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Protein

Tyrosine--tRNA ligase, mitochondrial

Gene

YARS2

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).2 Publications

Catalytic activityi

ATP + L-tyrosine + tRNA(Tyr) = AMP + diphosphate + L-tyrosyl-tRNA(Tyr).2 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei77TyrosineCombined sources1 Publication1
Binding sitei81ATPCombined sources1 Publication1
Binding sitei121TyrosineCombined sources1 Publication1
Binding sitei221TyrosineCombined sources1 Publication1
Binding sitei225TyrosineCombined sources1 Publication1
Binding sitei228TyrosineCombined sources1 Publication1
Binding sitei247TyrosineCombined sources1 Publication1
Binding sitei274ATP; via amide nitrogen and carbonyl oxygenCombined sources1 Publication1
Binding sitei284ATPBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi244 – 246ATPCombined sources1 Publication3

GO - Molecular functioni

  • ATP binding Source: BHF-UCL
  • protein homodimerization activity Source: BHF-UCL
  • RNA binding Source: UniProtKB
  • tRNA binding Source: BHF-UCL
  • tyrosine binding Source: BHF-UCL
  • tyrosine-tRNA ligase activity Source: BHF-UCL

GO - Biological processi

  • mitochondrial tyrosyl-tRNA aminoacylation Source: BHF-UCL
  • translation Source: UniProtKB
  • tRNA aminoacylation Source: BHF-UCL
  • tRNA aminoacylation for protein translation Source: Reactome

Keywordsi

Molecular functionAminoacyl-tRNA synthetase, Ligase
Biological processProtein biosynthesis
LigandATP-binding, Nucleotide-binding

Enzyme and pathway databases

BRENDAi6.1.1.1. 2681.
ReactomeiR-HSA-379726. Mitochondrial tRNA aminoacylation.

Names & Taxonomyi

Protein namesi
Recommended name:
Tyrosine--tRNA ligase, mitochondrial (EC:6.1.1.12 Publications)
Alternative name(s):
Tyrosyl-tRNA synthetase
Short name:
TyrRS1 Publication
Gene namesi
Name:YARS2
ORF Names:CGI-04
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 12

Organism-specific databases

EuPathDBiHostDB:ENSG00000139131.12.
HGNCiHGNC:24249. YARS2.

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Mitochondrion

Pathology & Biotechi

Involvement in diseasei

Myopathy with lactic acidosis and sideroblastic anemia 2 (MLASA2)2 Publications
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA rare oxidative phosphorylation disorder specific to skeletal muscle and bone marrow. Affected individuals manifest sideroblastic anemia, progressive lethargy, muscle weakness, and exercise intolerance associated with persistent lactic acidemia.
See also OMIM:613561
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_06864646G → D in MLASA2. 1 PublicationCorresponds to variant dbSNP:rs587777213Ensembl.1
Natural variantiVAR_06418852F → L in MLASA2; has a 2-fold reduction in catalytic activity and a reduction in affinity for tRNA-tyr resulting in an overall 9-fold loss of catalytic efficiency. 1 PublicationCorresponds to variant dbSNP:rs267607180Ensembl.1

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi200S → E: Loss of tRNA ligase activity. 1 Publication1
Mutagenesisi202Q → A: Mildly decreased tRNA ligase activity. 1 Publication1

Keywords - Diseasei

Disease mutation, Primary mitochondrial disease

Organism-specific databases

DisGeNETi51067.
MalaCardsiYARS2.
MIMi613561. phenotype.
OpenTargetsiENSG00000139131.
Orphaneti2598. Mitochondrial myopathy and sideroblastic anemia.
PharmGKBiPA142670559.

Chemistry databases

DrugBankiDB00135. L-Tyrosine.

