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Protein

Phenylalanine--tRNA ligase, mitochondrial

Gene

FARS2

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

Functioni

Is responsible for the charging of tRNA(Phe) with phenylalanine in mitochondrial translation. To a lesser extent, also catalyzes direct attachment of m-Tyr (an oxidized version of Phe) to tRNA(Phe), thereby opening the way for delivery of the misacylated tRNA to the ribosome and incorporation of ROS-damaged amino acid into proteins.2 Publications

Catalytic activityi

ATP + L-phenylalanine + tRNA(Phe) = AMP + diphosphate + L-phenylalanyl-tRNA(Phe).2 Publications

Kineticsi

kcat is 2.8 min(-1), 2.0 min(-1) and 3.1 min(-1) with L-phenylalanine, L-tyrosine and m-tyrosine as substrate, respectively. Thus, the catalytic efficiency of the m-Tyr attachment is only 5-fold lower than that of the correct amino acid, while that of Tyr attachment is 1000-fold lower (PubMed:19549855).1 Publication
  1. KM=2.2 µM for L-phenylalanine2 Publications
  2. KM=1900 µM for L-tyrosine2 Publications
  3. KM=11.7 µM for DL-m-tyrosine2 Publications
  4. KM=7.3 µM for L-phenylalanine2 Publications
  5. KM=2.9 mM for ATP2 Publications
  6. KM=1.2 µM for tRNA(Phe)2 Publications

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei179Substrate2 Publications1
    Binding sitei287Substrate; via carbonyl oxygen2 Publications1
    Binding sitei312Substrate; via carbonyl oxygen2 Publications1

    GO - Molecular functioni

    • ATP binding Source: UniProtKB-KW
    • phenylalanine-tRNA ligase activity Source: UniProtKB
    • tRNA binding Source: UniProtKB

    GO - Biological processi

    • phenylalanyl-tRNA aminoacylation Source: UniProtKB
    • tRNA aminoacylation for protein translation Source: Reactome
    • tRNA processing Source: UniProtKB

    Keywordsi

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

    Enzyme and pathway databases

    BRENDAi6.1.1.20. 2681.
    ReactomeiR-HSA-379726. Mitochondrial tRNA aminoacylation.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Phenylalanine--tRNA ligase, mitochondrial (EC:6.1.1.202 Publications)
    Alternative name(s):
    Phenylalanyl-tRNA synthetase
    Short name:
    PheRS
    Gene namesi
    Name:FARS2
    Synonyms:FARS1
    ORF Names:HSPC320
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    Proteomesi
    • UP000005640 Componenti: Chromosome 6

    Organism-specific databases

    EuPathDBiHostDB:ENSG00000145982.11.
    HGNCiHGNC:21062. FARS2.

    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

    Combined oxidative phosphorylation deficiency 14 (COXPD14)2 Publications
    The disease is caused by mutations affecting the gene represented in this entry.
    Disease descriptionA severe multisystemic autosomal recessive disorder characterized by neonatal onset of global developmental delay, refractory seizures, and lactic acidosis. Biochemical studies show deficiencies of multiple mitochondrial respiratory enzymes.
    See also OMIM:614946
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Natural variantiVAR_069487144Y → C in COXPD14; results in decreased affinity for tRNA causing a decrease in the catalytic efficiency for tRNA charging; does not affect ATP or Phe binding. 2 PublicationsCorresponds to variant dbSNP:rs397514610Ensembl.1
    Natural variantiVAR_069488329I → T in COXPD14; results in a 4-fold decrease in the catalytic efficiency of amino acid activation mainly due to a decreased affinity for ATP; does not affect Phe binding; affects the stability of the enzyme, leading to a significant decrease in overall charging capacity. 1 PublicationCorresponds to variant dbSNP:rs397514611Ensembl.1
    Natural variantiVAR_069489391D → V in COXPD14; results in a decrease in affinity for Phe causing a decrease in aminoacylation activity; affects the stability of the enzyme, leading to a significant decrease in overall charging capacity. 1 PublicationCorresponds to variant dbSNP:rs397514612Ensembl.1
    Spastic paraplegia 77, autosomal recessive (SPG77)1 Publication
    The disease is caused by mutations affecting the gene represented in this entry.
    Disease descriptionA form of spastic paraplegia, a neurodegenerative disorder characterized by a slow, gradual, progressive weakness and spasticity of the lower limbs. Rate of progression and the severity of symptoms are quite variable. Initial symptoms may include difficulty with balance, weakness and stiffness in the legs, muscle spasms, and dragging the toes when walking. In some forms of the disorder, bladder symptoms (such as incontinence) may appear, or the weakness and stiffness may spread to other parts of the body.
    See also OMIM:617046
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Natural variantiVAR_077044142D → Y in SPG77; resulted in severely impaired phenylalanine-tRNA ligase activity. 1 Publication1

