|Gene:||aspS||Accession Numbers: EG10097 (MetaCyc), b1866, ECK1867|
Species: Escherichia coli K-12 substr. MG1655
Aspartyl-tRNA synthetase (AspRS) is a member of the family of aminoacyl-tRNA synthetases, which interpret the genetic code by covalently linking amino acids to their specific tRNA molecules. The reaction is driven by ATP hydrolysis. AspRS belongs to the Class II aminoacyl tRNA synthetases, which share three regions of homology [Eriani90].
The enzyme is a dimer in solution [Eriani90a]. Crystal structures of AspRS have been determined and allow modelling of specific interactions with the tRNA and the reaction mechanism [Eiler99, Rees00, Moulinier01]. AspRS activity appears to be the target of processed Microcin C, which is an aspartyl adenylate analog [Metlitskaya06].
The tls-1 allele of aspS consists of a P555S mutation in the highly conserved proline residue of motif 3. It has no significant effect on substrate binding, but may affect the active site [Martin97]. Specific interactions of AspRS with tRNA(Asp) were deduced from the crystal structures and by mutagenesis of the tRNA substrate [Choi03a]. The L45 loop within the OB-fold domain of AspRS appears to be responsible for anticodon recognition [Brevet03]. Mutations that allow charging of an amber tRNAAsp with aspartate mostly localize to the anticodon binding domain of AspRS, although some are far from the anticodon binding domain [Martin04a].
Amino acid substrate specificity and discrimination by AspRS is complex. AspRS can misacylate tRNAAsp with D-Asp [Soutourina00, Thompson07a]. The misacylated D-Asp-tRNAAsp can be hydrolyzed by D-Tyr-tRNATyr deacylase [Soutourina00]. Molecular-dynamics free-energy simulations have been used to study substrate specificity [Archontis98, Archontis01, Archontis01a]. They suggest that a labile proton at His448 is mostly responsible for discrimination between Asp and Asn, that ATP acts as a mobile discriminator [Thompson06], and that strongly bound ATP-associated Mg2+ aids AspAMP recognition [Thompson06a]. Mutations in binding pocket residues have similar effects in experimental and simulation tests: discrimination between Asp and Asn is reduced, but not eliminated [Thompson08].
|Map Position: [1,946,774 <- 1,948,546]|
Molecular Weight of Polypeptide: 65.913 kD (from nucleotide sequence), 65 kD (experimental) [Eriani90a ]
Unification Links: ASAP:ABE-0006226 , CGSC:32508 , DIP:DIP-9182N , EchoBASE:EB0095 , EcoGene:EG10097 , EcoliWiki:b1866 , Mint:MINT-1249167 , ModBase:P21889 , OU-Microarray:b1866 , PortEco:aspS , PR:PRO_000022173 , Pride:P21889 , Protein Model Portal:P21889 , RefSeq:NP_416380 , RegulonDB:EG10097 , SMR:P21889 , String:511145.b1866 , UniProt:P21889
Relationship Links: InterPro:IN-FAMILY:IPR002312 , InterPro:IN-FAMILY:IPR004115 , InterPro:IN-FAMILY:IPR004364 , InterPro:IN-FAMILY:IPR004365 , InterPro:IN-FAMILY:IPR004524 , InterPro:IN-FAMILY:IPR006195 , InterPro:IN-FAMILY:IPR012340 , InterPro:IN-FAMILY:IPR018150 , InterPro:IN-FAMILY:IPR029351 , Panther:IN-FAMILY:PTHR22594 , Panther:IN-FAMILY:PTHR22594:SF5 , PDB:Structure:1C0A , PDB:Structure:1EQR , PDB:Structure:1IL2 , Pfam:IN-FAMILY:PF00152 , Pfam:IN-FAMILY:PF01336 , Pfam:IN-FAMILY:PF02938 , Prints:IN-FAMILY:PR01042 , Prosite:IN-FAMILY:PS50862
|Biological Process:||GO:0006422 - aspartyl-tRNA aminoacylation
GO:0006412 - translation [UniProtGOA11a]
GO:0006418 - tRNA aminoacylation for protein translation [GOA01a]
|Molecular Function:||GO:0004815 - aspartate-tRNA ligase activity
GO:0000166 - nucleotide binding [UniProtGOA11a, GOA01a]
GO:0003676 - nucleic acid binding [GOA01a]
GO:0004812 - aminoacyl-tRNA ligase activity [UniProtGOA11a, GOA01a]
GO:0005524 - ATP binding [UniProtGOA11a, GOA01a]
GO:0016874 - ligase activity [UniProtGOA11a, GOA01a]
|Cellular Component:||GO:0005829 - cytosol
[DiazMejia09, Ishihama08, Lasserre06]
GO:0005737 - cytoplasm [UniProtGOA11, UniProtGOA11a, GOA01a]
|MultiFun Terms:||information transfer → protein related → amino acid -activation|
Enzymatic reaction of: aspartyl-tRNA synthetase
EC Number: 188.8.131.52
The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.
The reaction is physiologically favored in the direction shown.
In Pathways: tRNA charging
Kinetic parameters were also measured in crude extracts of a strain overexpressing aspS [Eriani90a].
|Feature Class||Location||Attached Group||Citations||Comment|
|Protein-Segment||195 -> 198|
|Nucleotide-Phosphate-Binding-Region||217 -> 219||ATP|
|Nucleotide-Phosphate-Binding-Region||534 -> 537||ATP|
10/20/97 Gene b1866 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10097; confirmed by SwissProt match.
