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Protein

Proline--tRNA ligase

Gene

proS

Organism
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the attachment of proline to tRNA(Pro) in a two-step reaction: proline is first activated by ATP to form Pro-AMP and then transferred to the acceptor end of tRNA(Pro). Can inadvertently accommodate and process non-cognate amino acids such as cysteine and alanine.4 Publications

Catalytic activityi

ATP + L-proline + tRNA(Pro) = AMP + diphosphate + L-prolyl-tRNA(Pro).

Enzyme regulationi

Inhibited by high concentrations of prolinamide.

Kineticsi

  1. KM=0.28 mM for proline (at 60 degrees Celsius)3 Publications
  2. KM=0.09 mM for cysteine (at 60 degrees Celsius)3 Publications

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei101 – 1011ProlineBy similarity
    Binding sitei103 – 1031ProlineBy similarity
    Binding sitei132 – 1321ATPBy similarity
    Binding sitei132 – 1321ProlineBy similarity
    Binding sitei134 – 1341ATPBy similarity
    Binding sitei216 – 2161ATPBy similarity
    Binding sitei219 – 2191ATPBy similarity
    Binding sitei221 – 2211ProlineBy similarity
    Binding sitei253 – 2531ATPBy similarity
    Binding sitei255 – 2551ATPBy similarity

    GO - Molecular functioni

    GO - Biological processi

    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

    BRENDAi6.1.1.15. 3260.
    SABIO-RKQ58635.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Proline--tRNA ligase (EC:6.1.1.15)
    Alternative name(s):
    Prolyl-tRNA synthetase
    Short name:
    ProRS
    Gene namesi
    Name:proS
    Ordered Locus Names:MJ1238
    OrganismiMethanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii)
    Taxonomic identifieri243232 [NCBI]
    Taxonomic lineageiArchaeaEuryarchaeotaMethanococciMethanococcalesMethanocaldococcaceaeMethanocaldococcus
    Proteomesi
    • UP000000805 Componenti: Chromosome

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 455455Proline--tRNA ligasePRO_0000139351Add
    BLAST

    Interactioni

    Subunit structurei

    Homodimer. The dimer is functionally asymmetric: only one of the two active sites at a time is able to form prolyl-adenylate, and only one tRNA molecule binds per dimer.2 Publications

    Protein-protein interaction databases

    STRINGi243232.MJ_1238.

    Structurei

    Secondary structure

    1
    455
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi3 – 1311Combined sources
    Helixi31 – 5020Combined sources
    Beta strandi60 – 634Combined sources
    Helixi64 – 707Combined sources
    Beta strandi72 – 743Combined sources
    Helixi75 – 806Combined sources
    Beta strandi82 – 9817Combined sources
    Beta strandi100 – 1023Combined sources
    Helixi103 – 1119Combined sources
    Beta strandi124 – 1285Combined sources
    Turni140 – 1423Combined sources
    Beta strandi150 – 15910Combined sources
    Helixi160 – 18122Combined sources
    Beta strandi186 – 1905Combined sources
    Beta strandi200 – 2089Combined sources
    Beta strandi214 – 22411Combined sources
    Helixi226 – 2305Combined sources
    Beta strandi234 – 2363Combined sources
    Beta strandi240 – 2445Combined sources
    Beta strandi246 – 2527Combined sources
    Helixi255 – 26410Combined sources
    Beta strandi278 – 2858Combined sources
    Helixi292 – 30716Combined sources
    Beta strandi312 – 3143Combined sources
    Helixi321 – 33010Combined sources
    Beta strandi334 – 3396Combined sources
    Helixi341 – 3455Combined sources
    Beta strandi348 – 3536Combined sources
    Turni354 – 3563Combined sources
    Beta strandi359 – 3635Combined sources
    Helixi367 – 39327Combined sources
    Beta strandi394 – 3963Combined sources
    Helixi402 – 4087Combined sources
    Turni409 – 4124Combined sources
    Beta strandi414 – 4196Combined sources
    Helixi422 – 4243Combined sources
    Helixi427 – 4337Combined sources
    Beta strandi437 – 4426Combined sources
    Beta strandi444 – 4529Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1NJ8X-ray3.20A/B/C/D2-455[»]
    ProteinModelPortaliQ58635.
    SMRiQ58635. Positions 1-455.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ58635.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni329 – 35931Interaction with tRNABy similarityAdd
    BLAST

    Domaini

    Consists of three domains: the N-terminal catalytic domain, the anticodon-binding domain and the C-terminal extension.

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiarCOG00402. Archaea.
    COG0442. LUCA.
    InParanoidiQ58635.
    KOiK01881.
    OMAiQNSPGWK.
    PhylomeDBiQ58635.

