, Carter CW Jr (2003) Interconversion of ATP binding and conformational free energies by tryptophanyl-tRNA synthetase: structures of ATP bound to open and closed, pre-transition-state conformations. J Mol Biol 325:39–63
Shen N, Zhou M, Yang B, Yu Y, Dong X, Ding J (2008) Catalytic mechanism of the tryptophan activation reaction revealed by crystal structures of human tryptophanyl-tRNA synthetase in different enzymatic states. Nucleic Acids Res 36:1288–1299
Terada T, Nureki O, Ishitani R, Ambrogelly A, Ibba M, Soll D, Yokoyama S (2002) Functional convergence of two lysyl-tRNA synthetases with unrelated topologies. Nat Struct Biol 9:257–262
Schmitt E, Tanrikulu IC, Yoo TH, Panvert M, Tirrell DA, Mechulam Y (2009) Switching from an induced-fit to a lock-and-key mechanism in an aminoacyl-tRNA synthetase with modified specificity. J Mol Biol 394:843–851
Rath VL, Silvian LF, Beijer B, Sproat BS, Steitz TA (1998) How glutaminyl-tRNA synthetase selects glutamine. Structure 6:439–449
Bullock TL, Uter N, Nissan TA, Perona JJ (2003) Amino acid discrimination by a class I aminoacyl-tRNA synthetase specified by negative determinants. J Mol Biol 328:395–408
Corigliano EM, Perona JJ (2009) Architectural underpinnings of the genetic code for glutamine. Biochemistry 48:676–687
Konno M, Sumida T, Uchikawa E, Mori Y, Yanagisawa T, Sekine S, Yokoyama S (2009) Modeling of tRNA-assisted mechanism of Arg activation based on a structure of Arg-tRNA synthetase, tRNA, and an ATP analog (ANP). FEBS J 276:4763–4779
Fersht AR (1987) Dissection of the structure and activity of the tyrosyl-tRNA synthetase by site-directed mutagenesis. Biochemistry 26:8031–8037
First EA, Fersht AR (1993) Mutational and kinetic analysis of a mobile loop in tyrosyl-tRNA synthetase. Biochemistry 32:13658–13663
Cusack S, Yaremchuk A, Tukalo M (2000) The 2 A crystal structure of leucyl-tRNA synthetase and its complex with a leucyl-adenylate analogue. EMBO J 19:2351–2361
Kobayashi T, Takimura T, Sekine R, Kelly VP, Kamata K, Sakamoto K, Nishimura S, Yokoyama S (2005) Structural snapshots of the KMSKS loop rearrangement for amino acid activation by bacterial tyrosyl-tRNA synthetase. J Mol Biol 346:105–117
Sharma G, First EA (2009) Thermodynamic analysis reveals a temperature-dependent change in the catalytic mechanism of bacillus stearothermophilus tyrosyl-tRNA synthetase. J Biol Chem 284:4179–4190
Kapustina M, Carter CW Jr (2006) Computational studies of tryptophanyl-tRNA synthetase: activation of ATP by induced-fit. J Mol Biol 362:1159–1180
Retailleau P, Weinreb V, Hu M, Carter CW Jr (2007) Crystal structure of tryptophanyl-tRNA synthetase complexed with adenosine-5′ tetraphosphate: evidence for distributed use of catalytic binding energy in amino acid activation by class I aminoacyl-tRNA synthetases. J Mol Biol 369:108–128
Laowanapiban P, Kapustina M, Vonrhein C, Delarue M, Koehl P, Carter CW Jr (2009) Independent saturation of three TrpRS subsites generates a partially assembled state similar to those observed in molecular simulations. Proc Natl Acad Sci USA 106:1790–1795
Leatherbarrow RJ, Fersht AR, Winter G (1985) Transition-state stabilization in the mechanism of tyrosyl-tRNA synthetase revealed by protein engineering. Proc Natl Acad Sci USA 82:7840–7844
Weinreb V, Carter CW Jr (2008) Mg2+-free Bacillus stearothermophilus tryptophanyl-tRNA synthetase retains a major fraction of the overall rate enhancement for tryptophan activation. J Am Chem Soc 130:1488–1494
Weinreb V, Li L, Carter CW Jr (2012) A master switch couples Mg(2)(+)-assisted catalysis to domain motion in B. stearothermophilus tryptophanyl-tRNA Synthetase. Structure 20:128–138
Weinreb V, Li L, Campbell CL, Kaguni LS, Carter CW Jr (2009) Mg2+-assisted catalysis by B. stearothermophilus TrpRS is promoted by allosteric effects. Structure 17:952–964
Cammer S, Carter CW Jr (2010) Six Rossmannoid folds, including the class I aminoacyl-tRNA synthetases, share a partial core with the anti-codon-binding domain of a class II aminoacyl-tRNA synthetase. Bioinformatics 26:709–714
