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P04802

- SYDC_YEAST

UniProt

P04802 - SYDC_YEAST

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Protein

Aspartate--tRNA ligase, cytoplasmic

Gene

DPS1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

Catalytic activityi

ATP + L-aspartate + tRNA(Asp) = AMP + diphosphate + L-aspartyl-tRNA(Asp).

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei281 – 2811AspartateBy similarity
Binding sitei325 – 3251AspartateBy similarity
Binding sitei478 – 4781ATPBy similarity
Binding sitei481 – 4811AspartateBy similarity
Binding sitei485 – 4851AspartateBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi325 – 3273ATPBy similarity
Nucleotide bindingi333 – 3353ATPBy similarity
Nucleotide bindingi528 – 5314ATPBy similarity

GO - Molecular functioni

  1. aspartate-tRNA ligase activity Source: SGD
  2. ATP binding Source: UniProtKB-KW
  3. RNA binding Source: SGD

GO - Biological processi

  1. aspartyl-tRNA aminoacylation Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Aminoacyl-tRNA synthetase, Ligase

Keywords - Biological processi

Protein biosynthesis

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-32123-MONOMER.
SABIO-RKP04802.

Names & Taxonomyi

Protein namesi
Recommended name:
Aspartate--tRNA ligase, cytoplasmic (EC:6.1.1.12)
Alternative name(s):
Aspartyl-tRNA synthetase
Short name:
AspRS
Gene namesi
Name:DPS1
Synonyms:APS, APS1
Ordered Locus Names:YLL018C
ORF Names:L1295
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome XII

Organism-specific databases

SGDiS000003941. DPS1.

Subcellular locationi

GO - Cellular componenti

  1. cytoplasm Source: SGD
  2. nucleus Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi273 – 2731P → G: Loss of activity; important for dimerization. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed2 Publications
Chaini2 – 557556Aspartate--tRNA ligase, cytoplasmicPRO_0000111014Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylserine1 Publication
Modified residuei14 – 141Phosphoserine1 Publication
Modified residuei301 – 3011Phosphoserine3 Publications
Modified residuei502 – 5021Phosphoserine2 Publications
Modified residuei546 – 5461Phosphoserine1 Publication

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

MaxQBiP04802.
PaxDbiP04802.
PRIDEiP04802.

Expressioni

Gene expression databases

GenevestigatoriP04802.

Interactioni

Subunit structurei

Homodimer.

Protein-protein interaction databases

BioGridi31235. 56 interactions.
DIPiDIP-4093N.
IntActiP04802. 15 interactions.
MINTiMINT-510718.
STRINGi4932.YLL018C.

Structurei

Secondary structure

1
557
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi73 – 775
Helixi85 – 873
Helixi96 – 983
Turni101 – 1066
Beta strandi108 – 12013
Beta strandi122 – 13211
Beta strandi135 – 1428
Beta strandi145 – 1495
Helixi151 – 1577
Beta strandi165 – 17410
Beta strandi182 – 19817
Helixi208 – 2114
Helixi215 – 2206
Helixi228 – 2336
Helixi235 – 2384
Helixi242 – 26423
Beta strandi274 – 2785
Beta strandi280 – 2845
Beta strandi288 – 2914
Beta strandi294 – 2985
Helixi303 – 3119
Beta strandi316 – 3249
Beta strandi331 – 3333
Beta strandi336 – 34611
Helixi352 – 37221
Helixi374 – 38310
Beta strandi393 – 3953
Beta strandi398 – 4014
Helixi402 – 41110
Beta strandi418 – 4203
Helixi424 – 43714
Beta strandi441 – 4466
Helixi450 – 4523
Beta strandi461 – 4633
Beta strandi466 – 4749
Beta strandi477 – 4859
Helixi489 – 49810
Turni506 – 5083
Helixi509 – 5157
Beta strandi522 – 5287
Helixi529 – 5368
Helixi542 – 5454
Beta strandi546 – 5483

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1ASYX-ray2.90A/B68-557[»]
1ASZX-ray3.00A/B68-557[»]
1EOVX-ray2.30A71-557[»]
ProteinModelPortaliP04802.
SMRiP04802. Positions 68-557.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP04802.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni303 – 3064AspartateBy similarity

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0017.
GeneTreeiENSGT00550000074880.
HOGENOMiHOG000226032.
InParanoidiP04802.
KOiK01876.
OMAiFCVGPVF.
OrthoDBiEOG7PK972.

