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Protein

Tyrosine--tRNA ligase, cytoplasmic

Gene

YARS

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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 activityi

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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei39Tyrosine1 Publication1
Binding sitei166Tyrosine1 Publication1
Binding sitei170Tyrosine1 Publication1
Binding sitei173Tyrosine1 Publication1
Binding sitei188Tyrosine1 Publication1

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • interleukin-8 receptor binding Source: ProtInc
  • poly(A) RNA binding Source: UniProtKB
  • signal transducer activity Source: ProtInc
  • tRNA binding Source: UniProtKB-KW
  • tyrosine-tRNA ligase activity Source: Reactome
  • valine-tRNA ligase activity Source: GO_Central

GO - Biological processi

  • apoptotic process Source: ProtInc
  • tRNA aminoacylation for protein translation Source: Reactome
  • tyrosyl-tRNA aminoacylation Source: ProtInc
  • valyl-tRNA aminoacylation Source: GO_Central
Complete GO annotation...

Keywords - Molecular functioni

Aminoacyl-tRNA synthetase, Ligase

Keywords - Biological processi

Protein biosynthesis

Keywords - Ligandi

ATP-binding, Nucleotide-binding, RNA-binding, tRNA-binding

Enzyme and pathway databases

BioCyciZFISH:HS05899-MONOMER.
BRENDAi6.1.1.1. 2681.
ReactomeiR-HSA-379716. Cytosolic tRNA aminoacylation.

Names & Taxonomyi

Protein namesi
Recommended name:
Tyrosine--tRNA ligase, cytoplasmic (EC:6.1.1.1)
Alternative name(s):
Tyrosyl-tRNA synthetase
Short name:
TyrRS
Cleaved into the following chain:
Gene namesi
Name:YARS
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 1

Organism-specific databases

HGNCiHGNC:12840. YARS.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: HPA
  • cytosol Source: Reactome
  • extracellular space Source: ProtInc
  • nucleus Source: HPA
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Involvement in diseasei

Charcot-Marie-Tooth disease, dominant, intermediate type, C (CMTDIC)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA 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.
See also OMIM:608323
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_02668141G → R in CMTDIC; partial loss of activity. 1 PublicationCorresponds to variant rs121908833dbSNPEnsembl.1
Natural variantiVAR_026682153 – 156Missing in CMTDIC. 1 Publication4
Natural variantiVAR_026684196E → K in CMTDIC; partial loss of activity. 1 PublicationCorresponds to variant rs121908834dbSNPEnsembl.1

Keywords - Diseasei

Charcot-Marie-Tooth disease, Disease mutation, Neurodegeneration, Neuropathy

Organism-specific databases

DisGeNETi8565.
MalaCardsiYARS.
MIMi608323. phenotype.
OpenTargetsiENSG00000134684.
Orphaneti100045. Autosomal dominant intermediate Charcot-Marie-Tooth disease type C.
PharmGKBiPA37431.

Chemistry databases

ChEMBLiCHEMBL3179.
DrugBankiDB00135. L-Tyrosine.

Polymorphism and mutation databases

BioMutaiYARS.
DMDMi13638438.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00004232851 – 528Tyrosine--tRNA ligase, cytoplasmicAdd BLAST528
Initiator methionineiRemoved; alternateCombined sources2 Publications
ChainiPRO_00000556732 – 528Tyrosine--tRNA ligase, cytoplasmic, N-terminally processedAdd BLAST527

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei1N-acetylmethionineCombined sources1
Modified residuei2N-acetylglycine; in Tyrosine--tRNA ligase, cytoplasmic, N-terminally processedCombined sources1 Publication1
Modified residuei197N6-acetyllysineCombined sources1
Modified residuei205PhosphoserineCombined sources1
Modified residuei206N6-acetyllysineCombined sources1
Modified residuei386PhosphoserineCombined sources1
Modified residuei474N6-acetyllysineCombined sources1
Modified residuei482N6-acetyllysineCombined sources1
Modified residuei490N6-acetyllysineCombined sources1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

EPDiP54577.
MaxQBiP54577.
PaxDbiP54577.
PeptideAtlasiP54577.
PRIDEiP54577.

