EzCatDB: D00294

DB codeD00294
CATH domainDomain 12.40.50.140
Domain 23.30.930.10Catalytic domain
E.C.6.1.1.12
CSA1asy

CATH domainRelated DB codes (homologues)
2.40.50.140M00220,M00186,T00050,D00291,T00254
3.30.930.10S00413,D00291,D00293,D00295,M00049,T00113

Enzyme Name
Swiss-protKEGG

P04802Q52428
Protein nameAspartyl-tRNA synthetase, cytoplasmicAspartyl-tRNA synthetaseaspartate---tRNA ligase
aspartyl-tRNA synthetase
aspartyl ribonucleic synthetase
aspartyl-transfer RNA synthetase
aspartic acid translase
aspartyl-transfer ribonucleic acid synthetase
aspartyl ribonucleate synthetase
SynonymsEC 6.1.1.12
Aspartate--tRNA ligase
AspRS
EC 6.1.1.12
Aspartate--tRNA ligase
AspRS

KEGG pathways
MAP codePathways
MAP00252Alanine and aspartate metabolism
MAP00970Aminoacyl-tRNA biosynthesis

Swiss-prot:Accession NumberP04802Q52428
Entry nameSYDC_YEASTSYD_PYRKO
ActivityATP + L-aspartate + tRNA(Asp) = AMP + diphosphate + L-aspartyl-tRNA(Asp).ATP + L-aspartate + tRNA(Asp) = AMP + diphosphate + L-aspartyl-tRNA(Asp).
SubunitHomodimer.Homodimer.
Subcellular locationCytoplasm.Cytoplasm.
Cofactor
Binds 3 magnesium ions per subunit. The first one is coordinated by ATP and H(2)O.


CofactorsSubstratesProductsintermediates
KEGG-idC00305C00002C00049C01637C01638C00020C00013C06113C02984
CompoundMagnesiumATPL-AspartatetRNA(Asn)tRNA(Asp)AMPPyrophosphateL-Aspartyl-tRNA(Asn)L-Aspartyl-tRNA(Asp)Aspartyl-adenylate
Typedivalent metal (Ca2+, Mg2+)amine group,nucleotideamino acids,carboxyl groupnucleic acidsnucleic acidsamine group,nucleotidephosphate group/phosphate ionamino acids,carboxyl group,nucleic acidsamino acids,carboxyl group,nucleic acids
1asyA01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1asyB01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1aszA01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1aszB01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1eovA01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1b8aA01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1b8aB01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1asyA02UnboundUnboundUnboundUnboundBound:__A 676(chain R)UnboundUnboundUnboundUnbound
1asyB02UnboundUnboundUnboundUnboundBound:__A 676(chain S)UnboundUnboundUnboundUnbound
1aszA02UnboundBound:ATPUnboundUnboundBound:__A 676(chain R)UnboundUnboundUnboundUnbound
1aszB02UnboundBound:ATPUnboundUnboundBound:__A 676(chain S)UnboundUnboundUnboundUnbound
1eovA02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1b8aA02Analogue:3x_MNBound:ATPUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1b8aB02Analogue:3x_MNBound:ATPUnboundUnboundUnboundUnboundUnboundUnboundUnbound

Active-site residues
resource
Swiss-prot;P04802, Q52428 & literature [14]
pdbCatalytic residuesCofactor-binding residues
1asyA01                       

1asyB01                       

1aszA01                       

1aszB01                       

1eovA01                       

1b8aA01                       

1b8aB01                       

1asyA02ARG  325;ASP  342;ARG  531
GLU  478;SER  481(Magnesium binding)
1asyB02ARG  325;ASP  342;ARG  531
GLU  478;SER  481(Magnesium binding)
1aszA02ARG  325;ASP  342;ARG  531
GLU  478;SER  481(Magnesium binding)
1aszB02ARG  325;ASP  342;ARG  531
GLU  478;SER  481(Magnesium binding)
1eovA02ARG  325;ASP  342;ARG  531
GLU  478;SER  481(Magnesium binding)
1b8aA02ARG  214;ASP  231;ARG  412
GLU  361;SER  364(Magnesium binding)
1b8aB02ARG 1214;ASP 1231;ARG 1412
GLU 1361;SER 1364(Magnesium binding)

