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CATH domain | Related DB codes (homologues) |
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1.10.730.10 : Isoleucyl-tRNA Synthetase; Domain 1 | M00177 | 3.40.50.620 : Rossmann fold | S00314,S00549,S00316,S00317,S00318,S00315,T00085,T00249,D00300,M00177,M00178,T00114 |
KEGG pathways | MAP code | Pathways |
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MAP00330 | Arginine and proline metabolism | MAP00970 | Aminoacyl-tRNA biosynthesis |
UniProtKB:Accession Number | Q05506 | Q93RP5 |
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Entry name | SYRC_YEAST | Q93RP5_THETH |
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Activity | ATP + L-arginine + tRNA(Arg) = AMP + diphosphate + L-arginyl-tRNA(Arg). | ATP + L-arginine + tRNA(Arg) = AMP + diphosphate + L-arginyl-tRNA(Arg). |
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Subunit | Monomer. |
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Subcellular location | Cytoplasm. | Cytoplasm. |
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Cofactor |
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Compound table: links to PDB-related databases & PoSSuM |
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| Cofactors | Substrates | Products |
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KEGG-id | C00305 | C00002 | C00062 | C01636 | C00020 | C00013 | C02163 |
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Compound | Magnesium | ATP | L-Arginine | tRNA(Arg) | AMP | Pyrophosphate | L-Arginyl-tRNA(Arg) |
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Type | divalent metal (Ca2+, Mg2+) | amine group,nucleotide | amino acids,amine group,imine group,lipid | nucleic acids | amine group,nucleotide | phosphate group/phosphate ion | amino acids,amine group,imine group,lipid,nucleic acids |
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ChEBI | 18420
| 15422
| 16467
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| 16027
| 29888
|
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PubChem | 888
| 5957
| 6322 28782
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| 6083
| 21961011 1023
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| | | | | | | | | | | | | | |
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1bs2A01 |  |  |  |  |  |  |  | Unbound | Unbound | Bound:ARG | Unbound | Unbound | Unbound | Unbound |
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1f7uA01 |  |  |  |  |  |  |  | Unbound | Unbound | Bound:ARG | Bound:__G-__C-__C-__A 976(chain B) | Unbound | Unbound | Unbound |
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1f7vA01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Analogue:__G 973(chain B) | Unbound | Unbound | Unbound |
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1iq0A01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound |
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1bs2A02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound |
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1f7uA02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound |
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1f7vA02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound |
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1iq0A03 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound |
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1bs2A03 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound |
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1f7uA03 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound |
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1f7vA03 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound |
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1iq0A02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound |
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References for Catalytic Mechanism | References | Sections | No. of steps in catalysis |
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[11] | p.5443-5445 |
| [13] | p.5606, p.5608-5609 |
| [17] | p.3724-3725 |
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references | [1] |
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PubMed ID | 1253985 |
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Journal | FEBS Lett |
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Year | 1976 |
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Volume | 62 |
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Pages | 190-3 |
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Authors | Godeau JM |
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Title | Arginyl-tRNA synthetase from Bacillus stearothermophilus: subunit structure of enzyme. |
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[2] |
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PubMed ID | 679950 |
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Journal | Eur J Biochem |
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Year | 1978 |
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Volume | 87 |
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Pages | 583-90 |
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Authors | Carias JR, Mouricout M, Quintard B, Thomes JC, Julien R |
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Title | Leucyl-tRNA and arginyl-tRNA synthetases of wheat germ: inactivation and ribosome effects. |
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[3] |
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PubMed ID | 220092 |
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Journal | FEBS Lett |
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Year | 1979 |
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Volume | 99 |
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Pages | 25-8 |
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Authors | Gerlo E, Charlier J |
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Title | Irreversible inactivation of arginyl-tRNA ligase by periodate-oxidized tRNA. |
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[4] |
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PubMed ID | 6273159 |
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Journal | Eur J Biochem |
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Year | 1981 |
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Volume | 119 |
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Pages | 477-82 |
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Authors | Freist W, Sternbach H, Cramer F |
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Title | Arginyl-tRNA synthetase from Baker's yeast. Order of substrate addition and action of ATP analogs in the aminoacylation reaction; influence of pyrophosphate on the catalytic mechanism. |
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[5] |
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PubMed ID | 7042510 |