Family and domain databases

Gene3Di2.40.50.140. 1 hit.
InterProiIPR004364. aa-tRNA-synt_II.
IPR018150. aa-tRNA-synt_II-like.
IPR006195. aa-tRNA-synth_II.
IPR004523. Asp-tRNA_synthase.
IPR002312. Asp/Asn-tRNA-synth_IIb.
IPR012340. NA-bd_OB-fold.
IPR004365. NA-bd_OB_tRNA.
[Graphical view]
PANTHERiPTHR22594. PTHR22594. 1 hit.
PTHR22594:SF10. PTHR22594:SF10. 1 hit.
PfamiPF00152. tRNA-synt_2. 1 hit.
PF01336. tRNA_anti-codon. 1 hit.
[Graphical view]
PRINTSiPR01042. TRNASYNTHASP.
SUPFAMiSSF50249. SSF50249. 1 hit.
TIGRFAMsiTIGR00458. aspS_nondisc. 1 hit.
PROSITEiPS50862. AA_TRNA_LIGASE_II. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P04802-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MSQDENIVKA VEESAEPAQV ILGEDGKPLS KKALKKLQKE QEKQRKKEER
60 70 80 90 100
ALQLEAEREA REKKAAAEDT AKDNYGKLPL IQSRDSDRTG QKRVKFVDLD
110 120 130 140 150
EAKDSDKEVL FRARVHNTRQ QGATLAFLTL RQQASLIQGL VKANKEGTIS
160 170 180 190 200
KNMVKWAGSL NLESIVLVRG IVKKVDEPIK SATVQNLEIH ITKIYTISET
210 220 230 240 250
PEALPILLED ASRSEAEAEA AGLPVVNLDT RLDYRVIDLR TVTNQAIFRI
260 270 280 290 300
QAGVCELFRE YLATKKFTEV HTPKLLGAPS EGGSSVFEVT YFKGKAYLAQ
310 320 330 340 350
SPQFNKQQLI VADFERVYEI GPVFRAENSN THRHMTEFTG LDMEMAFEEH
360 370 380 390 400
YHEVLDTLSE LFVFIFSELP KRFAHEIELV RKQYPVEEFK LPKDGKMVRL
410 420 430 440 450
TYKEGIEMLR AAGKEIGDFE DLSTENEKFL GKLVRDKYDT DFYILDKFPL
460 470 480 490 500
EIRPFYTMPD PANPKYSNSY DFFMRGEEIL SGAQRIHDHA LLQERMKAHG
510 520 530 540 550
LSPEDPGLKD YCDGFSYGCP PHAGGGIGLE RVVMFYLDLK NIRRASLFPR

DPKRLRP
Length:557
Mass (Da):63,516
Last modified:January 23, 2007 - v3
Checksum:i6656279B3E9011A5
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X03606 Genomic DNA. Translation: CAA27269.1.
X06665 Genomic DNA. Translation: CAA29865.1.
X97560 Genomic DNA. Translation: CAA66172.1.
Z73123 Genomic DNA. Translation: CAA97464.1.
Z73122 Genomic DNA. Translation: CAA97463.1.
X91488 Genomic DNA. Translation: CAA62772.1.
BK006945 Genomic DNA. Translation: DAA09302.1.
PIRiA23508. SYBYDC.
RefSeqiNP_013083.1. NM_001181838.1.