2D gel databases

REPRODUCTION-2DPAGEIPI00007074.

PTM databases

iPTMnetiP54577.
PhosphoSitePlusiP54577.
SwissPalmiP54577.

Miscellaneous databases

PMAP-CutDBP54577.

Expressioni

Gene expression databases

BgeeiENSG00000134684.
CleanExiHS_YARS.
ExpressionAtlasiP54577. baseline and differential.
GenevisibleiP54577. HS.

Organism-specific databases

HPAiHPA017936.
HPA018950.
HPA018954.

Interactioni

Subunit structurei

Homodimer.2 Publications

GO - Molecular functioni

  • interleukin-8 receptor binding Source: ProtInc

Protein-protein interaction databases

BioGridi114134. 53 interactors.
DIPiDIP-50415N.
IntActiP54577. 16 interactors.
STRINGi9606.ENSP00000362576.

Chemistry databases

BindingDBiP54577.

Structurei

Secondary structure

1528
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi7 – 15Combined sources9
Beta strandi19 – 22Combined sources4
Helixi24 – 31Combined sources8
Beta strandi37 – 42Combined sources6
Helixi50 – 52Combined sources3
Helixi53 – 64Combined sources12
Beta strandi68 – 73Combined sources6
Helixi75 – 80Combined sources6
Turni81 – 84Combined sources4
Helixi87 – 108Combined sources22
Beta strandi115 – 119Combined sources5
Helixi120 – 122Combined sources3
Turni123 – 125Combined sources3
Helixi127 – 137Combined sources11
Helixi142 – 148Combined sources7
Turni149 – 152Combined sources4
Helixi161 – 176Combined sources16
Beta strandi180 – 185Combined sources6
Helixi186 – 188Combined sources3
Helixi189 – 198Combined sources10
Helixi199 – 202Combined sources4
Beta strandi208 – 212Combined sources5
Helixi238 – 246Combined sources9
Beta strandi247 – 249Combined sources3
Helixi259 – 266Combined sources8
Turni267 – 273Combined sources7
Beta strandi275 – 277Combined sources3
Helixi281 – 283Combined sources3
Beta strandi287 – 291Combined sources5
Helixi292 – 300Combined sources9
Helixi306 – 327Combined sources22
Helixi331 – 340Combined sources10
Helixi365 – 367Combined sources3
Beta strandi370 – 380Combined sources11
Beta strandi388 – 393Combined sources6
Beta strandi395 – 398Combined sources4
Beta strandi400 – 405Combined sources6
Turni407 – 409Combined sources3
Helixi412 – 414Combined sources3
Turni415 – 417Combined sources3
Beta strandi419 – 423Combined sources5
Beta strandi429 – 431Combined sources3
Beta strandi434 – 436Combined sources3
Beta strandi442 – 454Combined sources13
Beta strandi466 – 469Combined sources4
Beta strandi479 – 481Combined sources3
Helixi483 – 485Combined sources3
Helixi487 – 492Combined sources6
Beta strandi495 – 497Combined sources3
Beta strandi501 – 505Combined sources5
Beta strandi508 – 512Combined sources5
Beta strandi526 – 528Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1N3LX-ray1.18A1-364[»]
1NTGX-ray2.21A/B/C/D359-528[»]
1Q11X-ray1.60A1-364[»]
4Q93X-ray2.10A1-364[»]
4QBTX-ray2.10A1-364[»]
ProteinModelPortaliP54577.
SMRiP54577.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP54577.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini364 – 468tRNA-bindingPROSITE-ProRule annotationAdd BLAST105

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi44 – 52"HIGH" region9
Motifi222 – 226"KMSKS" region5

Sequence similaritiesi

Contains 1 tRNA-binding domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG2144. Eukaryota.
KOG2241. Eukaryota.
COG0073. LUCA.
COG0162. LUCA.
GeneTreeiENSGT00790000123100.
HOGENOMiHOG000228237.
HOVERGENiHBG080113.
InParanoidiP54577.
KOiK01866.
OMAiPIRKKFE.
OrthoDBiEOG091G03XO.
PhylomeDBiP54577.
TreeFamiTF300898.