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Journal | Hoppe Seylers Z Physiol Chem |
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Year | 1982 |
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Volume | 363 |
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Pages | 365-73 |
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Authors | Gerlo E, Freist W, Charlier J |
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Title | Arginyl-tRNA synthetase from Escherichia coli K12: specificity with regard to ATP analogs and their magnesium complexes. |
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[6] |
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PubMed ID | 1953742 |
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Journal | Biochem Biophys Res Commun |
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Year | 1991 |
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Volume | 180 |
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Pages | 702-8 |
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Authors | Huang S, Deutscher MP |
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Title | The NH2-terminal extension of rat liver arginyl-tRNA synthetase is responsible for its hydrophobic properties. |
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[7] |
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PubMed ID | 8224869 |
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Journal | Gene |
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Year | 1993 |
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Volume | 132 |
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Pages | 237-45 |
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Authors | Lazard M, Mirande M |
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Title | Cloning and analysis of a cDNA encoding mammalian arginyl-tRNA synthetase, a component of the multisynthetase complex with a hydrophobic N-terminal extension. |
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[8] |
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PubMed ID | 9396794 |
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Journal | Nucleic Acids Res |
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Year | 1997 |
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Volume | 25 |
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Pages | 4899-906 |
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Authors | Sissler M, Eriani G, Martin F, Giege R, Florentz C |
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Title | Mirror image alternative interaction patterns of the same tRNA with either class I arginyl-tRNA synthetase or class II aspartyl-tRNA synthetase. |
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[9] |
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PubMed ID | 9416614 |
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Journal | Protein Sci |
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Year | 1997 |
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Volume | 6 |
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Pages | 2636-8 |
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Authors | Zhou M, Wang ED, Campbell RL, Wang YL, Lin SX |
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Title | Crystallization and preliminary X-ray diffraction analysis of arginyl-tRNA synthetase from Escherichia coli. |
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[10] |
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PubMed ID | 9748544 |
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Journal | Biochim Biophys Acta |
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Year | 1998 |
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Volume | 1387 |
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Pages | 136-42 |
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Authors | Zhang QS, Wang ED, Wang YL |
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Title | The role of tryptophan residues in Escherichia coli arginyl-tRNA synthetase. |
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[11] |
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Comments | X-RAY CRYSTALLOGRAPHY (2.75 ANGSTROMS) |
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Medline ID | 98409547 |
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PubMed ID | 9736621 |
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Journal | EMBO J |
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Year | 1998 |
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Volume | 17 |
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Pages | 5438-48 |
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Authors | Cavarelli J, Delagoutte B, Eriani G, Gangloff J, Moras D |
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Title | L-arginine recognition by yeast arginyl-tRNA synthetase. |
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Related PDB | 1bs2 |
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Related UniProtKB | Q05506 |
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[12] |
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PubMed ID | 10333292 |
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Journal | J Protein Chem |
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Year | 1999 |
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Volume | 18 |
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Pages | 187-92 |
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Authors | Zhang QS, Shen L, Wang ED, Wang YL |
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Title | Biosynthesis and characterization of 4-fluorotryptophan-labeled Escherichia coli arginyl-tRNA synthetase. |
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[13] |
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Comments | X-ray crystallography |
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PubMed ID | 11060012 |
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Journal | EMBO J |
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Year | 2000 |
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Volume | 19 |
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Pages | 5599-610 |
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Authors | Delagoutte B, Moras D, Cavarelli J |
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Title | tRNA aminoacylation by arginyl-tRNA synthetase: induced conformations during substrates binding. |
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Related PDB | 1f7u,1f7v |
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[14] |
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PubMed ID | 10993737 |
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Journal | J Mol Biol |
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Year | 2000 |
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Volume | 302 |
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Pages | 991-1004 |