Uter NT, Perona JJ (2006) Active-site assembly in glutaminyl-tRNA synthetase by tRNA-mediated induced fit. Biochemistry 45:6858–6865
Xin Y, Li W, First EA (2000) Stabilization of the transition state for the transfer of tyrosine to tRNA(Tyr) by tyrosyl-tRNA synthetase. J Mol Biol 303:299–310
Lassila JK, Zalatan JG, Herschlag D (2011) Biological phosphoryl-transfer reactions: understanding mechanism and catalysis. Annu Rev Biochem 80:669–702
Black Pyrkosz A, Eargle J, Sethi A, Luthey-Schulten Z (2010) Exit strategies for charged tRNA from GluRS. J Mol Biol 397:1350–1371
Uter NT, Perona JJ (2004) Long-range intramolecular signaling in a tRNA synthetase complex revealed by pre-steady-state kinetics. Proc Natl Acad Sci USA 101:14396–14401
Fersht AR, Gangloff J, Dirheimer G (1978) Reaction pathway and rate-determining step in the aminoacylation of tRNAArg catalyzed by the arginyl-tRNA synthetase from yeast. Biochemistry 17:3740–3746
Liu C, Sanders JM, Pascal JM, Hou YM (2012) Adaptation to tRNA acceptor stem structure by flexible adjustment in the catalytic domain of class I tRNA synthetases. RNA 18:213–221
Mulvey RS, Fersht AR (1978) Mechanism of aminoacylation of transfer RNA. A pre-steady-state analysis of the reaction pathway catalyzed by the methionyl-tRNA synthetase of Bacillus stearothermophilus. Biochemistry 17:5591–5597
Cvetesic N, Perona JJ, Gruic-Sovulj I (2012) Kinetic partitioning between synthetic and editing pathways in class I aminoacyl-tRNA synthetases occurs at both pre-transfer and post-transfer hydrolytic steps. J Biol Chem 287:25381–25394
Ward WH, Fersht AR (1988) Tyrosyl-tRNA synthetase acts as an asymmetric dimer in charging tRNA. A rationale for half-of-the-sites activity. Biochemistry 27:5525–5530
Doublie S, Bricogne G, Gilmore C, Carter CW Jr (1995) Tryptophanyl-tRNA synthetase crystal structure reveals an unexpected homology to tyrosyl-tRNA synthetase. Structure 3:17–31
Eriani G, Delarue M, Poch O, Gangloff J, Moras D (1990) Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs. Nature 347:203–206
Cavarelli J, Eriani G, Rees B, Ruff M, Boeglin M, Mitschler A, Martin F, Gangloff J, Thierry JC, Moras D (1994) The active site of yeast aspartyl-tRNA synthetase: structural and functional aspects of the aminoacylation reaction. EMBO J 13:327–337
Dignam JD, Guo J, Griffith WP, Garbett NC, Holloway A, Mueser T (2011) Allosteric interaction of nucleotides and tRNA(ala) with E. coli alanyl-tRNA synthetase. Biochemistry 50:9886–9900
Cusack S (1993) Sequence, structure and evolutionary relationships between class 2 aminoacyl-tRNA synthetases: an update. Biochimie 75:1077–1081
Cavarelli J, Rees B, Ruff M, Thierry JC, Moras D (1993) Yeast tRNA(Asp) recognition by its cognate class II aminoacyl-tRNA synthetase. Nature 362:181–184
Belrhali H, Yaremchuk A, Tukalo M, Berthet-Colominas C, Rasmussen B, Bosecke P, Diat O, Cusack S (1995) The structural basis for seryl-adenylate and Ap4A synthesis by seryl-tRNA synthetase. Structure 3:341–352
Berthet-Colominas C, Seignovert L, Hartlein M, Grotli M, Cusack S, Leberman R (1998) The crystal structure of asparaginyl-tRNA synthetase from Thermus thermophilus and its complexes with ATP and asparaginyl-adenylate: the mechanism of discrimination between asparagine and aspartic acid. EMBO J 17:2947–2960
Schmitt E, Moulinier L, Fujiwara S, Imanaka T, Thierry JC, Moras D (1998) Crystal structure of aspartyl-tRNA synthetase from Pyrococcus kodakaraensis KOD: archaeon specificity and catalytic mechanism of adenylate formation. EMBO J 17:5227–5237
Arnez JG, Dock-Bregeon AC, Moras D (1999) Glycyl-tRNA synthetase uses a negatively charged pit for specific recognition and activation of glycine. J Mol Biol 286:1449–1459
Swairjo MA, Schimmel PR (2005) Breaking sieve for steric exclusion of a noncognate amino acid from active site of a tRNA synthetase. Proc Natl Acad Sci USA 102:988–993
Bilokapic S, Maier T, Ahel D, Gruic-Sovulj I, Soll D, Weygand-Durasevic I, Ban N (2006) Structure of the unusual seryl-tRNA synthetase reveals a distinct zinc-dependent mode of substrate recognition. EMBO J 25:2498–2509
