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MetaCyc Enzyme: aspartyl-tRNA synthetase

Gene: aspS Accession Numbers: EG10097 (MetaCyc), b1866, ECK1867

Synonyms: tls

Species: Escherichia coli K-12 substr. MG1655

Subunit composition of aspartyl-tRNA synthetase = [AspS]2
         aspartyl-tRNA synthetase = AspS

Summary:
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 [Martin97a]. Specific interactions of AspRS with tRNA(Asp) were deduced from the crystal structures and by mutagenesis of the tRNA substrate [Choi03]. 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].

Reviews: [Giege96, Ibba00]

Citations: [Akesson78, Neuenfeldt13]

Locations: cytosol

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 , 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

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0006422 - aspartyl-tRNA aminoacylation Inferred from experiment Inferred by computational analysis [GOA06, Martin97a]
GO:0006412 - translation Inferred by computational analysis [UniProtGOA11]
GO:0006418 - tRNA aminoacylation for protein translation Inferred by computational analysis [GOA01]
Molecular Function: GO:0004815 - aspartate-tRNA ligase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01a, Martin97a]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0003676 - nucleic acid binding Inferred by computational analysis [GOA01]
GO:0004812 - aminoacyl-tRNA ligase activity Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11, GOA06, GOA01]
GO:0016874 - ligase activity Inferred by computational analysis [UniProtGOA11, GOA01]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, Lasserre06]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, GOA06, GOA01]

MultiFun Terms: information transfer protein related amino acid -activation

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International


Enzymatic reaction of: aspartyl-tRNA synthetase

Synonyms: AspRS

EC Number: 6.1.1.12

tRNAasp + L-aspartate + ATP + H+ <=> L-aspartyl-tRNAasp + AMP + diphosphate

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.

In Pathways: tRNA charging

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International

Summary:
Kinetic parameters were also measured in crude extracts of a strain overexpressing aspS [Eriani90a].

Inhibitors (Competitive): 5'-O-[N-(L-Aspartyl)sulfamoyl]adenosine [Bernier05]

Inhibitors (Unknown Mechanism): L-aspartyl adenylate [Bernier05] , aspartyl-phosphonate-adenosine [Bernier05]

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
tRNAasp
0.4
[Akesson78, BRENDA14]
tRNAasp
0.6
[Martin97a]
tRNAasp
80.0
0.55
[Brevet03, BRENDA14]
L-aspartate
90.0
[Messmer09, BRENDA14]
L-aspartate
90.0, 60.0
[Martin97a, BRENDA14]
ATP
50.0
[Akesson78, BRENDA14]
ATP
91.0
[Martin04a, BRENDA14]
ATP
90.0
[Messmer09, BRENDA14]
ATP
90.0
[Martin97a, BRENDA14]

T(opt): 37 °C [BRENDA14, Messmer09]

pH(opt): 7.5 [BRENDA14, Messmer09], 8.5 [BRENDA14, Akesson78]


Sequence Features

Feature Class Location Citations
Acetylation-Modification 370
[Yu08]

History:
10/20/97 Gene b1866 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10097; confirmed by SwissProt match.


References

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

Bernier05: 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

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

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

Choi03: 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

Eiler99: 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(22);6532-41. PMID: 10562565

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

Giege96: Giege R, Florentz C, Kern D, Gangloff J, Eriani G, Moras D (1996). "Aspartate identity of transfer RNAs." Biochimie 78(7);605-23. PMID: 8955904

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Ibba00: Ibba M, Soll D (2000). "Aminoacyl-tRNA synthesis." Annu Rev Biochem 69;617-50. PMID: 10966471

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

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

Martin97a: 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

Soutourina00: Soutourina J, Plateau P, Blanquet S (2000). "Metabolism of D-aminoacyl-tRNAs in Escherichia coli and Saccharomyces cerevisiae cells." J Biol Chem 275(42);32535-42. PMID: 10918062

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

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

Yu08: Yu BJ, Kim JA, Moon JH, Ryu SE, Pan JG (2008). "The diversity of lysine-acetylated proteins in Escherichia coli." J Microbiol Biotechnol 18(9);1529-36. PMID: 18852508


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by SRI International Pathway Tools version 18.5 on Wed Nov 26, 2014, biocyc13.