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P54577 (SYYC_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 155. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (7) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Tyrosine--tRNA ligase, cytoplasmic

EC=6.1.1.1
Alternative name(s):
Tyrosyl-tRNA synthetase
Short name=TyrRS
Gene names
Name:YARS
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length528 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr) By similarity.

Catalytic activity

ATP + L-tyrosine + tRNA(Tyr) = AMP + diphosphate + L-tyrosyl-tRNA(Tyr).

Subunit structure

Homodimer. Ref.12

Subcellular location

Cytoplasm Ref.14.

Involvement in disease

Charcot-Marie-Tooth disease, dominant, intermediate type, C (CMTDIC) [MIM:608323]: A form of Charcot-Marie-Tooth disease, a disorder of the peripheral nervous system, characterized by progressive weakness and atrophy, initially of the peroneal muscles and later of the distal muscles of the arms. The dominant intermediate type C is characterized by clinical and pathologic features intermediate between demyelinating and axonal peripheral neuropathies, and motor median nerve conduction velocities ranging from 25 to 45 m/sec.
Note: The disease is caused by mutations affecting the gene represented in this entry. Ref.14

Sequence similarities

Belongs to the class-I aminoacyl-tRNA synthetase family.

Contains 1 tRNA-binding domain.

Sequence caution

The sequence AAB39406.1 differs from that shown. Reason: Frameshift at position 354.

Ontologies

Keywords
   Biological processProtein biosynthesis
   Cellular componentCytoplasm
   Coding sequence diversityPolymorphism
   DiseaseCharcot-Marie-Tooth disease
Disease mutation
Neurodegeneration
Neuropathy
   LigandATP-binding
Nucleotide-binding
RNA-binding
tRNA-binding
   Molecular functionAminoacyl-tRNA synthetase
Ligase
   PTMAcetylation
   Technical term3D-structure
Complete proteome
Direct protein sequencing
Reference proteome
Gene Ontology (GO)
   Biological_processapoptotic process

Traceable author statement PubMed 10102815. Source: ProtInc

gene expression

Traceable author statement. Source: Reactome

signal transduction

Non-traceable author statement PubMed 10102815. Source: GOC

tRNA aminoacylation for protein translation

Traceable author statement. Source: Reactome

tyrosyl-tRNA aminoacylation

Traceable author statement Ref.2. Source: ProtInc

   Cellular_componentcytoplasm

Inferred from direct assay. Source: HPA

cytosol

Traceable author statement. Source: Reactome

extracellular space

Traceable author statement PubMed 10102815. Source: ProtInc

nucleus

Inferred from direct assay. Source: HPA

   Molecular_functionATP binding

Inferred from electronic annotation. Source: UniProtKB-KW

interleukin-8 receptor binding

Traceable author statement PubMed 10102815. Source: ProtInc

poly(A) RNA binding

Inferred from direct assay PubMed 22658674. Source: UniProtKB

signal transducer activity

Non-traceable author statement PubMed 10102815. Source: ProtInc

tRNA binding

Inferred from electronic annotation. Source: UniProtKB-KW

tyrosine-tRNA ligase activity

Traceable author statement. Source: Reactome

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 528528Tyrosine--tRNA ligase, cytoplasmic
PRO_0000423285
Initiator methionine11Removed; alternate Ref.7 Ref.8
Chain2 – 528527Tyrosine--tRNA ligase, cytoplasmic, N-terminally processed
PRO_0000055673

Regions

Domain364 – 468105tRNA-binding
Motif44 – 529"HIGH" region
Motif222 – 2265"KMSKS" region

Sites

Binding site391Tyrosine
Binding site1661Tyrosine
Binding site1701Tyrosine
Binding site1731Tyrosine
Binding site1881Tyrosine

Amino acid modifications

Modified residue11N-acetylmethionine Ref.9
Modified residue21N-acetylglycine; in Tyrosine--tRNA ligase, cytoplasmic, N-terminally processed Ref.8 Ref.9
Modified residue1971N6-acetyllysine Ref.10
Modified residue2061N6-acetyllysine Ref.10
Modified residue4741N6-acetyllysine Ref.10
Modified residue4821N6-acetyllysine Ref.10
Modified residue4901N6-acetyllysine Ref.10

Natural variations

Natural variant411G → R in CMTDIC; partial loss of activity. Ref.14
VAR_026681
Natural variant153 – 1564Missing in CMTDIC.
VAR_026682
Natural variant1701Q → H.
Corresponds to variant rs2128600 [ dbSNP | Ensembl ].
VAR_026683
Natural variant1961E → K in CMTDIC; partial loss of activity. Ref.14
VAR_026684

Experimental info

Sequence conflict1431H → R in BAD97328. Ref.4

Secondary structure

............................................................................................ 528
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P54577 [UniParc].