Arnez JG, Sankaranarayanan R, Dock-Bregeon AC, Francklyn CS, Moras D (2000) Aminoacylation at the atomic level in class IIa aminoacyl-tRNA synthetases. J Biomol Struct Dyn 17:23–27
Sankaranarayanan R, Dock-Bregeon AC, Rees B, Bovee M, Caillet J, Romby P, Francklyn CS, Moras D (2000) Zinc ion mediated amino acid discrimination by threonyl-tRNA synthetase. Nat Struct Biol 7:461–465
Fishman R, Ankilova V, Moor N, Safro M (2001) Structure at 2.6 A resolution of phenylalanyl-tRNA synthetase complexed with phenylalanyl-adenylate in the presence of manganese. Acta Crystallogr D Biol Crystallogr 57:1534–1544
Guo M, Chong YE, Shapiro R, Beebe K, Yang XL, Schimmel P (2009) Paradox of mistranslation of serine for alanine caused by AlaRS recognition dilemma. Nature 462:808–812
Eiler S, Dock-Bregeon A, Moulinier L, Thierry JC, Moras D (1999) Synthesis of aspartyl-tRNA(Asp) in Escherichia coli – a snapshot of the second step. EMBO J 18:6532–6541
Arnez JG, Augustine JG, Moras D, Francklyn CS (1997) The first step of aminoacylation at the atomic level in histidyl-tRNA synthetase. Proc Natl Acad Sci USA 94:7144–7149
Guth EC, Francklyn CS (2007) Kinetic discrimination of tRNA identity by the conserved motif 2 loop of a class II aminoacyl-tRNA synthetase. Mol Cell 25:531–542
Dulic M, Pozar J, Bilokapic S, Weygand-Durasevic I, Gruic-Sovulj I (2011) An idiosyncratic serine ordering loop in methanogen seryl-tRNA synthetases guides substrates through seryl-tRNASer formation. Biochimie 93:1761–1769
Arnez JG, Harris DC, Mitschler A, Rees B, Francklyn CS, Moras D (1995) Crystal structure of histidyl-tRNA synthetase from Escherichia coli complexed with histidyl-adenylate. EMBO J 14:4143–4155
Banik SD, Nandi N (2010) Aminoacylation reaction in the histidyl-tRNA synthetase: fidelity mechanism of the activation step. J Phys Chem B 114:2301–2311
Ng JD, Sauter C, Lorber B, Kirkland N, Arnez J, Giege R (2002) Comparative analysis of space-grown and earth-grown crystals of an aminoacyl-tRNA synthetase: space-grown crystals are more useful for structural determination. Acta Crystallogr D Biol Crystallogr 58:645–652
Reshetnikova L, Moor N, Lavrik O, Vassylyev DG (1999) Crystal structures of phenylalanyl-tRNA synthetase complexed with phenylalanine and a phenylalanyl-adenylate analogue. J Mol Biol 287:555–568
Torres-Larios A, Sankaranarayanan R, Rees B, Dock-Bregeon AC, Moras D (2003) Conformational movements and cooperativity upon amino acid, ATP and tRNA binding in threonyl-tRNA synthetase. J Mol Biol 331:201–211
Yaremchuk A, Tukalo M, Grotli M, Cusack S (2001) A succession of substrate induced conformational changes ensures the amino acid specificity of Thermus thermophilus prolyl-tRNA synthetase: comparison with histidyl-tRNA synthetase. J Mol Biol 309:989–1002
Yanagisawa T, Ishii R, Fukunaga R, Kobayashi T, Sakamoto K, Yokoyama S (2008) Crystallographic studies on multiple conformational states of active-site loops in pyrrolysyl-tRNA synthetase. J Mol Biol 378:634–652
Bovee ML, Pierce MA, Francklyn CS (2003) Induced fit and kinetic mechanism of adenylation catalyzed by Escherichia coli threonyl-tRNA synthetase. Biochemistry 42:15102–15113
Cusack S, Yaremchuk A, Tukalo M (1996) The crystal structure of the ternary complex of T. thermophilus seryl-tRNA synthetase with tRNA(Ser) and a seryl-adenylate analogue reveals a conformational switch in the active site. EMBO J 15:2834–2842
Qiu X, Janson CA, Blackburn MN, Chhohan IK, Hibbs M, Abdel-Meguid SS (1999) Cooperative structural dynamics and a novel fidelity mechanism in histidyl-tRNA synthetase. Biochemistry 38:12296–12304
Moulinier L, Eiler S, Eriani G, Gangloff J, Thierry JC, Gabriel K, McClain WH, Moras D (2001) The structure of an AspRS-tRNA(Asp) complex reveals a tRNA-dependent control mechanism. EMBO J 20:5290–5301
Onesti S, Desogus G, Brevet A, Chen J, Plateau P, Blanquet S, Brick P (2000) Structural studies of lysyl-tRNA synthetase: conformational changes induced by substrate binding. Biochemistry 39:12853–12861
Moor N, Kotik-Kogan O, Tworowski D, Sukhanova M, Safro M (2006) The crystal structure of the ternary complex of phenylalanyl-tRNA synthetase with tRNAPhe and a phenylalanyl-adenylate analogue reveals a conformational switch of the CCA end. Biochemistry 45:10572–10583
