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Protein

Proline--tRNA ligase

Gene

proS

Organism
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Status
Reviewed-Annotation score: Annotation score: 5 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 cysteine.2 Publications

Catalytic activityi

ATP + L-proline + tRNA(Pro) = AMP + diphosphate + L-prolyl-tRNA(Pro).UniRule annotation2 Publications

Kineticsi

  1. KM=0.15 mM for proline (at 60 degrees Celsius)1 Publication
  2. KM=0.02 mM for cysteine (at 60 degrees Celsius)1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei111 – 1111Proline1 Publication
    Binding sitei113 – 1131Proline1 Publication
    Binding sitei142 – 1421ATP1 Publication
    Binding sitei142 – 1421Proline1 Publication
    Binding sitei153 – 1531ATP1 Publication
    Binding sitei225 – 2251ATP1 Publication
    Binding sitei228 – 2281ATP1 Publication
    Binding sitei230 – 2301Proline1 Publication
    Binding sitei262 – 2621ATP1 Publication
    Binding sitei264 – 2641ATP1 Publication
    Metal bindingi427 – 4271Zinc; structural2 Publications
    Metal bindingi432 – 4321Zinc; structural2 Publications
    Metal bindingi458 – 4581Zinc; structural2 Publications
    Metal bindingi461 – 4611Zinc; structural2 Publications

    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, Metal-binding, Nucleotide-binding, Zinc

    Enzyme and pathway databases

    BioCyciTTHE300852:GH8R-121-MONOMER.
    BRENDAi6.1.1.15. 2305.
    SABIO-RKQ5SM28.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Proline--tRNA ligaseUniRule annotationCurated (EC:6.1.1.15UniRule annotation2 Publications)
    Alternative name(s):
    Prolyl-tRNA synthetase1 PublicationUniRule annotation
    Short name:
    ProRS1 PublicationUniRule annotation
    Gene namesi
    Name:proS
    Ordered Locus Names:TTHA0115
    OrganismiThermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
    Taxonomic identifieri300852 [NCBI]
    Taxonomic lineageiBacteriaDeinococcus-ThermusDeinococciThermalesThermaceaeThermus
    Proteomesi
    • UP000000532 Componenti: Chromosome

    Subcellular locationi

    • Cytoplasm UniRule annotation

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi477 – 4771Y → A: Slightly reduces the aminoacylation activity. 1 Publication
    Mutagenesisi477 – 4771Y → F: Little change in the aminoacylation activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 477477Proline--tRNA ligasePRO_0000248229Add
    BLAST

    Interactioni

    Subunit structurei

    Homodimer. Only one tRNA molecule binds per dimer.2 Publications

    Protein-protein interaction databases

    STRINGi300852.TTHA0115.

    Structurei

    Secondary structure

    1
    477
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi10 – 2415Combined sources
    Beta strandi27 – 304Combined sources
    Beta strandi37 – 393Combined sources
    Helixi41 – 6020Combined sources
    Beta strandi70 – 745Combined sources
    Helixi81 – 877Combined sources
    Helixi88 – 903Combined sources
    Beta strandi92 – 10817Combined sources
    Helixi113 – 12311Combined sources
    Helixi127 – 1293Combined sources
    Beta strandi132 – 14110Combined sources
    Turni149 – 1513Combined sources
    Beta strandi154 – 16714Combined sources
    Helixi168 – 19023Combined sources
    Beta strandi195 – 1984Combined sources
    Turni201 – 2033Combined sources
    Beta strandi208 – 21710Combined sources
    Beta strandi223 – 23311Combined sources
    Helixi235 – 2395Combined sources
    Beta strandi243 – 2453Combined sources
    Beta strandi251 – 2533Combined sources
    Beta strandi255 – 2628Combined sources
    Helixi264 – 27310Combined sources
    Beta strandi278 – 2803Combined sources
    Turni283 – 2853Combined sources
    Beta strandi289 – 2946Combined sources
    Turni298 – 3003Combined sources
    Helixi301 – 31717Combined sources
    Beta strandi322 – 3243Combined sources
    Beta strandi328 – 3303Combined sources
    Helixi332 – 34110Combined sources
    Beta strandi345 – 3506Combined sources
    Helixi352 – 3565Combined sources
    Beta strandi359 – 3646Combined sources
    Turni365 – 3673Combined sources
    Beta strandi371 – 3733Combined sources
    Helixi374 – 3763Combined sources
    Helixi377 – 40226Combined sources
    Beta strandi404 – 4063Combined sources
    Helixi410 – 4167Combined sources
    Turni417 – 4193Combined sources
    Beta strandi420 – 4245Combined sources
    Helixi430 – 44011Combined sources
    Beta strandi443 – 4519Combined sources
    Turni459 – 4613Combined sources
    Beta strandi471 – 4744Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1H4QX-ray3.00A/B1-477[»]
    1H4SX-ray2.85A/B1-477[»]
    1H4TX-ray2.90A/B/C/D1-477[»]
    1HC7X-ray2.43A/B/C/D1-477[»]
    ProteinModelPortaliQ5SM28.
    SMRiQ5SM28. Positions 5-477.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ5SM28.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni340 – 36930Interaction with tRNAAdd
    BLAST