Akesson78: Akesson B, Lundvik L (1978). "Simultaneous purification and some properties of aspartate: tRNA ligase and seven other amino-acid:tRNA ligases from Escherichia coli." Eur J Biochem 83(1);29-36. PMID: 342244
Archontis01: Archontis G, Simonson T (2001). "Dielectric relaxation in an enzyme active site: molecular dynamics simulations interpreted with a macroscopic continuum model." J Am Chem Soc 123(44);11047-56. PMID: 11686711
Archontis01a: Archontis G, Simonson T, Karplus M (2001). "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 306(2);307-27. PMID: 11237602
Archontis98: Archontis G, Simonson T, Moras D, Karplus M (1998). "Specific amino acid recognition by aspartyl-tRNA synthetase studied by free energy simulations." J Mol Biol 275(5);823-46. PMID: 9480772
Bernier05a: Bernier S, Akochy PM, Lapointe J, Chenevert R (2005). "Synthesis and aminoacyl-tRNA synthetase inhibitory activity of aspartyl adenylate analogs." Bioorg Med Chem 13(1);69-75. PMID: 15582453
Brevet03: Brevet A, Chen J, Commans S, Lazennec C, Blanquet S, Plateau P (2003). "Anticodon recognition in evolution: switching tRNA specificity of an aminoacyl-tRNA synthetase by site-directed peptide transplantation." J Biol Chem 278(33);30927-35. PMID: 12766171
Choi03a: Choi H, Gabriel K, Schneider J, Otten S, McClain WH (2003). "Recognition of acceptor-stem structure of tRNA(Asp) by Escherichia coli aspartyl-tRNA synthetase." RNA 9(4);386-93. PMID: 12649491
DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114
Eriani90: 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(6289);203-6. PMID: 2203971
Eriani90a: Eriani G, Dirheimer G, Gangloff J (1990). "Aspartyl-tRNA synthetase from Escherichia coli: cloning and characterisation of the gene, homologies of its translated amino acid sequence with asparaginyl- and lysyl-tRNA synthetases." Nucleic Acids Res 18(23);7109-18. PMID: 2129559
Lasserre06: Lasserre JP, Beyne E, Pyndiah S, Lapaillerie D, Claverol S, Bonneu M (2006). "A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis." Electrophoresis 27(16);3306-21. PMID: 16858726
Martin04a: Martin F, Barends S, Eriani G (2004). "Single amino acid changes in AspRS reveal alternative routes for expanding its tRNA repertoire in vivo." Nucleic Acids Res 32(13);4081-9. PMID: 15289581
Martin97: Martin F, Sharples GJ, Lloyd RG, Eiler S, Moras D, Gangloff J, Eriani G (1997). "Characterization of a thermosensitive Escherichia coli aspartyl-tRNA synthetase mutant." J Bacteriol 179(11);3691-6. PMID: 9171418
Messmer09: Messmer M, Blais SP, Balg C, Chenevert R, Grenier L, Lague P, Sauter C, Sissler M, Giege R, Lapointe J, Florentz C (2009). "Peculiar inhibition of human mitochondrial aspartyl-tRNA synthetase by adenylate analogs." Biochimie 91(5);596-603. PMID: 19254750
Metlitskaya06: Metlitskaya A, Kazakov T, Kommer A, Pavlova O, Praetorius-Ibba M, Ibba M, Krasheninnikov I, Kolb V, Khmel I, Severinov K (2006). "Aspartyl-tRNA synthetase is the target of peptide nucleotide antibiotic Microcin C." J Biol Chem 281(26);18033-42. PMID: 16574659
Moulinier01: 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(18);5290-301. PMID: 11566892
Neuenfeldt13: Neuenfeldt A, Lorber B, Ennifar E, Gaudry A, Sauter C, Sissler M, Florentz C (2013). "Thermodynamic properties distinguish human mitochondrial aspartyl-tRNA synthetase from bacterial homolog with same 3D architecture." Nucleic Acids Res 41(4);2698-708. PMID: 23275545
Rees00: Rees B, Webster G, Delarue M, Boeglin M, Moras D (2000). "Aspartyl tRNA-synthetase from Escherichia coli: flexibility and adaptability to the substrates." J Mol Biol 299(5);1157-64. PMID: 10873442
Thompson06: Thompson D, Plateau P, Simonson T (2006). "Free-energy simulations and experiments reveal long-range electrostatic interactions and substrate-assisted specificity in an aminoacyl-tRNA synthetase." Chembiochem 7(2);337-44. PMID: 16408313
Thompson06a: Thompson D, Simonson T (2006). "Molecular dynamics simulations show that bound Mg2+ contributes to amino acid and aminoacyl adenylate binding specificity in aspartyl-tRNA synthetase through long range electrostatic interactions." J Biol Chem 281(33);23792-803. PMID: 16774919
Thompson07a: Thompson D, Lazennec C, Plateau P, Simonson T (2007). "Ammonium scanning in an enzyme active site. The chiral specificity of aspartyl-tRNA synthetase." J Biol Chem 282(42);30856-68. PMID: 17690095
Thompson08: Thompson D, Lazennec C, Plateau P, Simonson T (2008). "Probing electrostatic interactions and ligand binding in aspartyl-tRNA synthetase through site-directed mutagenesis and computer simulations." Proteins 71(3):1450-60. PMID: 18076053
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