Dibbelt L, Pachmann U, Zachau HG (1980) Serine activation is the rate limiting step of tRNASer aminoacylation by yeast seryl tRNA synthetase. Nucleic Acids Res 8:4021–4039
Dibbelt L, Zachau HG (1981) On the rate limiting step of yeast tRNAPhe aminoacylation. FEBS Lett 129:173–176
Sankaranarayanan R, Dock-Bregeon AC, Romby P, Caillet J, Springer M, Rees B, Ehresmann C, Ehresmann B, Moras D (1999) The structure of threonyl-tRNA synthetase-tRNA(Thr) complex enlightens its repressor activity and reveals an essential zinc ion in the active site. Cell 97:371–381
Nozawa K, O'Donoghue P, Gundllapalli S, Araiso Y, Ishitani R, Umehara T, Soll D, Nureki O (2009) Pyrrolysyl-tRNA synthetase-tRNA(Pyl) structure reveals the molecular basis of orthogonality. Nature 457:1163–1167
Biou V, Yaremchuk A, Tukalo M, Cusack S (1994) The 2.9 A crystal structure of T. thermophilus seryl-tRNA synthetase complexed with tRNA(Ser). Science 263:1404–1410
Borel F, Vincent C, Leberman R, Hartlein M (1994) Seryl-tRNA synthetase from Escherichia coli: implication of its N-terminal domain in aminoacylation activity and specificity. Nucleic Acids Res 22:2963–2969
Eriani G, Cavarelli J, Martin F, Dirheimer G, Moras D, Gangloff J (1993) Role of dimerization in yeast aspartyl-tRNA synthetase and importance of the class II invariant proline. Proc Natl Acad Sci USA 90:10816–10820
Yaremchuk A, Cusack S, Tukalo M (2000) Crystal structure of a eukaryote/archaeon-like protyl-tRNA synthetase and its complex with tRNAPro(CGG). EMBO J 19:4745–4758
Yang XL, Otero FJ, Ewalt KL, Liu J, Swairjo MA, Kohrer C, RajBhandary UL, Skene RJ, McRee DE, Schimmel P (2006) Two conformations of a crystalline human tRNA synthetase-tRNA complex: implications for protein synthesis. EMBO J 25:2919–2929
Hauenstein SI, Hou YM, Perona JJ (2008) The homotetrameric phosphoseryl-tRNA synthetase from Methanosarcina mazei exhibits half-of-the-sites activity. J Biol Chem 283:21997–22006
Ambrogelly A, Kamtekar S, Stathopoulos C, Kennedy D, Soll D (2005) Asymmetric behavior of archaeal prolyl-tRNA synthetase. FEBS Lett 579:6017–6022
Coleman DE, Carter CW Jr (1984) Crystals of Bacillus stearothermophilus tryptophanyl-tRNA synthetase containing enzymatically formed acyl transfer product tryptophanyl-ATP, an active site maker for the 3′ CCA terminus of tryptophanyl-tRNATrp. Biochemistry 23:381–385
Liu H, Gauld JW (2008) Substrate-assisted catalysis in the aminoacyl transfer mechanism of histidyl-tRNA synthetase: a density functional theory study. J Phys Chem B 112:16874–16882
Huang W, Bushnell EA, Francklyn CS, Gauld JW (2011) The alpha-amino group of the threonine substrate as the general base during tRNA aminoacylation: a new version of substrate-assisted catalysis predicted by hybrid DFT. J Phys Chem A 115:13050–13060
Lee JW, Beebe K, Nangle LA, Jang J, Longo-Guess CM, Cook SA, Davisson MT, Sundberg JP, Schimmel P, Ackerman SL (2006) Editing-defective tRNA synthetase causes protein misfolding and neurodegeneration. Nature 443:50–55
Ruan B, Palioura S, Sabina J, Marvin-Guy L, Kochhar S, Larossa RA, Soll D (2008) Quality control despite mistranslation caused by an ambiguous genetic code. Proc Natl Acad Sci USA 105:16502–16507
Reynolds NM, Ling J, Roy H, Banerjee R, Repasky SE, Hamel P, Ibba M (2010) Cell-specific differences in the requirements for translation quality control. Proc Natl Acad Sci USA 107:4063–4068
Roy H, Ling J, Alfonzo J, Ibba M (2005) Loss of editing activity during the evolution of mitochondrial phenylalanyl-tRNA synthetase. J Biol Chem 280:38186–38192
Lue SW, Kelley SO (2005) An aminoacyl-tRNA synthetase with a defunct editing site. Biochemistry 44:3010–3016
Netzer N, Goodenbour JM, David A, Dittmar KA, Jones RB, Schneider JR, Boone D, Eves EM, Rosner MR, Gibbs JS, Embry A, Dolan B, Das S, Hickman HD, Berglund P, Bennink JR, Yewdell JW, Pan T (2009) Innate immune and chemically triggered oxidative stress modifies translational fidelity. Nature 462:522–526
