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
15422
17053
16027
29888
PubChem 888
5957
44367445
5960
6083
1023
21961011
1asyA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1asyB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1aszA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1aszB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1eovA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1b8aA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1b8aB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1asyA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Bound:__A_676 (chain R) Unbound Unbound Unbound Unbound
1asyB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Bound:__A_676 (chain S) Unbound Unbound Unbound Unbound
1aszA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:ATP Unbound Unbound Bound:__A_676 (chain R) Unbound Unbound Unbound Unbound
1aszB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:ATP Unbound Unbound Bound:__A_676 (chain S) Unbound Unbound Unbound Unbound
1eovA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1b8aA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:3x_MN Bound:ATP Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1b8aB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain 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 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1asyB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1aszA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1aszB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1eovA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1b8aA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1b8aB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1asyA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 325;ASP 342;ARG 531 GLU 478;SER 481(Magnesium binding)
1asyB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 325;ASP 342;ARG 531 GLU 478;SER 481(Magnesium binding)
1aszA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 325;ASP 342;ARG 531 GLU 478;SER 481(Magnesium binding)
1aszB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 325;ASP 342;ARG 531 GLU 478;SER 481(Magnesium binding)
1eovA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 325;ASP 342;ARG 531 GLU 478;SER 481(Magnesium binding)
1b8aA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 214;ASP 231;ARG 412 GLU 361;SER 364(Magnesium binding)
1b8aB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain 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. The crystalline aminoacyl-tRNA synthetase.
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 . aminoacyl-tRNA synthetase complex. Characterization and first crystallographic data.
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), AND MUTAGENESIS.
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, hinge region, and anticodon-binding domain.
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, forming an aspartyl-adenylate intermediate:
(B) Transfer of acyl group from the intermediate to the 3'-end of tRNA:

Created Updated
2004-08-31 2009-02-26