Genome annotation databases

EnsemblFungiiYLL018C; YLL018C; YLL018C.
GeneIDi850643.
KEGGisce:YLL018C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X03606 Genomic DNA. Translation: CAA27269.1 .
X06665 Genomic DNA. Translation: CAA29865.1 .
X97560 Genomic DNA. Translation: CAA66172.1 .
Z73123 Genomic DNA. Translation: CAA97464.1 .
Z73122 Genomic DNA. Translation: CAA97463.1 .
X91488 Genomic DNA. Translation: CAA62772.1 .
BK006945 Genomic DNA. Translation: DAA09302.1 .
PIRi A23508. SYBYDC.
RefSeqi NP_013083.1. NM_001181838.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1ASY X-ray 2.90 A/B 68-557 [» ]
1ASZ X-ray 3.00 A/B 68-557 [» ]
1EOV X-ray 2.30 A 71-557 [» ]
ProteinModelPortali P04802.
SMRi P04802. Positions 68-557.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 31235. 56 interactions.
DIPi DIP-4093N.
IntActi P04802. 15 interactions.
MINTi MINT-510718.
STRINGi 4932.YLL018C.

Proteomic databases

MaxQBi P04802.
PaxDbi P04802.
PRIDEi P04802.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YLL018C ; YLL018C ; YLL018C .
GeneIDi 850643.
KEGGi sce:YLL018C.

Organism-specific databases

SGDi S000003941. DPS1.

Phylogenomic databases

eggNOGi COG0017.
GeneTreei ENSGT00550000074880.
HOGENOMi HOG000226032.
InParanoidi P04802.
KOi K01876.
OMAi FCVGPVF.
OrthoDBi EOG7PK972.

Enzyme and pathway databases

BioCyci YEAST:G3O-32123-MONOMER.
SABIO-RK P04802.

Miscellaneous databases

EvolutionaryTracei P04802.
NextBioi 966579.
PROi P04802.

Gene expression databases

Genevestigatori P04802.