Silvian LF, Wang J, Steitz TA (1999) Insights into editing from an ile-tRNA synthetase structure with tRNAile and mupirocin. Science 285:1074–1077
Fukai S, Nureki O, Sekine S, Shimada A, Tao J, Vassylyev DG, Yokoyama S (2000) Structural basis for double-sieve discrimination of L-valine from L-isoleucine and L-threonine by the complex of tRNA(Val) and valyl-tRNA synthetase. Cell 103:793–803
Lincecum TL Jr, Tukalo M, Yaremchuk A, Mursinna RS, Williams AM, Sproat BS, Van Den Eynde W, Link A, Van Calenbergh S, Grotli M, Martinis SA, Cusack S (2003) Structural and mechanistic basis of pre- and posttransfer editing by leucyl-tRNA synthetase. Mol Cell 11:951–963
Roy H, Ling J, Irnov M, Ibba M (2004) Post-transfer editing in vitro and in vivo by the beta subunit of phenylalanyl-tRNA synthetase. EMBO J 23:4639–4648
Kotik-Kogan O, Moor N, Tworowski D, Safro M (2005) Structural basis for discrimination of L-phenylalanine from L-tyrosine by phenylalanyl-tRNA synthetase. Structure 13:1799–1807
Beebe K, Ribas De Pouplana L, Schimmel P (2003) Elucidation of tRNA-dependent editing by a class II tRNA synthetase and significance for cell viability. EMBO J 22:668–675
Francklyn CS (2008) DNA polymerases and aminoacyl-tRNA synthetases: shared mechanisms for ensuring the fidelity of gene expression. Biochemistry 47:11695–11703
Ling J, So BR, Yadavalli SS, Roy H, Shoji S, Fredrick K, Musier-Forsyth K, Ibba M (2009) Resampling and editing of mischarged tRNA prior to translation elongation. Mol Cell 33:654–660
An S, Musier-Forsyth K (2004) Trans-editing of Cys-tRNAPro by Haemophilus influenzae YbaK protein. J Biol Chem 279:42359–42362
Minajigi A, Francklyn CS (2010) Aminoacyl transfer rate dictates choice of editing pathway in threonyl-tRNA synthetase. J Biol Chem 285:23810–23817
Splan KE, Ignatov ME, Musier-Forsyth K (2008) Transfer RNA modulates the editing mechanism used by class II prolyl-tRNA synthetase. J Biol Chem 283:7128–7134
Gruic-Sovulj I, Rokov-Plavec J, Weygand-Durasevic I (2007) Hydrolysis of non-cognate aminoacyl-adenylates by a class II aminoacyl-tRNA synthetase lacking an editing domain. FEBS Lett 581:5110–5114
Ling J, Peterson KM, Simonovic I, Soll D, Simonovic M (2012) The mechanism of pre-transfer editing in yeast mitochondrial threonyl-tRNA synthetase. J Biol Chem 287:28518–28525
Rokov-Plavec J, Lesjak S, Gruic-Sovulj I, Mocibob M, Dulic M, Weygand-Durasevic I (2013) Substrate recognition and fidelity of maize seryl-tRNA synthetases. Arch Biochem Biophys 529:122–130
Gruic-Sovulj I, Dulic M, Weygand-Durasevic I (2011) Pre-transfer editing of serine hydroxamate within the active site of methanogenic-type seryl-tRNA synthetase. Croat Chim Acta 84:179–184
Gruic-Sovulj I, Dulic M, Cvetesic N, Majsec K, Weygand-Durasevic I (2010) Efficiently activated serine analog is not transferred to yeast tRNA(Ser). Croat Chim Acta 83:163–169
Jakubowski H (1980) Valyl-tRNA synthetase form yellow lupin seeds: hydrolysis of the enzyme-bound noncognate aminoacyl adenylate as a possible mechanism of increasing specificity of the aminoacyl-tRNA synthetase. Biochemistry 19:5071–5078
Zhu B, Yao P, Tan M, Eriani G, Wang ED (2009) tRNA-independent pretransfer editing by class I leucyl-tRNA synthetase. J Biol Chem 284:3418–3424
Jakubowski H (1991) Proofreading in vivo: editing of homocysteine by methionyl-tRNA synthetase in the yeast Saccharomyces cerevisiae. EMBO J 10:593–598
Serre L, Verdon G, Choinowski T, Hervouet N, Risler JL, Zelwer C (2001) How methionyl-tRNA synthetase creates its amino acid recognition pocket upon L-methionine binding. J Mol Biol 306:863–876
Jakubowski H (1999) Misacylation of tRNALys with noncognate amino acids by lysyl-tRNA synthetase. Biochemistry 38:8088–8093
Jakubowski H (1997) Aminoacyl thioester chemistry of class II aminoacyl-tRNA synthetases. Biochemistry 36:11077–11085
Levengood J, Ataide SF, Roy H, Ibba M (2004) Divergence in noncognate amino acid recognition between class I and class II lysyl-tRNA synthetases. J Biol Chem 279:17707–17714
Hopfield JJ, Yamane T, Yue V, Coutts SM (1976) Direct experimental evidence for kinetic proofreading in amino acylation of tRNAIle. Proc Natl Acad Sci USA 73:1164–1168
