DB code: D00294
| CATH domain | 2.40.50.140 : OB fold (Dihydrolipoamide Acetyltransferase, E2P) | |
|---|---|---|
| 3.30.930.10 : BirA Bifunctional Protein; domain 2 | Catalytic domain | |
| E.C. | 6.1.1.12 | |
| CSA | 1asy | |
| M-CSA | 1asy | |
| MACiE | ||
| CATH domain | Related DB codes (homologues) |
|---|---|
| 2.40.50.140 : OB fold (Dihydrolipoamide Acetyltransferase, E2P) | M00220 M00186 T00050 D00291 T00254 |
| 3.30.930.10 : BirA Bifunctional Protein; domain 2 | S00413 D00291 D00293 D00295 M00049 T00113 |
| Uniprot Enzyme Name | UniprotKB | Protein name | Synonyms | RefSeq | Pfam |
|---|---|---|---|---|
| P04802 |
Aspartyl-tRNA synthetase, cytoplasmic
|
EC
6.1.1.12
Aspartate--tRNA ligase AspRS |
NP_013083.1
(Protein)
NM_001181838.1 (DNA/RNA sequence) |
PF00152
(tRNA-synt_2)
PF01336 (tRNA_anti) [Graphical View] |
| Q52428 |
Aspartyl-tRNA synthetase
|
EC
6.1.1.12
Aspartate--tRNA ligase AspRS |
YP_182905.1
(Protein)
NC_006624.1 (DNA/RNA sequence) |
PF00152
(tRNA-synt_2)
PF01336 (tRNA_anti) [Graphical View] |
| KEGG enzyme name |
|---|
|
aspartate---tRNA ligase
aspartyl-tRNA synthetase aspartyl ribonucleic synthetase aspartyl-transfer RNA synthetase aspartic acid translase aspartyl-transfer ribonucleic acid synthetase aspartyl ribonucleate synthetase |
| UniprotKB: Accession Number | Entry name | Activity | Subunit | Subcellular location | Cofactor |
|---|---|---|---|---|---|
| P04802 | SYDC_YEAST | ATP + L-aspartate + tRNA(Asp) = AMP + diphosphate + L-aspartyl-tRNA(Asp). | Homodimer. | Cytoplasm. | |
| Q52428 | SYD_PYRKO | ATP + L-aspartate + tRNA(Asp) = AMP + diphosphate + L-aspartyl-tRNA(Asp). | Homodimer. | Cytoplasm. | Binds 3 magnesium ions per subunit. The first one is coordinated by ATP and H(2)O. |
| KEGG Pathways | Map code | Pathways | E.C. |
|---|---|---|
| MAP00252 | Alanine and aspartate metabolism | |
| MAP00970 | Aminoacyl-tRNA biosynthesis |
| Compound table | |||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Cofactors | Substrates | Products | Intermediates | ||||||||||||
| KEGG-id | C00305 | C00002 | C00049 | C01637 | C01638 | C00020 | C00013 | C06113 | C02984 | ||||||
| E.C. | |||||||||||||||
| Compound | Magnesium | ATP | L-Aspartate | tRNA(Asn) | tRNA(Asp) | AMP | Pyrophosphate | L-Aspartyl-tRNA(Asn) | L-Aspartyl-tRNA(Asp) | Aspartyl-adenylate | |||||
| Type | divalent metal (Ca2+, Mg2+) | amine group,nucleotide | amino acids,carboxyl group | nucleic acids | nucleic acids | amine group,nucleotide | phosphate group/phosphate ion | amino acids,carboxyl group,nucleic acids | amino acids,carboxyl group,nucleic acids | ||||||
| ChEBI |
18420 18420 |
15422 15422 |
17053 17053 |
16027 16027 |
29888 29888 |
||||||||||
| PubChem |
888 888 |
5957 5957 |
44367445 5960 44367445 5960 |
6083 6083 |
1023 21961011 1023 21961011 |
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| 1asyA01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1asyB01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1aszA01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1aszB01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1eovA01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1b8aA01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1b8aB01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1asyA02 |
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Unbound | Unbound | Unbound | Unbound | Bound:__A_676 (chain R) | Unbound | Unbound | Unbound | Unbound | |
| 1asyB02 |
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Unbound | Unbound | Unbound | Unbound | Bound:__A_676 (chain S) | Unbound | Unbound | Unbound | Unbound | |
| 1aszA02 |
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Unbound | Bound:ATP | Unbound | Unbound | Bound:__A_676 (chain R) | Unbound | Unbound | Unbound | Unbound | |
| 1aszB02 |
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Unbound | Bound:ATP | Unbound | Unbound | Bound:__A_676 (chain S) | Unbound | Unbound | Unbound | Unbound | |
| 1eovA02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1b8aA02 |
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Analogue:3x_MN | Bound:ATP | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1b8aB02 |
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Analogue:3x_MN | Bound:ATP | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| Reference for Active-site residues | ||