Last modified January 23, 2007. Version 4.
Checksum: 00C7E88843905780

FASTA52859,143
        10         20         30         40         50         60 
MGDAPSPEEK LHLITRNLQE VLGEEKLKEI LKERELKIYW GTATTGKPHV AYFVPMSKIA 

        70         80         90        100        110        120 
DFLKAGCEVT ILFADLHAYL DNMKAPWELL ELRVSYYENV IKAMLESIGV PLEKLKFIKG 

       130        140        150        160        170        180 
TDYQLSKEYT LDVYRLSSVV TQHDSKKAGA EVVKQVEHPL LSGLLYPGLQ ALDEEYLKVD 

       190        200        210        220        230        240 
AQFGGIDQRK IFTFAEKYLP ALGYSKRVHL MNPMVPGLTG SKMSSSEEES KIDLLDRKED 

       250        260        270        280        290        300 
VKKKLKKAFC EPGNVENNGV LSFIKHVLFP LKSEFVILRD EKWGGNKTYT AYVDLEKDFA 

       310        320        330        340        350        360 
AEVVHPGDLK NSVEVALNKL LDPIREKFNT PALKKLASAA YPDPSKQKPM AKGPAKNSEP 

       370        380        390        400        410        420 
EEVIPSRLDI RVGKIITVEK HPDADSLYVE KIDVGEAEPR TVVSGLVQFV PKEELQDRLV 

       430        440        450        460        470        480 
VVLCNLKPQK MRGVESQGML LCASIEGINR QVEPLDPPAG SAPGEHVFVK GYEKGQPDEE 

       490        500        510        520 
LKPKKKVFEK LQADFKISEE CIAQWKQTNF MTKLGSISCK SLKGGNIS 

« Hide

References

« Hide 'large scale' references
[1]"Evidence that two present-day components needed for the genetic code appeared after nucleated cells separated from eubacteria."
Ribas de Pouplana L., Frugier M., Quinn C.L., Schimmel P.
Proc. Natl. Acad. Sci. U.S.A. 93:166-170(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[2]"Human tyrosyl-tRNA synthetase shares amino acid sequence homology with a putative cytokine."
Kleeman T.A., Wei D., Simpson K.L., First E.A.
J. Biol. Chem. 272:14420-14425(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[3]"Complete sequencing and characterization of 21,243 full-length human cDNAs."
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. expand/collapse author list , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Tissue: Brain.
[4]Totoki Y., Toyoda A., Takeda T., Sakaki Y., Tanaka A., Yokoyama S.
Submitted (APR-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[5]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[6]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Tissue: Bone and Lung.
[7]"Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides."
Gevaert K., Goethals M., Martens L., Van Damme J., Staes A., Thomas G.R., Vandekerckhove J.
Nat. Biotechnol. 21:566-569(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 2-16.
Tissue: Platelet.
[8]Bienvenut W.V.
Submitted (OCT-2004) to UniProtKB
Cited for: PROTEIN SEQUENCE OF 2-16, ACETYLATION AT GLY-2, IDENTIFICATION BY MASS SPECTROMETRY.
Tissue: B-cell lymphoma.
[9]"Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach."
Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.
Anal. Chem. 81:4493-4501(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1 AND GLY-2, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[10]"Lysine acetylation targets protein complexes and co-regulates major cellular functions."
Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T.C., Olsen J.V., Mann M.
Science 325:834-840(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-197; LYS-206; LYS-474; LYS-482 AND LYS-490, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[11]"Initial characterization of the human central proteome."
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.
BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[12]"Crystal structure of a human aminoacyl-tRNA synthetase cytokine."
Yang X.-L., Skene R.J., McRee D.E., Schimmel P.
Proc. Natl. Acad. Sci. U.S.A. 99:15369-15374(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.18 ANGSTROMS) OF 1-342, SUBUNIT.
[13]"Crystal structures that suggest late development of genetic code components for differentiating aromatic side chains."
Yang X.-L., Otero F.J., Skene R.J., McRee D.E., Schimmel P., Ribas de Pouplana L.
Proc. Natl. Acad. Sci. U.S.A. 100:15376-15380(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) OF 1-364 IN COMPLEX WITH TYROSINE.
[14]"Disrupted function and axonal distribution of mutant tyrosyl-tRNA synthetase in dominant intermediate Charcot-Marie-Tooth neuropathy."
Jordanova A., Irobi J., Thomas F.P., Van Dijck P., Meerschaert K., Dewil M., Dierick I., Jacobs A., De Vriendt E., Guergueltcheva V., Rao C.V., Tournev I., Gondim F.A.A., D'Hooghe M., Van Gerwen V., Callaerts P., Van Den Bosch L., Timmermans J.-P. expand/collapse author list , Robberecht W., Gettemans J., Thevelein J.M., De Jonghe P., Kremensky I., Timmerman V.
Nat. Genet. 38:197-202(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION, VARIANTS CMTDIC 153-VAL--VAL-156 DEL; ARG-41 AND LYS-196, CHARACTERIZATION OF VARIANTS CMTDIC ARG-41 AND LYS-196.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
U40714 mRNA. Translation: AAB39406.1. Frameshift.
U89436 mRNA. Translation: AAB88409.1.
AK125213 mRNA. Translation: BAG54166.1.
AK223608 mRNA. Translation: BAD97328.1.
CH471059 Genomic DNA. Translation: EAX07506.1.
CH471059 Genomic DNA. Translation: EAX07507.1.
BC001933 mRNA. Translation: AAH01933.1.
BC004151 mRNA. Translation: AAH04151.1.
BC016689 mRNA. Translation: AAH16689.1.
CCDSCCDS368.1.
RefSeqNP_003671.1. NM_003680.3.
UniGeneHs.213264.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1N3LX-ray1.18A1-364[»]
1NTGX-ray2.21A/B/C/D359-528[»]
1Q11X-ray1.60A1-364[»]
ProteinModelPortalP54577.
SMRP54577. Positions 4-342, 360-528.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid114134. 15 interactions.
IntActP54577. 1 interaction.
STRING9606.ENSP00000362576.