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[11]p.1121
[14]Fig.5, p.335-336
[18]p.5234-5235

references
[1]
PubMed ID6997491
JournalJ Mol Biol
Year1980
Volume138
Pages129-35
AuthorsDietrich A, Giege R, Comarmond MB, Thierry JC, Moras D
TitleCrystallographic studies on the aspartyl-tRNA synthetase-tRNAAsp system from yeast. The crystalline aminoacyl-tRNA synthetase.
[2]
PubMed ID7049254
JournalBiochimie
Year1982
Volume64
Pages357-62
AuthorsGiege R, Lorber B, Ebel JP, Moras D, Thierry JC, Jacrot B, Zaccai G
TitleFormation of a catalytically active complex between tRNAAsp and aspartyl-tRNA synthetase from yeast in high concentrations of ammonium sulphate.
[3]
PubMed ID6345542
JournalJ Biol Chem
Year1983
Volume258
Pages8429-35
AuthorsLorber B, Giege R, Ebel JP, Berthet C, Thierry JC, Moras D
TitleCrystallization of a tRNA . aminoacyl-tRNA synthetase complex. Characterization and first crystallographic data.
[4]
PubMed ID3078234
JournalJ Biomol Struct Dyn
Year1987
Volume5
Pages187-98
AuthorsPodjarny A, Rees B, Thierry JC, Cavarelli J, Jesior JC, Roth M, Lewitt-Bentley A, Kahn R, Lorber B, Ebel JP, et al
TitleYeast tRNA(Asp)-aspartyl-tRNA synthetase complex: low resolution crystal structure.
[5]
PubMed ID3134944
JournalBiochimie
Year1988
Volume70
Pages205-13
AuthorsTheobald A, Kern D, Giege R
TitleNon-essential role of lysine residues for the catalytic activities of aspartyl-tRNA synthetase and comparison with other aminoacyl-tRNA synthetases.
[6]
PubMed ID3286258
JournalEur J Biochem
Year1988
Volume174
Pages155-61
AuthorsLorber B, Mejdoub H, Reinbolt J, Boulanger Y, Giege R
TitleProperties of N-terminal truncated yeast aspartyl-tRNA synthetase and structural characteristics of the cleaved domain.
[7]
PubMed ID3047397
JournalJ Mol Biol
Year1988
Volume201
Pages235-6
AuthorsRuff M, Cavarelli J, Mikol V, Lorber B, Mitschler A, Giege R, Thierry JC, Moras D
TitleA high resolution diffracting crystal form of the complex between yeast tRNAAsp and aspartyl-tRNA synthetase.
[8]
PubMed ID2047878
JournalScience
Year1991
Volume252
Pages1696-9
AuthorsPutz J, Puglisi JD, Florentz C, Giege R
TitleIdentity elements for specific aminoacylation of yeast tRNA(Asp) by cognate aspartyl-tRNA synthetase.
[9]
CommentsX-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS).
Medline ID91262650
PubMed ID2047877
JournalScience
Year1991
Volume252
Pages1682-9
AuthorsRuff M, Krishnaswamy S, Boeglin M, Poterszman A, Mitschler A, Podjarny A, Rees B, Thierry JC, Moras D
TitleClass II aminoacyl transfer RNA synthetases: crystal structure of yeast aspartyl-tRNA synthetase complexed with tRNA(Asp).
Related PDB1asy
Related Swiss-protP04802
[10]
PubMed ID1445684
JournalActa Crystallogr A
Year1992
Volume48
Pages756-64
AuthorsCura V, Krishnaswamy S, Podjarny AD
TitleHeavy-atom refinement against solvent-flattened phases.
[11]
PubMed ID8199247
JournalBiochimie
Year1993
Volume75
Pages1117-23
AuthorsCavarelli J, Rees B, Thierry JC, Moras D
TitleYeast aspartyl-tRNA synthetase: a structural view of the aminoacylation reaction.
[12]
PubMed ID8450889
JournalNature
Year1993
Volume362
Pages181-4
AuthorsCavarelli J, Rees B, Ruff M, Thierry JC, Moras D
TitleYeast tRNA(Asp) recognition by its cognate class II aminoacyl-tRNA synthetase.
[13]
PubMed ID8248175
JournalProc Natl Acad Sci U S A
Year1993
Volume90
Pages10816-20
AuthorsEriani G, Cavarelli J, Martin F, Dirheimer G, Moras D, Gangloff J
TitleRole of dimerization in yeast aspartyl-tRNA synthetase and importance of the class II invariant proline.
[14]
CommentsX-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS), AND MUTAGENESIS.
Medline ID94147977
PubMed ID8313877
JournalEMBO J
Year1994
Volume13
Pages327-37