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Authors | Lazard M, Agou F, Kerjan P, Mirande M |
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Title | The tRNA-dependent activation of arginine by arginyl-tRNA synthetase requires inter-domain communication. |
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[15] |
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PubMed ID | 10744027 |
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Journal | RNA |
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Year | 2000 |
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Volume | 6 |
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Pages | 434-48 |
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Authors | Geslain R, Martin F, Delagoutte B, Cavarelli J, Gangloff J, Eriani G |
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Title | In vivo selection of lethal mutations reveals two functional domains in arginyl-tRNA synthetase. |
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[16] |
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PubMed ID | 11733016 |
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Journal | Eur J Biochem |
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Year | 2001 |
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Volume | 268 |
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Pages | 6207-13 |
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Authors | Kiga D, Sakamoto K, Sato S, Hirao I, Yokoyama S |
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Title | Shifted positioning of the anticodon nucleotide residues of amber suppressor tRNA species by Escherichia coli arginyl-tRNA synthetase. |
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[17] |
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PubMed ID | 11106639 |
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Journal | J Biol Chem |
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Year | 2001 |
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Volume | 276 |
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Pages | 3723-6 |
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Authors | Sekine S, Shimada A, Nureki O, Cavarelli J, Moras D, Vassylyev DG, Yokoyama S |
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Title | Crucial role of the high-loop lysine for the catalytic activity of arginyl-tRNA synthetase. |
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[18] |
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PubMed ID | 11717415 |
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Journal | Proc Natl Acad Sci U S A |
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Year | 2001 |
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Volume | 98 |
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Pages | 13473-5 |
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Authors | Hendrickson TL |
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Title | Recognizing the D-loop of transfer RNAs. |
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[19] |
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PubMed ID | 11698642 |
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Journal | Proc Natl Acad Sci U S A |
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Year | 2001 |
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Volume | 98 |
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Pages | 13537-42 |
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Authors | Shimada A, Nureki O, Goto M, Takahashi S, Yokoyama S |
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Title | Structural and mutational studies of the recognition of the arginine tRNA-specific major identity element, A20, by arginyl-tRNA synthetase. |
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Related PDB | 1iq0,1ir4 |
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[20] |
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PubMed ID | 14690419 |
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Journal | Biochemistry |
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Year | 2003 |
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Volume | 42 |
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Pages | 15092-101 |
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Authors | Geslain R, Bey G, Cavarelli J, Eriani G |
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Title | Limited set of amino acid residues in a class Ia aminoacyl-tRNA synthetase is crucial for tRNA binding. |
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[21] |
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PubMed ID | 12860413 |
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Journal | FEBS Lett |
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Year | 2003 |
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Volume | 547 |
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Pages | 197-200 |
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Authors | Yao YN, Zhang QS, Yan XZ, Zhu G, Wang ED |
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Title | Substrate-induced conformational changes in Escherichia coli arginyl-tRNA synthetase observed by 19F NMR spectroscopy. |
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[22] |
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PubMed ID | 14672708 |
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Journal | Biochem Biophys Res Commun |
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Year | 2004 |
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Volume | 313 |
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Pages | 129-34 |
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Authors | Yao YN, Zhang QS, Yan XZ, Zhu G, Wang ED |
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Title | Escherichia coli tRNA(4)(Arg)(UCU) induces a constrained conformation of the crucial Omega-loop of arginyl-tRNA synthetase. |
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comments | This enzyme belongs to class-I aminoacyl-tRNA synthetase family. Although the tertiary structures with magnesium ions have not been determined yet, Mg2+ ions are required for the first step of catalysis, according to the paper [13]. According to the literature [11] and [13], this enzyme catalyzes two successive transfer reactions. (A) Transfer of the adenylate from ATP (the first substrate) to the carboxylate of the second substrate, arginine: This reaction results in the formation of arginyl-adenylate (intermediate) and the release of the inorganic pyrophosphate. (B) Transfer of the acyl group from the intermediate to the 2'-OH of tRNA(Arg). The detailed catalytic mechanism has not been elucidated yet, though.
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created | updated |
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2004-09-14 | 2012-06-25 |
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