Polymorphism and mutation databases

BioMutaiYARS2.
DMDMi50401709.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Transit peptidei1 – 16MitochondrionSequence analysisAdd BLAST16
ChainiPRO_000003583017 – 477Tyrosine--tRNA ligase, mitochondrialAdd BLAST461

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei355N6-acetyllysineCombined sources1
Modified residuei367N6-acetyllysineBy similarity1

Keywords - PTMi

Acetylation

Proteomic databases

EPDiQ9Y2Z4.
MaxQBiQ9Y2Z4.
PaxDbiQ9Y2Z4.
PeptideAtlasiQ9Y2Z4.
PRIDEiQ9Y2Z4.

PTM databases

iPTMnetiQ9Y2Z4.
PhosphoSitePlusiQ9Y2Z4.
SwissPalmiQ9Y2Z4.

Expressioni

Gene expression databases

BgeeiENSG00000139131.
CleanExiHS_YARS2.
ExpressionAtlasiQ9Y2Z4. baseline and differential.
GenevisibleiQ9Y2Z4. HS.

Organism-specific databases

HPAiHPA038721.
HPA057610.
HPA074097.

Interactioni

Subunit structurei

Homodimer.2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
FAM9BQ8IZU03EBI-1049286,EBI-10175124

GO - Molecular functioni

  • protein homodimerization activity Source: BHF-UCL

Protein-protein interaction databases

BioGridi119258. 53 interactors.
DIPiDIP-29487N.
IntActiQ9Y2Z4. 16 interactors.
MINTiMINT-4832075.
STRINGi9606.ENSP00000320658.

Structurei

Secondary structure

1477
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi38 – 45Combined sources8
Beta strandi50 – 52Combined sources3
Helixi61 – 64Combined sources4
Beta strandi67 – 70Combined sources4
Beta strandi75 – 80Combined sources6
Beta strandi83 – 86Combined sources4
Helixi89 – 103Combined sources15
Beta strandi107 – 112Combined sources6
Helixi116 – 118Combined sources3
Helixi134 – 158Combined sources25
Beta strandi168 – 172Combined sources5
Helixi174 – 177Combined sources4
Helixi182 – 189Combined sources8
Helixi190 – 192Combined sources3
Helixi195 – 200Combined sources6
Helixi202 – 208Combined sources7
Beta strandi210 – 212Combined sources3
Helixi216 – 236Combined sources21
Beta strandi240 – 244Combined sources5
Helixi245 – 247Combined sources3
Helixi248 – 261Combined sources14
Beta strandi267 – 271Combined sources5
Beta strandi291 – 293Combined sources3
Turni294 – 296Combined sources3
Helixi299 – 307Combined sources9
Helixi311 – 321Combined sources11
Helixi326 – 338Combined sources13
Helixi340 – 342Combined sources3
Helixi344 – 372Combined sources29

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2PIDX-ray2.20A/B32-375[»]
3ZXIX-ray2.75A/B32-375[»]
ProteinModelPortaliQ9Y2Z4.
SMRiQ9Y2Z4.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9Y2Z4.

Family & Domainsi

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi82 – 91"HIGH" regionCurated10
Motifi281 – 285"KMSKS" regionCurated5

Sequence similaritiesi

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiKOG2623. Eukaryota.
COG0162. LUCA.
GeneTreeiENSGT00390000013709.
HOGENOMiHOG000242790.
HOVERGENiHBG056052.
InParanoidiQ9Y2Z4.
KOiK01866.
OMAiDLMWRYY.
OrthoDBiEOG091G06NG.
PhylomeDBiQ9Y2Z4.
TreeFamiTF105974.

Family and domain databases

CDDicd00805. TyrRS_core. 1 hit.
Gene3Di3.10.290.10. 1 hit.
3.40.50.620. 1 hit.
InterProiView protein in InterPro
IPR001412. aa-tRNA-synth_I_CS.
IPR002305. aa-tRNA-synth_Ic.
IPR014729. Rossmann-like_a/b/a_fold.
IPR002942. S4_RNA-bd.
IPR002307. Tyr-tRNA-ligase.
IPR024088. Tyr-tRNA-ligase_bac-type.
PANTHERiPTHR11766. PTHR11766. 1 hit.
PfamiView protein in Pfam
PF00579. tRNA-synt_1b. 1 hit.
PRINTSiPR01040. TRNASYNTHTYR.
TIGRFAMsiTIGR00234. tyrS. 1 hit.
PROSITEiView protein in PROSITE
PS00178. AA_TRNA_LIGASE_I. 1 hit.