Chemistry

BindingDBP54577.
ChEMBLCHEMBL3179.
DrugBankDB00135. L-Tyrosine.

PTM databases

PhosphoSiteP54577.

Polymorphism databases

DMDM13638438.

2D gel databases

REPRODUCTION-2DPAGEIPI00007074.

Proteomic databases

MaxQBP54577.
PaxDbP54577.
PeptideAtlasP54577.
PRIDEP54577.

Protocols and materials databases

DNASU8565.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000373477; ENSP00000362576; ENSG00000134684.
GeneID8565.
KEGGhsa:8565.
UCSCuc001bvy.1. human.

Organism-specific databases

CTD8565.
GeneCardsGC01M033240.
HGNCHGNC:12840. YARS.
HPAHPA017936.
HPA018950.
HPA018954.
MIM603623. gene.
608323. phenotype.
neXtProtNX_P54577.
Orphanet100045. Autosomal dominant intermediate Charcot-Marie-Tooth disease type C.
PharmGKBPA37431.
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG0162.
HOGENOMHOG000228237.
HOVERGENHBG080113.
InParanoidP54577.
KOK01866.
OMANRQVEPL.
OrthoDBEOG79CXZ2.
PhylomeDBP54577.
TreeFamTF300898.

Enzyme and pathway databases

ReactomeREACT_71. Gene Expression.

Gene expression databases

BgeeP54577.
CleanExHS_YARS.
GenevestigatorP54577.

Family and domain databases

Gene3D2.40.50.140. 1 hit.
3.40.50.620. 1 hit.
InterProIPR002305. aa-tRNA-synth_Ic.
IPR012340. NA-bd_OB-fold.
IPR014729. Rossmann-like_a/b/a_fold.
IPR002547. tRNA-bd_dom.
IPR002307. Tyr-tRNA-ligase.
[Graphical view]
PfamPF00579. tRNA-synt_1b. 1 hit.
PF01588. tRNA_bind. 1 hit.
[Graphical view]
PRINTSPR01040. TRNASYNTHTYR.
SUPFAMSSF50249. SSF50249. 1 hit.
TIGRFAMsTIGR00234. tyrS. 1 hit.
PROSITEPS50886. TRBD. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSYARS. human.
EvolutionaryTraceP54577.
GeneWikiYARS.
GenomeRNAi8565.
NextBio32113.
PMAP-CutDBP54577.
PROP54577.
SOURCESearch...

Entry information

Entry nameSYYC_HUMAN
AccessionPrimary (citable) accession number: P54577
Secondary accession number(s): B3KWK4 expand/collapse secondary AC list , D3DPQ4, O43276, Q53EN1
Entry history
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: January 23, 2007
Last modified: July 9, 2014
This is version 155 of the entry and version 4 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 1

Human chromosome 1: entries, gene names and cross-references to MIM

Aminoacyl-tRNA synthetases

List of aminoacyl-tRNA synthetase entries