    Family and domain databases

    Gene3Di3.30.110.30. 1 hit.
    3.40.50.800. 1 hit.
    HAMAPiMF_01571. Pro_tRNA_synth_type3.
    InterProiIPR002314. aa-tRNA-synt_IIb.
    IPR006195. aa-tRNA-synth_II.
    IPR004154. Anticodon-bd.
    IPR002316. Pro-tRNA-ligase_IIa.
    IPR004499. Pro-tRNA-ligase_IIa_arc-type.
    IPR016061. Pro-tRNA_ligase_II_C.
    IPR017449. Pro-tRNA_synth_II.
    IPR015264. Pro-tRNA_synth_II_arc.
    [Graphical view]
    PANTHERiPTHR11451:SF6. PTHR11451:SF6. 1 hit.
    PfamiPF03129. HGTP_anticodon. 1 hit.
    PF09181. ProRS-C_2. 1 hit.
    PF00587. tRNA-synt_2b. 1 hit.
    [Graphical view]
    PRINTSiPR01046. TRNASYNTHPRO.
    SUPFAMiSSF52954. SSF52954. 1 hit.
    SSF64586. SSF64586. 1 hit.
    TIGRFAMsiTIGR00408. proS_fam_I. 1 hit.
    PROSITEiPS50862. AA_TRNA_LIGASE_II. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q58635-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MEFSEWYSDI LEKAEIYDVR YPIKGCGVYL PYGFKIRRYT FEIIRNLLDE
    60 70 80 90 100
    SGHDEALFPM LIPEDLLAKE AEHIKGFEDE VYWVTHGGKT QLDVKLALRP
    110 120 130 140 150
    TSETPIYYMM KLWVKVHTDL PIKIYQIVNT FRYETKHTRP LIRLREIMTF
    160 170 180 190 200
    KEAHTAHSTK EEAENQVKEA ISIYKKFFDT LGIPYLISKR PEWDKFPGAE
    210 220 230 240 250
    YTMAFDTIFP DGRTMQIATV HNLGQNFSKT FEIIFETPTG DKDYAYQTCY
    260 270 280 290 300
    GISDRVIASI IAIHGDEKGL ILPPIVAPIQ VVIVPLIFKG KEDIVMEKAK
    310 320 330 340 350
    EIYEKLKGKF RVHIDDRDIR PGRKFNDWEI KGVPLRIEVG PKDIENKKIT
    360 370 380 390 400
    LFRRDTMEKF QVDETQLMEV VEKTLNNIME NIKNRAWEKF ENFITILEDI
    410 420 430 440 450
    NPDEIKNILS EKRGVILVPF KEEIYNEELE EKVEATILGE TEYKGNKYIA

    IAKTY
    Length:455
    Mass (Da):53,309
    Last modified:November 1, 1996 - v1
    Checksum:i3D155A36AFE0CC3B
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    L77117 Genomic DNA. Translation: AAB99242.1.
    PIRiE64454.

    Genome annotation databases

    EnsemblBacteriaiAAB99242; AAB99242; MJ_1238.
    KEGGimja:MJ_1238.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    L77117 Genomic DNA. Translation: AAB99242.1.
    PIRiE64454.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1NJ8X-ray3.20A/B/C/D2-455[»]
    ProteinModelPortaliQ58635.
    SMRiQ58635. Positions 1-455.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi243232.MJ_1238.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAB99242; AAB99242; MJ_1238.
    KEGGimja:MJ_1238.

    Phylogenomic databases

    eggNOGiarCOG00402. Archaea.
    COG0442. LUCA.
    InParanoidiQ58635.
    KOiK01881.
    OMAiQNSPGWK.
    PhylomeDBiQ58635.

    Enzyme and pathway databases

    BRENDAi6.1.1.15. 3260.
    SABIO-RKQ58635.

    Miscellaneous databases

    EvolutionaryTraceiQ58635.