    Keywords - Diseasei

    Disease mutation, Hereditary spastic paraplegia, Neurodegeneration, Primary mitochondrial disease

    Organism-specific databases

    DisGeNETi10667.
    MalaCardsiFARS2.
    MIMi614946. phenotype.
    617046. phenotype.
    OpenTargetsiENSG00000145982.
    Orphaneti319519. Combined oxidative phosphorylation defect type 14.
    PharmGKBiPA134954893.

    Chemistry databases

    ChEMBLiCHEMBL2511.
    DrugBankiDB00120. L-Phenylalanine.

    Polymorphism and mutation databases

    BioMutaiFARS2.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_0000035813? – 451Phenylalanine--tRNA ligase, mitochondrial
    Transit peptidei1 – ?MitochondrionSequence analysis

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Modified residuei202N6-acetyllysineCombined sources1

    Keywords - PTMi

    Acetylation

    Proteomic databases

    EPDiO95363.
    MaxQBiO95363.
    PaxDbiO95363.
    PeptideAtlasiO95363.
    PRIDEiO95363.

    PTM databases

    iPTMnetiO95363.
    PhosphoSitePlusiO95363.

    Expressioni

    Gene expression databases

    BgeeiENSG00000145982.
    CleanExiHS_FARS2.
    ExpressionAtlasiO95363. baseline and differential.
    GenevisibleiO95363. HS.

    Organism-specific databases

    HPAiHPA018148.
    HPA028836.

    Interactioni

    Subunit structurei

    Monomer.3 Publications

    Binary interactionsi

    Show more details

    Protein-protein interaction databases

    BioGridi115909. 52 interactors.
    IntActiO95363. 68 interactors.
    MINTiMINT-3077661.
    STRINGi9606.ENSP00000274680.

    Chemistry databases

    BindingDBiO95363.

    Structurei

    Secondary structure

    1451
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi49 – 53Combined sources5
    Beta strandi56 – 59Combined sources4
    Helixi68 – 71Combined sources4
    Turni72 – 75Combined sources4
    Helixi78 – 80Combined sources3
    Beta strandi81 – 84Combined sources4
    Helixi85 – 103Combined sources19
    Beta strandi105 – 107Combined sources3
    Beta strandi111 – 113Combined sources3
    Beta strandi118 – 121Combined sources4
    Helixi122 – 125Combined sources4
    Helixi127 – 129Combined sources3
    Helixi136 – 138Combined sources3
    Helixi140 – 142Combined sources3
    Beta strandi145 – 152Combined sources8
    Helixi156 – 159Combined sources4
    Helixi160 – 165Combined sources6
    Beta strandi169 – 178Combined sources10
    Beta strandi184 – 186Combined sources3
    Beta strandi189 – 201Combined sources13
    Helixi202 – 205Combined sources4
    Turni206 – 208Combined sources3
    Helixi212 – 214Combined sources3
    Helixi233 – 255Combined sources23
    Helixi256 – 258Combined sources3
    Beta strandi261 – 268Combined sources8
    Beta strandi271 – 281Combined sources11
    Beta strandi284 – 294Combined sources11
    Helixi296 – 301Combined sources6
    Beta strandi307 – 315Combined sources9
    Helixi316 – 323Combined sources8
    Helixi329 – 333Combined sources5
    Helixi337 – 340Combined sources4
    Helixi341 – 343Combined sources3
    Beta strandi363 – 370Combined sources8
    Helixi378 – 389Combined sources12
    Helixi390 – 392Combined sources3
    Beta strandi393 – 403Combined sources11
    Turni405 – 407Combined sources3
    Beta strandi410 – 418Combined sources9
    Beta strandi421 – 423Combined sources3
    Helixi427 – 444Combined sources18
    Beta strandi448 – 451Combined sources4