Boniecki MT, Vu MT, Betha AK, Martinis SA (2008) CP1-dependent partitioning of pretransfer and posttransfer editing in leucyl-tRNA synthetase. Proc Natl Acad Sci USA 105:19223–19228
Williams AM, Martinis SA (2006) Mutational unmasking of a tRNA-dependent pathway for preventing genetic code ambiguity. Proc Natl Acad Sci USA 103:3586–3591
Eldred EW, Schimmel PR (1972) Rapid deacylation by isoleucyl transfer ribonucleic acid synthetase of isoleucine-specific transfer ribonucleic acid aminoacylated with valine. J Biol Chem 247:2961–2964
Hati S, Ziervogel B, Sternjohn J, Wong FC, Nagan MC, Rosen AE, Siliciano PG, Chihade JW, Musier-Forsyth K (2006) Pre-transfer editing by class II prolyl-tRNA synthetase: role of aminoacylation active site in “selective release” of noncognate amino acids. J Biol Chem 281:27862–27872
Ling J, Peterson KM, Simonovic I, Cho C, Soll D, Simonovic M (2012) Yeast mitochondrial threonyl-tRNA synthetase recognizes tRNA isoacceptors by distinct mechanisms and promotes CUN codon reassignment. Proc Natl Acad Sci USA 109:3281–3286
Lin SX, Baltzinger M, Remy P (1984) Fast kinetic study of yeast phenylalanyl-tRNA synthetase: role of tRNAPhe in the discrimination between tyrosine and phenylalanine. Biochemistry 23:4109–4116
Nomanbhoy TK, Hendrickson TL, Schimmel P (1999) Transfer RNA-dependent translocation of misactivated amino acids to prevent errors in protein synthesis. Mol Cell 4:519–528
Farrow MA, Schimmel P (2001) Editing by a tRNA synthetase: DNA aptamer-induced translocation and hydrolysis of a misactivated amino acid. Biochemistry 40:4478–4483
Hendrickson TL, Nomanbhoy TK, de Crecy-Lagard V, Fukai S, Nureki O, Yokoyama S, Schimmel P (2002) Mutational separation of two pathways for editing by a class I tRNA synthetase. Mol Cell 9:353–362
Bishop AC, Nomanbhoy TK, Schimmel P (2002) Blocking site-to-site translocation of a misactivated amino acid by mutation of a class I tRNA synthetase. Proc Natl Acad Sci USA 99:585–590
Dock-Bregeon AC, Rees B, Torres-Larios A, Bey G, Caillet J, Moras D (2004) Achieving error-free translation; the mechanism of proofreading of threonyl-tRNA synthetase at atomic resolution. Mol Cell 16:375–386
Lin L, Hale SP, Schimmel P (1996) Aminoacylation error correction. Nature 384:33–34
Betha AK, Williams AM, Martinis SA (2007) Isolated CP1 domain of Escherichia coli leucyl-tRNA synthetase is dependent on flanking hinge motifs for amino acid editing activity. Biochemistry 46:6258–6267
Beuning PJ, Musier-Forsyth K (2001) Species-specific differences in amino acid editing by class II prolyl-tRNA synthetase. J Biol Chem 276:30779–30785
SternJohn J, Hati S, Siliciano PG, Musier-Forsyth K (2007) Restoring species-specific posttransfer editing activity to a synthetase with a defunct editing domain. Proc Natl Acad Sci USA 104:2127–2132
Guo LT, Helgadottir S, Soll D, Ling J (2012) Rational design and directed evolution of a bacterial-type glutaminyl-tRNA synthetase precursor. Nucleic Acids Res 40:7967–7974
Wong FC, Beuning PJ, Silvers C, Musier-Forsyth K (2003) An isolated class II aminoacyl-tRNA synthetase insertion domain is functional in amino acid editing. J Biol Chem 278:52857–52864
Nureki O, Vassylyev DG, Tateno M, Shimada A, Nakama T, Fukai S, Konno M, Hendrickson TL, Schimmel P, Yokoyama S (1998) Enzyme structure with two catalytic sites for double-sieve selection of substrate. Science 280:578–582
Mascarenhas AP, Martinis SA (2009) A glycine hinge for tRNA-dependent translocation of editing substrates to prevent errors by leucyl-tRNA synthetase. FEBS Lett 583:3443–3447
Rock FL, Mao W, Yaremchuk A, Tukalo M, Crepin T, Zhou H, Zhang YK, Hernandez V, Akama T, Baker SJ, Plattner JJ, Shapiro L, Martinis SA, Benkovic SJ, Cusack S, Alley MR (2007) An antifungal agent inhibits an aminoacyl-tRNA synthetase by trapping tRNA in the editing site. Science 316:1759–1761
Fukunaga R, Yokoyama S (2007) Structure of the AlaX-M trans-editing enzyme from Pyrococcus horikoshii. Acta Crystallogr D Biol Crystallogr 63:390–400