|---|---|---|
| resource | references | E.C. |
| Swiss-prot;P04802, Q52428 & literature [14] | ||
| Active-site residues | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| PDB | Catalytic residues | Cofactor-binding residues | Modified residues | Main-chain involved in catalysis | Comment | |||||
| 1asyA01 |
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| 1asyB01 |
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| 1aszA01 |
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| 1aszB01 |
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| 1eovA01 |
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| 1b8aA01 |
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| 1b8aB01 |
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| 1asyA02 |
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ARG 325;ASP 342;ARG 531 | GLU 478;SER 481(Magnesium binding) | |||
| 1asyB02 |
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ARG 325;ASP 342;ARG 531 | GLU 478;SER 481(Magnesium binding) | |||
| 1aszA02 |
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ARG 325;ASP 342;ARG 531 | GLU 478;SER 481(Magnesium binding) | |||
| 1aszB02 |
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ARG 325;ASP 342;ARG 531 | GLU 478;SER 481(Magnesium binding) | |||
| 1eovA02 |
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ARG 325;ASP 342;ARG 531 | GLU 478;SER 481(Magnesium binding) | |||
| 1b8aA02 |
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ARG 214;ASP 231;ARG 412 | GLU 361;SER 364(Magnesium binding) | |||
| 1b8aB02 |
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ARG 1214;ASP 1231;ARG 1412 | GLU 1361;SER 1364(Magnesium binding) | |||
| References for Catalytic Mechanism | ||
|---|---|---|
| References | Sections | No. of steps in catalysis |
|
[11]
|
p.1121 | |
|
[14]
|
Fig.5, p.335-336 | |
|
[18]
|
p.5234-5235 | |
| References | |
|---|---|
| [1] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 6997491 |
| Journal | J Mol Biol |
| Year | 1980 |
| Volume | 138 |
| Pages | 129-35 |
| Authors | Dietrich A, Giege R, Comarmond MB, Thierry JC, Moras D |
| Title |
Crystallographic studies on the aspartyl-tRNA synthetase-tRNAAsp system from yeast. |
| Related PDB | |
| Related UniProtKB | |
| [2] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 7049254 |
| Journal | Biochimie |
| Year | 1982 |
| Volume | 64 |
| Pages | 357-62 |
| Authors | Giege R, Lorber B, Ebel JP, Moras D, Thierry JC, Jacrot B, Zaccai G |
| Title | Formation of a catalytically active complex between tRNAAsp and aspartyl-tRNA synthetase from yeast in high concentrations of ammonium sulphate. |
| Related PDB | |
| Related UniProtKB | |
| [3] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 6345542 |
| Journal | J Biol Chem |
| Year | 1983 |
| Volume | 258 |
| Pages | 8429-35 |
| Authors | Lorber B, Giege R, Ebel JP, Berthet C, Thierry JC, Moras D |
| Title |
Crystallization of a tRNA . |
| Related PDB | |
| Related UniProtKB | |
| [4] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 3078234 |
| Journal | J Biomol Struct Dyn |
| Year | 1987 |
| Volume | 5 |
| Pages | 187-98 |
| Authors | Podjarny A, Rees B, Thierry JC, Cavarelli J, Jesior JC, Roth M, Lewitt-Bentley A, Kahn R, Lorber B, Ebel JP, et al |
| Title | Yeast tRNA(Asp)-aspartyl-tRNA synthetase complex: low resolution crystal structure. |
| Related PDB | |
| Related UniProtKB | |
| [5] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 3134944 |
| Journal | Biochimie |
| Year | 1988 |
| Volume | 70 |
| Pages | 205-13 |
| Authors | Theobald A, Kern D, Giege R |
| Title | Non-essential role of lysine residues for the catalytic activities of aspartyl-tRNA synthetase and comparison with other aminoacyl-tRNA synthetases. |
| Related PDB | |
| Related UniProtKB | |
| [6] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 3286258 |
| Journal | Eur J Biochem |
| Year | 1988 |
| Volume | 174 |
| Pages | 155-61 |
| Authors | Lorber B, Mejdoub H, Reinbolt J, Boulanger Y, Giege R |
| Title | Properties of N-terminal truncated yeast aspartyl-tRNA synthetase and structural characteristics of the cleaved domain. |
| Related PDB | |
| Related UniProtKB | |
| [7] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 3047397 |
| Journal | J Mol Biol |