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    3CMQX-ray2.20A38-451[»]
    3HFVX-ray2.60A38-451[»]
    3TEGX-ray2.20A38-451[»]
    3TUPX-ray3.05A38-451[»]
    5MGHX-ray1.87A47-451[»]
    5MGUX-ray1.89A46-451[»]
    5MGVX-ray2.05A47-451[»]
    5MGWX-ray1.46A46-451[»]
    ProteinModelPortaliO95363.
    SMRiO95363.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiO95363.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Domaini358 – 450FDX-ACBPROSITE-ProRule annotationAdd BLAST93

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni157 – 160Substrate binding4
    Regioni186 – 188Substrate binding3
    Regioni193 – 195Substrate binding3

    Sequence similaritiesi

    Keywords - Domaini

    Transit peptide

    Phylogenomic databases

    eggNOGiKOG2783. Eukaryota.
    COG0016. LUCA.
    COG0072. LUCA.
    GeneTreeiENSGT00530000063467.
    HOGENOMiHOG000165163.
    HOVERGENiHBG082540.
    InParanoidiO95363.
    KOiK01889.
    OMAiVKLMEHE.
    OrthoDBiEOG091G07OD.
    PhylomeDBiO95363.
    TreeFamiTF105798.

    Family and domain databases

    Gene3Di3.30.70.380. 1 hit.
    InterProiView protein in InterPro
    IPR006195. aa-tRNA-synth_II.
    IPR005121. Fdx_antiC-bd.
    IPR036690. Fdx_antiC-bd_sf.
    IPR004530. Phe-tRNA-synth_IIc_mito.
    IPR002319. Phenylalanyl-tRNA_Synthase.
    PANTHERiPTHR11538:SF41. PTHR11538:SF41. 1 hit.
    PfamiView protein in Pfam
    PF03147. FDX-ACB. 1 hit.
    PF01409. tRNA-synt_2d. 2 hits.
    SMARTiView protein in SMART
    SM00896. FDX-ACB. 1 hit.
    SUPFAMiSSF54991. SSF54991. 1 hit.
    TIGRFAMsiTIGR00469. pheS_mito. 1 hit.
    PROSITEiView protein in PROSITE
    PS50862. AA_TRNA_LIGASE_II. 1 hit.
    PS51447. FDX_ACB. 1 hit.

    Sequencei

    Sequence statusi: Complete.

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

    O95363-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MVGSALRRGA HAYVYLVSKA SHISRGHQHQ AWGSRPPAAE CATQRAPGSV
    60 70 80 90 100
    VELLGKSYPQ DDHSNLTRKV LTRVGRNLHN QQHHPLWLIK ERVKEHFYKQ
    110 120 130 140 150
    YVGRFGTPLF SVYDNLSPVV TTWQNFDSLL IPADHPSRKK GDNYYLNRTH
    160 170 180 190 200
    MLRAHTSAHQ WDLLHAGLDA FLVVGDVYRR DQIDSQHYPI FHQLEAVRLF
    210 220 230 240 250
    SKHELFAGIK DGESLQLFEQ SSRSAHKQET HTMEAVKLVE FDLKQTLTRL
    260 270 280 290 300
    MAHLFGDELE IRWVDCYFPF THPSFEMEIN FHGEWLEVLG CGVMEQQLVN
    310 320 330 340 350
    SAGAQDRIGW AFGLGLERLA MILYDIPDIR LFWCEDERFL KQFCVSNINQ
    360 370 380 390 400
    KVKFQPLSKY PAVINDISFW LPSENYAEND FYDLVRTIGG DLVEKVDLID
    410 420 430 440 450
    KFVHPKTHKT SHCYRITYRH MERTLSQREV RHIHQALQEA AVQLLGVEGR