Family and domain databases

Gene3Di 2.40.50.140. 1 hit.
InterProi IPR004364. aa-tRNA-synt_II.
IPR018150. aa-tRNA-synt_II-like.
IPR006195. aa-tRNA-synth_II.
IPR004523. Asp-tRNA_synthase.
IPR002312. Asp/Asn-tRNA-synth_IIb.
IPR012340. NA-bd_OB-fold.
IPR004365. NA-bd_OB_tRNA.
[Graphical view ]
PANTHERi PTHR22594. PTHR22594. 1 hit.
PTHR22594:SF10. PTHR22594:SF10. 1 hit.
Pfami PF00152. tRNA-synt_2. 1 hit.
PF01336. tRNA_anti-codon. 1 hit.
[Graphical view ]
PRINTSi PR01042. TRNASYNTHASP.
SUPFAMi SSF50249. SSF50249. 1 hit.
TIGRFAMsi TIGR00458. aspS_nondisc. 1 hit.
PROSITEi PS50862. AA_TRNA_LIGASE_II. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Sequence polymorphisms in the yeast gene encoding aspartyl tRNA synthase."
    Reid G.A.
    Nucleic Acids Res. 16:1212-1212(1988) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  2. "Nucleotide sequence of the gene coding for yeast cytoplasmic aspartyl-tRNA synthetase (APS); mapping of the 5' and 3' termini of AspRS mRNA."
    Sellami M., Fasiolo F., Dirheimer G., Ebel J.-P., Gangloff J.
    Nucleic Acids Res. 14:1657-1666(1986) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  3. "The sequence of 32kb on the left arm of yeast chromosome XII reveals six known genes, a new member of the seripauperins family and a new ABC transporter homologous to the human multidrug resistance protein."
    Purnelle B., Goffeau A.
    Yeast 13:183-188(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  4. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XII."
    Johnston M., Hillier L.W., Riles L., Albermann K., Andre B., Ansorge W., Benes V., Brueckner M., Delius H., Dubois E., Duesterhoeft A., Entian K.-D., Floeth M., Goffeau A., Hebling U., Heumann K., Heuss-Neitzel D., Hilbert H.
    , Hilger F., Kleine K., Koetter P., Louis E.J., Messenguy F., Mewes H.-W., Miosga T., Moestl D., Mueller-Auer S., Nentwich U., Obermaier B., Piravandi E., Pohl T.M., Portetelle D., Purnelle B., Rechmann S., Rieger M., Rinke M., Rose M., Scharfe M., Scherens B., Scholler P., Schwager C., Schwarz S., Underwood A.P., Urrestarazu L.A., Vandenbol M., Verhasselt P., Vierendeels F., Voet M., Volckaert G., Voss H., Wambutt R., Wedler E., Wedler H., Zimmermann F.K., Zollner A., Hani J., Hoheisel J.D.
    Nature 387:87-90(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  5. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  6. "The complete amino acid sequence of cytoplasmic aspartyl-tRNA synthetase from Saccharomyces cerevisiae."
    Amiri I., Mejdoub H., Hounwanou N., Boulanger Y., Reinbolt J.
    Biochimie 67:607-613(1985) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 2-557.
  7. "Sequence analysis of the CEN12 region of Saccharomyces cerevisiae on a 43.7 kb fragment of chromosome XII including an open reading frame homologous to the human cystic fibrosis transmembrane conductance regulator protein CFTR."
    Miosga T., Zimmermann F.K.
    Yeast 12:693-708(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-81.
    Strain: ATCC 90840 / EAY235 / FY23.
  8. "Identification of structurally and functionally important histidine residues in cytoplasmic aspartyl-tRNA synthetase from Saccharomyces cerevisiae."
    Gasparini S., Vincendon P., Eriani G., Gangloff J., Boulanger Y., Reinbolt J., Kern D.
    Biochemistry 30:4284-4289(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: PARTIAL PROTEIN SEQUENCE, MUTAGENESIS.
  9. "Role of dimerization in yeast aspartyl-tRNA synthetase and importance of the class II invariant proline."
    Eriani G., Cavarelli J., Martin F., Dirheimer G., Moras D., Gangloff J.
    Proc. Natl. Acad. Sci. U.S.A. 90:10816-10820(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF PRO-273.
  10. "Proteome studies of Saccharomyces cerevisiae: identification and characterization of abundant proteins."
    Garrels J.I., McLaughlin C.S., Warner J.R., Futcher B., Latter G.I., Kobayashi R., Schwender B., Volpe T., Anderson D.S., Mesquita-Fuentes R., Payne W.E.
    Electrophoresis 18:1347-1360(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION AT SER-2.
  11. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  12. "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae."
    Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P.
    J. Proteome Res. 6:1190-1197(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-301, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Strain: ADR376.
  13. "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry."
    Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L., Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F.
    Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-546, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  14. "A multidimensional chromatography technology for in-depth phosphoproteome analysis."
    Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
    Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-14; SER-301 AND SER-502, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  15. "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
    Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
    Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-301 AND SER-502, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  16. "Class II aminoacyl transfer RNA synthetases: crystal structure of yeast aspartyl-tRNA synthetase complexed with tRNA(Asp)."
    Ruff M., Krishnaswamy S., Boeglin M., Poterszman A., Mitschler A., Podjarny A., Rees B., Thierry J.-C., Moras D.
    Science 252:1682-1689(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS).
  17. "The active site of yeast aspartyl-tRNA synthetase: structural and functional aspects of the aminoacylation reaction."
    Cavarelli J., Eriani G., Rees B., Ruff M., Boeglin M., Mitschler A., Martin F., Gangloff J., Thierry J.-C., Moras D.
    EMBO J. 13:327-337(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS), MUTAGENESIS.

Entry informationi

Entry nameiSYDC_YEAST
AccessioniPrimary (citable) accession number: P04802
Secondary accession number(s): D6VXY6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 13, 1987
Last sequence update: January 23, 2007
Last modified: October 29, 2014
This is version 164 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 5750 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Aminoacyl-tRNA synthetases
    List of aminoacyl-tRNA synthetase entries
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families
  4. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  5. Yeast chromosome XII
    Yeast (Saccharomyces cerevisiae) chromosome XII: entries and gene names

External Data

Dasty 3