| Year | 1988 |
| Volume | 201 |
| Pages | 235-6 |
| Authors | Ruff M, Cavarelli J, Mikol V, Lorber B, Mitschler A, Giege R, Thierry JC, Moras D |
| Title | A high resolution diffracting crystal form of the complex between yeast tRNAAsp and aspartyl-tRNA synthetase. |
| Related PDB | |
| Related UniProtKB | |
| [8] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 2047878 |
| Journal | Science |
| Year | 1991 |
| Volume | 252 |
| Pages | 1696-9 |
| Authors | Putz J, Puglisi JD, Florentz C, Giege R |
| Title | Identity elements for specific aminoacylation of yeast tRNA(Asp) by cognate aspartyl-tRNA synthetase. |
| Related PDB | |
| Related UniProtKB | |
| [9] | |
| Resource | |
| Comments | X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS). |
| Medline ID | 91262650 |
| PubMed ID | 2047877 |
| Journal | Science |
| Year | 1991 |
| Volume | 252 |
| Pages | 1682-9 |
| Authors | Ruff M, Krishnaswamy S, Boeglin M, Poterszman A, Mitschler A, Podjarny A, Rees B, Thierry JC, Moras D |
| Title | Class II aminoacyl transfer RNA synthetases: crystal structure of yeast aspartyl-tRNA synthetase complexed with tRNA(Asp). |
| Related PDB | 1asy |
| Related UniProtKB | P04802 |
| [10] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 1445684 |
| Journal | Acta Crystallogr A |
| Year | 1992 |
| Volume | 48 |
| Pages | 756-64 |
| Authors | Cura V, Krishnaswamy S, Podjarny AD |
| Title | Heavy-atom refinement against solvent-flattened phases. |
| Related PDB | |
| Related UniProtKB | |
| [11] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 8199247 |
| Journal | Biochimie |
| Year | 1993 |
| Volume | 75 |
| Pages | 1117-23 |
| Authors | Cavarelli J, Rees B, Thierry JC, Moras D |
| Title | Yeast aspartyl-tRNA synthetase: a structural view of the aminoacylation reaction. |
| Related PDB | |
| Related UniProtKB | |
| [12] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 8450889 |
| Journal | Nature |
| Year | 1993 |
| Volume | 362 |
| Pages | 181-4 |
| Authors | Cavarelli J, Rees B, Ruff M, Thierry JC, Moras D |
| Title | Yeast tRNA(Asp) recognition by its cognate class II aminoacyl-tRNA synthetase. |
| Related PDB | |
| Related UniProtKB | |
| [13] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 8248175 |
| Journal | Proc Natl Acad Sci U S A |
| Year | 1993 |
| Volume | 90 |
| Pages | 10816-20 |
| Authors | Eriani G, Cavarelli J, Martin F, Dirheimer G, Moras D, Gangloff J |
| Title | Role of dimerization in yeast aspartyl-tRNA synthetase and importance of the class II invariant proline. |
| Related PDB | |
| Related UniProtKB | |
| [14] | |
| Resource | |
| Comments |
X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS), |
| Medline ID | 94147977 |
| PubMed ID | 8313877 |
| Journal | EMBO J |
| Year | 1994 |
| Volume | 13 |
| Pages | 327-37 |
| Authors | Cavarelli J, Eriani G, Rees B, Ruff M, Boeglin M, Mitschler A, Martin F, Gangloff J, Thierry JC, Moras D |
| Title | The active site of yeast aspartyl-tRNA synthetase: structural and functional aspects of the aminoacylation reaction. |
| Related PDB | 1asz |
| Related UniProtKB | P04802 |
| [15] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 7819251 |
| Journal | Biochemistry |
| Year | 1995 |
| Volume | 34 |
| Pages | 569-76 |
| Authors | Agou F, Yang Y, Gesquiere JC, Waller JP, Guittet E |
| Title | Polyanion-induced alpha-helical structure of a synthetic 23-residue peptide representing the lysine-rich segment of the N-terminal extension of yeast cytoplasmic aspartyl-tRNA synthetase. |
| Related PDB | |
| Related UniProtKB | |
| [16] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 8955905 |
| Journal | Biochimie |
| Year | 1996 |
| Volume | 78 |
| Pages | 624-31 |
| Authors | Rees B, Cavarelli J, Moras D |
| Title | Conformational flexibility of tRNA: structural changes in yeast tRNA(Asp) upon binding to aspartyl-tRNA synthetase. |
| Related PDB | |
| Related UniProtKB | |
| [17] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 9396794 |
| Journal | Nucleic Acids Res |
| Year | 1997 |
| Volume | 25 |
| Pages | 4899-906 |
| Authors | Sissler M, Eriani G, Martin F, Giege R, Florentz C |
| Title | Mirror image alternative interaction patterns of the same tRNA with either class I arginyl-tRNA synthetase or class II aspartyl-tRNA synthetase. |
| Related PDB | |
| Related UniProtKB | |