Family and domain databases

CDDicd00805. TyrRS_core. 1 hit.
Gene3Di3.40.50.620. 1 hit.
InterProiIPR002305. 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]
PfamiPF00579. tRNA-synt_1b. 1 hit.
PF01588. tRNA_bind. 1 hit.
[Graphical view]
PRINTSiPR01040. TRNASYNTHTYR.
SUPFAMiSSF50249. SSF50249. 1 hit.
TIGRFAMsiTIGR00234. tyrS. 1 hit.
PROSITEiPS50886. TRBD. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

P54577-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGDAPSPEEK LHLITRNLQE VLGEEKLKEI LKERELKIYW GTATTGKPHV
60 70 80 90 100
AYFVPMSKIA DFLKAGCEVT ILFADLHAYL DNMKAPWELL ELRVSYYENV
110 120 130 140 150
IKAMLESIGV PLEKLKFIKG TDYQLSKEYT LDVYRLSSVV TQHDSKKAGA
160 170 180 190 200
EVVKQVEHPL LSGLLYPGLQ ALDEEYLKVD AQFGGIDQRK IFTFAEKYLP
210 220 230 240 250
ALGYSKRVHL MNPMVPGLTG SKMSSSEEES KIDLLDRKED VKKKLKKAFC
260 270 280 290 300
EPGNVENNGV LSFIKHVLFP LKSEFVILRD EKWGGNKTYT AYVDLEKDFA
310 320 330 340 350
AEVVHPGDLK NSVEVALNKL LDPIREKFNT PALKKLASAA YPDPSKQKPM
360 370 380 390 400
AKGPAKNSEP EEVIPSRLDI RVGKIITVEK HPDADSLYVE KIDVGEAEPR
410 420 430 440 450
TVVSGLVQFV PKEELQDRLV VVLCNLKPQK MRGVESQGML LCASIEGINR
460 470 480 490 500
QVEPLDPPAG SAPGEHVFVK GYEKGQPDEE LKPKKKVFEK LQADFKISEE
510 520
CIAQWKQTNF MTKLGSISCK SLKGGNIS
Length:528
Mass (Da):59,143
Last modified:January 23, 2007 - v4
Checksum:i00C7E88843905780
GO

Sequence cautioni

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

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti143H → R in BAD97328 (Ref. 4) Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_02668141G → R in CMTDIC; partial loss of activity. 1 PublicationCorresponds to variant rs121908833dbSNPEnsembl.1
Natural variantiVAR_026682153 – 156Missing in CMTDIC. 1 Publication4
Natural variantiVAR_026683170Q → H.Corresponds to variant rs2128600dbSNPEnsembl.1
Natural variantiVAR_026684196E → K in CMTDIC; partial loss of activity. 1 PublicationCorresponds to variant rs121908834dbSNPEnsembl.1
Natural variantiVAR_073292274E → K Found in a patient with hereditary motor and sensory neuropathy; unknown pathological significance. 1 PublicationCorresponds to variant rs758897498dbSNPEnsembl.1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
CCDSiCCDS368.1.
RefSeqiNP_003671.1. NM_003680.3.
UniGeneiHs.213264.