    F
    Length:451
    Mass (Da):52,357
    Last modified:May 1, 1999 - v1
    Checksum:i1E5CC647A4A7193B
    GO

    Sequence cautioni

    The sequence AAF28998 differs from that shown. Reason: Frameshift at position 414.Curated

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti158A → T in BAD97143 (Ref. 4) Curated1
    Sequence conflicti361P → T in AAF28998 (Ref. 7) Curated1

    Natural variant

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Natural variantiVAR_05264257S → C. Corresponds to variant dbSNP:rs34382405Ensembl.1
    Natural variantiVAR_077044142D → Y in SPG77; resulted in severely impaired phenylalanine-tRNA ligase activity. 1 Publication1
    Natural variantiVAR_069487144Y → C in COXPD14; results in decreased affinity for tRNA causing a decrease in the catalytic efficiency for tRNA charging; does not affect ATP or Phe binding. 2 PublicationsCorresponds to variant dbSNP:rs397514610Ensembl.1
    Natural variantiVAR_052643280N → S3 PublicationsCorresponds to variant dbSNP:rs11243011Ensembl.1
    Natural variantiVAR_069488329I → T in COXPD14; results in a 4-fold decrease in the catalytic efficiency of amino acid activation mainly due to a decreased affinity for ATP; does not affect Phe binding; affects the stability of the enzyme, leading to a significant decrease in overall charging capacity. 1 PublicationCorresponds to variant dbSNP:rs397514611Ensembl.1
    Natural variantiVAR_069489391D → V in COXPD14; results in a decrease in affinity for Phe causing a decrease in aminoacylation activity; affects the stability of the enzyme, leading to a significant decrease in overall charging capacity. 1 PublicationCorresponds to variant dbSNP:rs397514612Ensembl.1

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AF097441 mRNA. Translation: AAC83802.1.
    AK312454 mRNA. Translation: BAG35361.1.
    CR542279 mRNA. Translation: CAG47075.1.
    AK223423 mRNA. Translation: BAD97143.1.
    AL133473 Genomic DNA. No translation available.
    AL022097 Genomic DNA. No translation available.
    AL392184 Genomic DNA. No translation available.
    AL121978 Genomic DNA. No translation available.
    AL590868 Genomic DNA. No translation available.
    BC020239 mRNA. Translation: AAH20239.1.
    BC021112 mRNA. Translation: AAH21112.1.
    AF161438 mRNA. Translation: AAF28998.1. Frameshift.
    CCDSiCCDS4494.1.
    RefSeqiNP_001305801.1. NM_001318872.1.
    NP_006558.1. NM_006567.4.
    XP_005248869.1. XM_005248812.3.
    XP_016865675.1. XM_017010186.1.
    XP_016865676.1. XM_017010187.1.
    UniGeneiHs.484547.

    Genome annotation databases

    EnsembliENST00000274680; ENSP00000274680; ENSG00000145982.
    ENST00000324331; ENSP00000316335; ENSG00000145982.
    GeneIDi10667.
    KEGGihsa:10667.
    UCSCiuc003mwr.3. human.

    Keywords - Coding sequence diversityi

    Polymorphism

    Similar proteinsi

    Entry informationi

    Entry nameiSYFM_HUMAN
    AccessioniPrimary (citable) accession number: O95363
    Secondary accession number(s): B2R664
    , Q53F66, Q5TCS3, Q6FG29, Q9NPY7, Q9P062
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 23, 2004
    Last sequence update: May 1, 1999
    Last modified: November 22, 2017
    This is version 161 of the entry and version 1 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 6
      Human chromosome 6: 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