Sequencei

Sequence statusi: Complete.

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

Q9Y2Z4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAAPILRSFS WGRWSGTLNL SVLLPLGLRK AHSGAQGLLA AQKARGLFKD
60 70 80 90 100
FFPETGTKIE LPELFDRGTA SFPQTIYCGF DPTADSLHVG HLLALLGLFH
110 120 130 140 150
LQRAGHNVIA LVGGATARLG DPSGRTKERE ALETERVRAN ARALRLGLEA
160 170 180 190 200
LAANHQQLFT DGRSWGSFTV LDNSAWYQKQ HLVDFLAAVG GHFRMGTLLS
210 220 230 240 250
RQSVQLRLKS PEGMSLAEFF YQVLQAYDFY YLFQRYGCRV QLGGSDQLGN
260 270 280 290 300
IMSGYEFINK LTGEDVFGIT VPLITSTTGA KLGKSAGNAV WLNRDKTSPF
310 320 330 340 350
ELYQFFVRQP DDSVERYLKL FTFLPLPEID HIMQLHVKEP ERRGPQKRLA
360 370 380 390 400
AEVTKLVHGR EGLDSAKRCT QALYHSSIDA LEVMSDQELK ELFKEAPFSE
410 420 430 440 450
FFLDPGTSVL DTCRKANAIP DGPRGYRMIT EGGVSINHQQ VTNPESVLIV
460 470
GQHILKNGLS LLKIGKRNFY IIKWLQL
Length:477
Mass (Da):53,199
Last modified:July 19, 2004 - v2
Checksum:iC513B8FE1E7A09E4
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti1 – 4MAAP → MGA in AAD27714 (PubMed:10810093).Curated4
Sequence conflicti118R → A in AAD27714 (PubMed:10810093).Curated1
Sequence conflicti272P → T in AAD27714 (PubMed:10810093).Curated1
Sequence conflicti311D → E in AAD27714 (PubMed:10810093).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_06864646G → D in MLASA2. 1 PublicationCorresponds to variant dbSNP:rs587777213Ensembl.1
Natural variantiVAR_06418852F → L in MLASA2; has a 2-fold reduction in catalytic activity and a reduction in affinity for tRNA-tyr resulting in an overall 9-fold loss of catalytic efficiency. 1 PublicationCorresponds to variant dbSNP:rs267607180Ensembl.1
Natural variantiVAR_034534191G → V1 PublicationCorresponds to variant dbSNP:rs11539445Ensembl.1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF132939 mRNA. Translation: AAD27714.1.
AK024057 mRNA. Translation: BAB14806.1.
AC087588 Genomic DNA. No translation available.
CH471116 Genomic DNA. Translation: EAW88517.1.
CH471116 Genomic DNA. Translation: EAW88518.1.
BC015625 mRNA. Translation: AAH15625.1.
CCDSiCCDS31770.1.
RefSeqiNP_001035526.1. NM_001040436.2.
UniGeneiHs.505231.
Hs.706015.

Genome annotation databases

EnsembliENST00000324868; ENSP00000320658; ENSG00000139131.
GeneIDi51067.
KEGGihsa:51067.
UCSCiuc001rli.4. human.

Keywords - Coding sequence diversityi

Polymorphism

Similar proteinsi

Entry informationi

Entry nameiSYYM_HUMAN
AccessioniPrimary (citable) accession number: Q9Y2Z4
Secondary accession number(s): D3DUW8, Q9H817
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 19, 2004
Last sequence update: July 19, 2004
Last modified: September 27, 2017
This is version 149 of the entry and version 2 of the sequence. See 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, Reference proteome

Documents

  1. Aminoacyl-tRNA synthetases
    List of aminoacyl-tRNA synthetase entries
  2. Human chromosome 12
    Human chromosome 12: 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