Genome annotation databases

EnsembliENST00000373477; ENSP00000362576; ENSG00000134684.
GeneIDi8565.
KEGGihsa:8565.
UCSCiuc001bvy.2. human.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
CCDSiCCDS368.1.
RefSeqiNP_003671.1. NM_003680.3.
UniGeneiHs.213264.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1N3LX-ray1.18A1-364[»]
1NTGX-ray2.21A/B/C/D359-528[»]
1Q11X-ray1.60A1-364[»]
4Q93X-ray2.10A1-364[»]
4QBTX-ray2.10A1-364[»]
ProteinModelPortaliP54577.
SMRiP54577.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi114134. 53 interactors.
DIPiDIP-50415N.
IntActiP54577. 16 interactors.
STRINGi9606.ENSP00000362576.

Chemistry databases

BindingDBiP54577.
ChEMBLiCHEMBL3179.
DrugBankiDB00135. L-Tyrosine.

PTM databases

iPTMnetiP54577.
PhosphoSitePlusiP54577.
SwissPalmiP54577.

Polymorphism and mutation databases

BioMutaiYARS.
DMDMi13638438.

2D gel databases

REPRODUCTION-2DPAGEIPI00007074.

Proteomic databases

EPDiP54577.
MaxQBiP54577.
PaxDbiP54577.
PeptideAtlasiP54577.
PRIDEiP54577.

Protocols and materials databases

DNASUi8565.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000373477; ENSP00000362576; ENSG00000134684.
GeneIDi8565.
KEGGihsa:8565.
UCSCiuc001bvy.2. human.

Organism-specific databases

CTDi8565.
DisGeNETi8565.
GeneCardsiYARS.
HGNCiHGNC:12840. YARS.
HPAiHPA017936.
HPA018950.
HPA018954.
MalaCardsiYARS.
MIMi603623. gene.
608323. phenotype.
neXtProtiNX_P54577.
OpenTargetsiENSG00000134684.
Orphaneti100045. Autosomal dominant intermediate Charcot-Marie-Tooth disease type C.
PharmGKBiPA37431.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2144. Eukaryota.
KOG2241. Eukaryota.
COG0073. LUCA.
COG0162. LUCA.
GeneTreeiENSGT00790000123100.
HOGENOMiHOG000228237.
HOVERGENiHBG080113.
InParanoidiP54577.
KOiK01866.
OMAiPIRKKFE.
OrthoDBiEOG091G03XO.
PhylomeDBiP54577.
TreeFamiTF300898.

Enzyme and pathway databases

BioCyciZFISH:HS05899-MONOMER.
BRENDAi6.1.1.1. 2681.
ReactomeiR-HSA-379716. Cytosolic tRNA aminoacylation.

Miscellaneous databases

ChiTaRSiYARS. human.
EvolutionaryTraceiP54577.
GeneWikiiYARS.
GenomeRNAii8565.
PMAP-CutDBP54577.
PROiP54577.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000134684.
CleanExiHS_YARS.
ExpressionAtlasiP54577. baseline and differential.
GenevisibleiP54577. HS.

Family and domain databases

CDDicd00805. TyrRS_core. 1 hit.
Gene3Di3.40.50.620. 1 hit.
InterProiIPR002305. 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]
PfamiPF00579. tRNA-synt_1b. 1 hit.
PF01588. tRNA_bind. 1 hit.
[Graphical view]
PRINTSiPR01040. TRNASYNTHTYR.
SUPFAMiSSF50249. SSF50249. 1 hit.
TIGRFAMsiTIGR00234. tyrS. 1 hit.
PROSITEiPS50886. TRBD. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiSYYC_HUMAN
AccessioniPrimary (citable) accession number: P54577
Secondary accession number(s): B3KWK4
, D3DPQ4, O43276, Q53EN1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: January 23, 2007
Last modified: November 30, 2016
This is version 181 of the entry and version 4 of the sequence. [Complete history]
Entry statusiReviewed (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.

Miscellaneousi

Keywords - Technical termi

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

Documents

  1. Aminoacyl-tRNA synthetases
    List of aminoacyl-tRNA synthetase entries
  2. Human chromosome 1
    Human chromosome 1: entries, gene names and cross-references to MIM
  3. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  4. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  5. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  6. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  7. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.