| [18] | |
| Resource | |
| Comments | X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS). |
| Medline ID | 98393563 |
| PubMed ID | 9724658 |
| Journal | EMBO J |
| Year | 1998 |
| Volume | 17 |
| Pages | 5227-37 |
| Authors | Schmitt E, Moulinier L, Fujiwara S, Imanaka T, Thierry JC, Moras D |
| Title | Crystal structure of aspartyl-tRNA synthetase from Pyrococcus kodakaraensis KOD: archaeon specificity and catalytic mechanism of adenylate formation. |
| Related PDB | 1b8a |
| Related UniProtKB | Q52428 |
| [19] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 10089405 |
| Journal | Acta Crystallogr D Biol Crystallogr |
| Year | 1999 |
| Volume | 55 |
| Pages | 149-56 |
| Authors | Sauter C, Lorber B, Kern D, Cavarelli J, Moras D, Giege R |
| Title | Crystallogenesis studies on yeast aspartyl-tRNA synthetase: use of phase diagram to improve crystal quality. |
| Related PDB | |
| Related UniProtKB | |
| [20] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 10508395 |
| Journal | Biochemistry |
| Year | 1999 |
| Volume | 38 |
| Pages | 11926-32 |
| Authors | Wolfson AD, Khvorova AM, Sauter C, Florentz C, Giege R |
| Title | Mimics of yeast tRNAAsp and their recognition by aspartyl-tRNA synthetase. |
| Related PDB | |
| Related UniProtKB | |
| [21] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 10452887 |
| Journal | J Mol Biol |
| Year | 1999 |
| Volume | 291 |
| Pages | 761-73 |
| Authors | Eriani G, Gangloff J |
| Title | Yeast aspartyl-tRNA synthetase residues interacting with tRNA(Asp) identity bases connectively contribute to tRNA(Asp) binding in the ground and transition-state complex and discriminate against non-cognate tRNAs. |
| Related PDB | |
| Related UniProtKB | |
| [22] | |
| Resource | |
| Comments | X-ray crystallography |
| Medline ID | |
| PubMed ID | 10873455 |
| Journal | J Mol Biol |
| Year | 2000 |
| Volume | 299 |
| Pages | 1313-24 |
| Authors | Sauter C, Lorber B, Cavarelli J, Moras D, Giege R |
| Title |
The free yeast aspartyl-tRNA synthetase differs from the tRNA(Asp)-complexed enzyme by structural changes in the catalytic site, |
| Related PDB | 1eov |
| Related UniProtKB | |
| [23] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 11686711 |
| Journal | J Am Chem Soc |
| Year | 2001 |
| Volume | 123 |
| Pages | 11047-56 |
| Authors | Archontis G, Simonson T |
| Title | Dielectric relaxation in an enzyme active site: molecular dynamics simulations interpreted with a macroscopic continuum model. |
| Related PDB | |
| Related UniProtKB | |
| [24] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 12660169 |
| Journal | EMBO J |
| Year | 2003 |
| Volume | 22 |
| Pages | 1632-43 |
| Authors | Charron C, Roy H, Blaise M, Giege R, Kern D |
| Title | Non-discriminating and discriminating aspartyl-tRNA synthetases differ in the anticodon-binding domain. |
| Related PDB | |
| Related UniProtKB | |
| [25] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 12486031 |
| Journal | J Biol Chem |
| Year | 2003 |
| Volume | 278 |
| Pages | 9683-90 |
| Authors | Ryckelynck M, Giege R, Frugier M |
| Title | Yeast tRNA(Asp) charging accuracy is threatened by the N-terminal extension of aspartyl-tRNA synthetase. |
| Related PDB | |
| Related UniProtKB | |
| [26] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 12730374 |
| Journal | Proc Natl Acad Sci U S A |
| Year | 2003 |
| Volume | 100 |
| Pages | 5676-81 |
| Authors | Feng L, Tumbula-Hansen D, Toogood H, Soll D |
| Title | Expanding tRNA recognition of a tRNA synthetase by a single amino acid change. |
| Related PDB | |
| Related UniProtKB | |
| [27] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 15170340 |
| Journal | Biochemistry |
| Year | 2004 |
| Volume | 43 |
| Pages | 7028-37 |
| Authors | Ador L, Jaeger S, Geslain R, Martin F, Cavarelli J, Eriani G |
| Title | Mutation and evolution of the magnesium-binding site of a class II aminoacyl-tRNA synthetase. |
| Related PDB | |
| Related UniProtKB | |
| Comments |
|---|
|
This enzyme is class IIb aminoacyl-tRNA synthetases.
This enzyme catalyzes the following reactions (see [14]): (A) Transfer of adenylate from ATP to carboxyl oxygen of Aspartate, (B) Transfer of acyl group from the intermediate to the 3'-end of tRNA: |
| Created | Updated |
|---|---|
| 2004-08-31 | 2009-02-26 |