    Family and domain databases

    Gene3Di3.30.110.30. 1 hit.
    3.40.50.800. 1 hit.
    HAMAPiMF_01571. Pro_tRNA_synth_type3.
    InterProiIPR002314. aa-tRNA-synt_IIb.
    IPR006195. aa-tRNA-synth_II.
    IPR004154. Anticodon-bd.
    IPR002316. Pro-tRNA-ligase_IIa.
    IPR004499. Pro-tRNA-ligase_IIa_arc-type.
    IPR016061. Pro-tRNA_ligase_II_C.
    IPR017449. Pro-tRNA_synth_II.
    IPR015264. Pro-tRNA_synth_II_arc.
    [Graphical view]
    PANTHERiPTHR11451:SF6. PTHR11451:SF6. 1 hit.
    PfamiPF03129. HGTP_anticodon. 1 hit.
    PF09181. ProRS-C_2. 1 hit.
    PF00587. tRNA-synt_2b. 1 hit.
    [Graphical view]
    PRINTSiPR01046. TRNASYNTHPRO.
    SUPFAMiSSF52954. SSF52954. 1 hit.
    SSF64586. SSF64586. 1 hit.
    TIGRFAMsiTIGR00408. proS_fam_I. 1 hit.
    PROSITEiPS50862. AA_TRNA_LIGASE_II. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440.
    2. "One polypeptide with two aminoacyl-tRNA synthetase activities."
      Stathopoulos C., Li T., Longman R., Vothknecht U.C., Becker H.D., Ibba M., Soell D.
      Science 287:479-482(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 1-18, FUNCTION AS A PROLYL-TRNA SYNTHETASE, PUTATIVE FUNCTION AS A CYSTEINYL-TRNA SYNTHETASE.
    3. "Synthesis of cysteinyl-tRNA(Cys) by a genome that lacks the normal cysteine-tRNA synthetase."
      Lipman R.S.A., Sowers K.R., Hou Y.-M.
      Biochemistry 39:7792-7798(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION AS A PROLYL-TRNA SYNTHETASE, PUTATIVE FUNCTION AS A CYSTEINYL-TRNA SYNTHETASE, INHIBITION BY PROLINAMIDE.
      Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440.
    4. "Methanococcus jannaschii prolyl-cysteinyl-tRNA synthetase possesses overlapping amino acid binding sites."
      Stathopoulos C., Jacquin-Becker C., Becker H.D., Li T., Ambrogelly A., Longman R., Soell D.
      Biochemistry 40:46-52(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION AS A PROLYL-TRNA SYNTHETASE, PUTATIVE FUNCTION AS A CYSTEINYL-TRNA SYNTHETASE, KINETIC PARAMETERS.
    5. "Species-specific differences in amino acid editing by class II prolyl-tRNA synthetase."
      Beuning P.J., Musier-Forsyth K.
      J. Biol. Chem. 276:30779-30785(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: MISAMINOACYLATION OF TRNA(PRO) WITH ALANINE OR CYSTEINE, EDITING ACTIVITY AGAINST ALANINE, KINETIC PARAMETERS.
    6. "Cysteine activation is an inherent in vitro property of prolyl-tRNA synthetases."
      Ahel I., Stathopoulos C., Ambrogelly A., Sauerwald A., Toogood H., Hartsch T., Soell D.
      J. Biol. Chem. 277:34743-34748(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: MISAMINOACYLATION OF TRNA(PRO) WITH CYSTEINE, KINETIC PARAMETERS.
    7. Cited for: MISAMINOACYLATION OF TRNA(PRO) WITH CYSTEINE, INABILITY TO SYNTHESIZE CYSTEINYL-TRNA(CYS), LACK OF EDITING ACTIVITY.
    8. "Amino acid activation of a dual-specificity tRNA synthetase is independent of tRNA."
      Lipman R.S.A., Beuning P.J., Musier-Forsyth K., Hou Y.-M.
      J. Mol. Biol. 316:421-427(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION IN CYSTEINE ACTIVATION.
    9. "Cysteinyl-tRNA(Cys) formation in Methanocaldococcus jannaschii: the mechanism is still unknown."
      Ruan B., Nakano H., Tanaka M., Mills J.A., DeVito J.A., Min B., Low K.B., Battista J.R., Soell D.
      J. Bacteriol. 186:8-14(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: INABILITY TO SYNTHESIZE CYSTEINYL-TRNA(CYS).
    10. "Asymmetric behavior of archaeal prolyl-tRNA synthetase."
      Ambrogelly A., Kamtekar S., Stathopoulos C., Kennedy D., Soell D.
      FEBS Lett. 579:6017-6022(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBUNIT.
    11. "The structural basis of cysteine aminoacylation of tRNAPro by prolyl-tRNA synthetases."
      Kamtekar S., Kennedy W.D., Wang J., Stathopoulos C., Soell D., Steitz T.A.
      Proc. Natl. Acad. Sci. U.S.A. 100:1673-1678(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (3.2 ANGSTROMS) OF APOENZYME, SUBUNIT.

    Entry informationi

    Entry nameiSYP_METJA
    AccessioniPrimary (citable) accession number: Q58635
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1997
    Last sequence update: November 1, 1996
    Last modified: June 8, 2016
    This is version 116 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Caution

    Was originally (PubMed:10642548, PubMed:10869184 and PubMed:11141055) thought to have both prolyl- and cysteinyl-tRNA synthetase activities (ProCysRS). However, recent biochemical and structural studies show that ProRS misaminoacylates tRNA(Pro) with cysteine but is unable to aminoacylate tRNA(Cys). These conflicting results may be due to the fact that much of the previous work was done with unfractionated tRNA.Curated
    According to PubMed:12130658, ProRS is unable to edit the misacylated Cys-tRNA(Pro) and Ala-tRNA(Pro), whereas according to PubMed:11408489, it hydrolyzes Ala-AMP and Ala-tRNA(Pro) by 'pretransfer' and 'posttransfer' editing activities, respectively.Curated

    Keywords - Technical termi

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

    Documents

    1. Aminoacyl-tRNA synthetases
      List of aminoacyl-tRNA synthetase entries
    2. Methanococcus jannaschii
      Methanococcus jannaschii: entries and gene names
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. 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.