Sokabe M, Okada A, Yao M, Nakashima T, Tanaka I (2005) Molecular basis of alanine discrimination in editing site. Proc Natl Acad Sci USA 102:11669–11674
Sasaki HM, Sekine S, Sengoku T, Fukunaga R, Hattori M, Utsunomiya Y, Kuroishi C, Kuramitsu S, Shirouzu M, Yokoyama S (2006) Structural and mutational studies of the amino acid-editing domain from archaeal/eukaryal phenylalanyl-tRNA synthetase. Proc Natl Acad Sci USA 103:14744–14749
Hussain T, Kruparani SP, Pal B, Dock-Bregeon AC, Dwivedi S, Shekar MR, Sureshbabu K, Sankaranarayanan R (2006) Post-transfer editing mechanism of a D-aminoacyl-tRNA deacylase-like domain in threonyl-tRNA synthetase from archaea. EMBO J 25:4152–4162
Murayama K, Kato-Murayama M, Katsura K, Uchikubo-Kamo T, Yamaguchi-Hirafuji M, Kawazoe M, Akasaka R, Hanawa-Suetsugu K, Hori-Takemoto C, Terada T, Shirouzu M, Yokoyama S (2005) Structure of a putative trans-editing enzyme for prolyl-tRNA synthetase from Aeropyrum pernix K1 at 1.7 A resolution. Acta Crystallogr Sect F Struct Biol Cryst Commun 61:26–29
Fukunaga R, Yokoyama S (2005) Structural basis for non-cognate amino acid discrimination by the valyl-tRNA synthetase editing domain. J Biol Chem 280:29937–29945
Fukunaga R, Fukai S, Ishitani R, Nureki O, Yokoyama S (2004) Crystal structures of the CP1 domain from Thermus thermophilus isoleucyl-tRNA synthetase and its complex with L-valine. J Biol Chem 279:8396–8402
Seiradake E, Mao W, Hernandez V, Baker SJ, Plattner JJ, Alley MR, Cusack S (2009) Crystal structures of the human and fungal cytosolic leucyl-tRNA synthetase editing domains: a structural basis for the rational design of antifungal benzoxaboroles. J Mol Biol 390:196–207
Fukunaga R, Yokoyama S (2006) Structural basis for substrate recognition by the editing domain of isoleucyl-tRNA synthetase. J Mol Biol 359:901–912
Liu Y, Liao J, Zhu B, Wang ED, Ding J (2006) Crystal structures of the editing domain of Escherichia coli leucyl-tRNA synthetase and its complexes with Met and Ile reveal a lock-and-key mechanism for amino acid discrimination. Biochem J 394:399–407
Mursinna RS, Lincecum TL Jr, Martinis SA (2001) A conserved threonine within Escherichia coli leucyl-tRNA synthetase prevents hydrolytic editing of leucyl-tRNALeu. Biochemistry 40:5376–5381
Hussain T, Kamarthapu V, Kruparani SP, Deshmukh MV, Sankaranarayanan R (2010) Mechanistic insights into cognate substrate discrimination during proofreading in translation. Proc Natl Acad Sci USA 107:22117–22121
Kumar S, Das M, Hadad CM, Musier-Forsyth K (2012) Substrate specificity of bacterial prolyl-tRNA synthetase editing domain is controlled by a tunable hydrophobic pocket. J Biol Chem 287:3175–3184
Ahel I, Stathopoulos C, Ambrogelly A, Sauerwald A, Toogood H, Hartsch T, Soll D (2002) Cysteine activation is an inherent in vitro property of prolyl-tRNA synthetases. J Biol Chem 277:34743–34748
Ahel I, Korencic D, Ibba M, Soll D (2003) Trans-editing of mischarged tRNAs. Proc Natl Acad Sci USA 100:15422–15427
Pasman Z, Robey-Bond S, Mirando AC, Smith GJ, Lague A, Francklyn CS (2011) Substrate specificity and catalysis by the editing active site of alanyl-tRNA synthetase from Escherichia coli. Biochemistry 50:1474–1482
Waas WF, Schimmel P (2007) Evidence that tRNA synthetase-directed proton transfer stops mistranslation. Biochemistry 46:12062–12070
Beebe K, Merriman E, Ribas De Pouplana L, Schimmel P (2004) A domain for editing by an archaebacterial tRNA synthetase. Proc Natl Acad Sci USA 101:5958–5963
Korencic D, Ahel I, Schelert J, Sacher M, Ruan B, Stathopoulos C, Blum P, Ibba M, Soll D (2004) A freestanding proofreading domain is required for protein synthesis quality control in archaea. Proc Natl Acad Sci USA 101:10260–10265
Dwivedi S, Kruparani SP, Sankaranarayanan R (2005) A D-amino acid editing module coupled to the translational apparatus in archaea. Nat Struct Mol Biol 12:556–557
Hagiwara Y, Field MJ, Nureki O, Tateno M (2010) Editing mechanism of aminoacyl-tRNA synthetases operates by a hybrid ribozyme/protein catalyst. J Am Chem Soc 132:2751–2758
Ling J, Roy H, Ibba M (2007) Mechanism of tRNA-dependent editing in translational quality control. Proc Natl Acad Sci USA 104:72–77