AuthorsCavarelli J, Eriani G, Rees B, Ruff M, Boeglin M, Mitschler A, Martin F, Gangloff J, Thierry JC, Moras D
TitleThe active site of yeast aspartyl-tRNA synthetase: structural and functional aspects of the aminoacylation reaction.
Related PDB1asz
Related Swiss-protP04802
[15]
PubMed ID7819251
JournalBiochemistry
Year1995
Volume34
Pages569-76
AuthorsAgou F, Yang Y, Gesquiere JC, Waller JP, Guittet E
TitlePolyanion-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.
[16]
PubMed ID8955905
JournalBiochimie
Year1996
Volume78
Pages624-31
AuthorsRees B, Cavarelli J, Moras D
TitleConformational flexibility of tRNA: structural changes in yeast tRNA(Asp) upon binding to aspartyl-tRNA synthetase.
[17]
PubMed ID9396794
JournalNucleic Acids Res
Year1997
Volume25
Pages4899-906
AuthorsSissler M, Eriani G, Martin F, Giege R, Florentz C
TitleMirror image alternative interaction patterns of the same tRNA with either class I arginyl-tRNA synthetase or class II aspartyl-tRNA synthetase.
[18]
CommentsX-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
Medline ID98393563
PubMed ID9724658
JournalEMBO J
Year1998
Volume17
Pages5227-37
AuthorsSchmitt E, Moulinier L, Fujiwara S, Imanaka T, Thierry JC, Moras D
TitleCrystal structure of aspartyl-tRNA synthetase from Pyrococcus kodakaraensis KOD: archaeon specificity and catalytic mechanism of adenylate formation.
Related PDB1b8a
Related Swiss-protQ52428
[19]
PubMed ID10089405
JournalActa Crystallogr D Biol Crystallogr
Year1999
Volume55
Pages149-56
AuthorsSauter C, Lorber B, Kern D, Cavarelli J, Moras D, Giege R
TitleCrystallogenesis studies on yeast aspartyl-tRNA synthetase: use of phase diagram to improve crystal quality.
[20]
PubMed ID10508395
JournalBiochemistry
Year1999
Volume38
Pages11926-32
AuthorsWolfson AD, Khvorova AM, Sauter C, Florentz C, Giege R
TitleMimics of yeast tRNAAsp and their recognition by aspartyl-tRNA synthetase.
[21]
PubMed ID10452887
JournalJ Mol Biol
Year1999
Volume291
Pages761-73
AuthorsEriani G, Gangloff J
TitleYeast 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.
[22]
CommentsX-ray crystallography
PubMed ID10873455
JournalJ Mol Biol
Year2000
Volume299
Pages1313-24
AuthorsSauter C, Lorber B, Cavarelli J, Moras D, Giege R
TitleThe 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 PDB1eov
[23]
PubMed ID11686711
JournalJ Am Chem Soc
Year2001
Volume123
Pages11047-56
AuthorsArchontis G, Simonson T
TitleDielectric relaxation in an enzyme active site: molecular dynamics simulations interpreted with a macroscopic continuum model.
[24]
PubMed ID12660169
JournalEMBO J
Year2003
Volume22
Pages1632-43
AuthorsCharron C, Roy H, Blaise M, Giege R, Kern D
TitleNon-discriminating and discriminating aspartyl-tRNA synthetases differ in the anticodon-binding domain.
[25]
PubMed ID12486031
JournalJ Biol Chem
Year2003
Volume278
Pages9683-90
AuthorsRyckelynck M, Giege R, Frugier M
TitleYeast tRNA(Asp) charging accuracy is threatened by the N-terminal extension of aspartyl-tRNA synthetase.
[26]
PubMed ID12730374
JournalProc Natl Acad Sci U S A
Year2003
Volume100
Pages5676-81
AuthorsFeng L, Tumbula-Hansen D, Toogood H, Soll D
TitleExpanding tRNA recognition of a tRNA synthetase by a single amino acid change.
[27]
PubMed ID15170340
JournalBiochemistry
Year2004
Volume43
Pages7028-37
AuthorsAdor L, Jaeger S, Geslain R, Martin F, Cavarelli J, Eriani G
TitleMutation and evolution of the magnesium-binding site of a class II aminoacyl-tRNA synthetase.

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:

createdupdated
2004-08-312009-02-26
Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2010)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)

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