Sheoran A, Sharma G, First EA (2008) Activation of D-tyrosine by Bacillus stearothermophilus tyrosyl-tRNA synthetase: 1. Pre-steady-state kinetic analysis reveals the mechanistic basis for the recognition of D-tyrosine. J Biol Chem 283:12960–12970
Sheoran A, First EA (2008) Activation of D-tyrosine by Bacillus stearothermophilus tyrosyl-tRNA synthetase: 2. Cooperative binding of ATP is limited to the initial turnover of the enzyme. J Biol Chem 283:12971–12980
Calendar R, Berg P (1967) D-Tyrosyl RNA: formation, hydrolysis and utilization for protein synthesis. J Mol Biol 26:39–54
An S, Musier-Forsyth K (2005) Cys-tRNA(Pro) editing by Haemophilus influenzae YbaK via a novel synthetase.YbaK.tRNA ternary complex. J Biol Chem 280:34465–34472
Ruan B, Soll D (2005) The bacterial YbaK protein is a Cys-tRNAPro and Cys-tRNA Cys deacylase. J Biol Chem 280:25887–25891
So BR, An S, Kumar S, Das M, Turner DA, Hadad CM, Musier-Forsyth K (2011) Substrate-mediated fidelity mechanism ensures accurate decoding of proline codons. J Biol Chem 286:31810–31820
Kumar S, Das M, Hadad CM, Musier-Forsyth K (2013) Aminoacyl-tRNA substrate and enzyme backbone atoms contribute to translational quality control by YbaK. J Phys Chem B 117:4521–4527
Sanford B, Cao B, Johnson JM, Zimmerman K, Strom AM, Mueller RM, Bhattacharyya S, Musier-Forsyth K, Hati S (2012) Role of coupled dynamics in the catalytic activity of prokaryotic-like prolyl-tRNA synthetases. Biochemistry 51:2146–2156
Beebe K, Mock M, Merriman E, Schimmel P (2008) Distinct domains of tRNA synthetase recognize the same base pair. Nature 451:90–93
Guo M, Chong YE, Beebe K, Shapiro R, Yang XL, Schimmel P (2009) The C-Ala domain brings together editing and aminoacylation functions on one tRNA. Science 325:744–747
Chong YE, Yang XL, Schimmel P (2008) Natural homolog of tRNA synthetase editing domain rescues conditional lethality caused by mistranslation. J Biol Chem 283:30073–30078
O'Donoghue P, Luthey-Schulten Z (2003) On the evolution of structure in aminoacyl-tRNA synthetases. Microbiol Mol Biol Rev 67:550–573
Ibba M, Morgan S, Curnow AW, Pridmore DR, Vothknecht UC, Gardner W, Lin W, Woese CR, Soll D (1997) A euryarchaeal lysyl-tRNA synthetase: resemblance to class I synthetases. Science 278:1119–1122
Sauerwald A, Zhu W, Major TA, Roy H, Palioura S, Jahn D, Whitman WB, Yates JR 3rd, Ibba M, Soll D (2005) RNA-dependent cysteine biosynthesis in archaea. Science 307:1969–1972
Hao B, Gong W, Ferguson TK, James CM, Krzycki JA, Chan MK (2002) A new UAG-encoded residue in the structure of a methanogen methyltransferase. Science 296:1462–1466
Srinivasan G, James CM, Krzycki JA (2002) Pyrrolysine encoded by UAG in archaea: charging of a UAG-decoding specialized tRNA. Science 296:1459–1462
Polycarpo C, Ambrogelly A, Berube A, Winbush SM, McCloskey JA, Crain PF, Wood JL, Soll D (2004) An aminoacyl-tRNA synthetase that specifically activates pyrrolysine. Proc Natl Acad Sci USA 101:12450–12454
Blight SK, Larue RC, Mahapatra A, Longstaff DG, Chang E, Zhao G, Kang PT, Green-Church KB, Chan MK, Krzycki JA (2004) Direct charging of tRNA(CUA) with pyrrolysine in vitro and in vivo. Nature 431:333–335
Acknowledgments
We thank Nevena Cvetesic and Andrew Hadd for assistance with figures. This work was supported by the National Institutes of Health (GM63713 and 1RO3TW008024) and by the Croatian Science Foundation (grant 09.01/293). I.G.S. thanks the Adris foundation for support.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2013 Springer-Verlag Berlin Heidelberg
About this chapter
Cite this chapter
Perona, J.J., Gruic-Sovulj, I. (2013). Synthetic and Editing Mechanisms of Aminoacyl-tRNA Synthetases. In: Kim, S. (eds) Aminoacyl-tRNA Synthetases in Biology and Medicine. Topics in Current Chemistry, vol 344. Springer, Dordrecht. https://doi.org/10.1007/128_2013_456
Download citation
DOI: https://doi.org/10.1007/128_2013_456
Published:
Publisher Name: Springer, Dordrecht
Print ISBN: 978-94-017-8700-0
Online ISBN: 978-94-017-8701-7
eBook Packages: Chemistry and Materials ScienceChemistry and Material Science (R0)