    Domaini

    Consists of three domains: the N-terminal catalytic domain, the anticodon-binding domain and the C-terminal extension. The C-terminal extension binds a zinc ion, which probably plays a non-essential structural role in stabilizing the fold of C-terminal domain.

    Sequence similaritiesi

    Belongs to the class-II aminoacyl-tRNA synthetase family. ProS type 3 subfamily.UniRule annotationCurated

    Phylogenomic databases

    eggNOGiENOG4107R1M. Bacteria.
    COG0442. LUCA.
    HOGENOMiHOG000167538.
    KOiK01881.
    OMAiVYWGKAY.
    OrthoDBiEOG6G7R2R.
    PhylomeDBiQ5SM28.

    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.
    [Graphical view]
    PANTHERiPTHR11451:SF6. PTHR11451:SF6. 1 hit.
    PfamiPF03129. HGTP_anticodon. 1 hit.
    PF09180. ProRS-C_1. 1 hit.
    PF00587. tRNA-synt_2b. 1 hit.
    [Graphical view]
    PRINTSiPR01046. TRNASYNTHPRO.
    SMARTiSM00946. ProRS-C_1. 1 hit.
    [Graphical view]
    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.

    Q5SM28-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MAKEKGLTPQ SQDFSEWYLE VIQKAELADY GPVRGTIVVR PYGYAIWENI
    60 70 80 90 100
    QQVLDRMFKE TGHQNAYFPL FIPMSFLRKE AEHVEGFSPE LAVVTHAGGE
    110 120 130 140 150
    ELEEPLAVRP TSETVIGYMW SKWIRSWRDL PQLLNQWGNV VRWEMRTRPF
    160 170 180 190 200
    LRTSEFLWQE GHTAHATREE AEEEVRRMLS IYARLAREYA AIPVIEGLKT
    210 220 230 240 250
    EKEKFAGAVY TTTIEALMKD GKALQAGTSH YLGENFARAF DIKFQDRDLQ
    260 270 280 290 300
    VKYVHTTSWG LSWRFIGAII MTHGDDRGLV LPPRLAPIQV VIVPIYKDES
    310 320 330 340 350
    RERVLEAAQG LRQALLAQGL RVHLDDRDQH TPGYKFHEWE LKGVPFRVEL
    360 370 380 390 400
    GPKDLEGGQA VLASRLGGKE TLPLAALPEA LPGKLDAFHE ELYRRALAFR
    410 420 430 440 450
    EDHTRKVDTY EAFKEAVQEG FALAFHCGDK ACERLIQEET TATTRCVPFE
    460 470
    AEPEEGFCVR CGRPSAYGKR VVFAKAY
    Length:477
    Mass (Da):54,488
    Last modified:December 21, 2004 - v1
    Checksum:i6AA477F1EC4D12F5
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AF384553 Genomic DNA. Translation: AAK62359.1.
    AP008226 Genomic DNA. Translation: BAD69938.1.
    RefSeqiWP_011227720.1. NC_006461.1.
    YP_143381.1. NC_006461.1.

    Genome annotation databases

    EnsemblBacteriaiBAD69938; BAD69938; BAD69938.
    GeneIDi3169620.
    KEGGittj:TTHA0115.
    PATRICi23955165. VBITheThe93045_0113.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AF384553 Genomic DNA. Translation: AAK62359.1.
    AP008226 Genomic DNA. Translation: BAD69938.1.
    RefSeqiWP_011227720.1. NC_006461.1.
    YP_143381.1. NC_006461.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1H4QX-ray3.00A/B1-477[»]
    1H4SX-ray2.85A/B1-477[»]
    1H4TX-ray2.90A/B/C/D1-477[»]
    1HC7X-ray2.43A/B/C/D1-477[»]
    ProteinModelPortaliQ5SM28.
    SMRiQ5SM28. Positions 5-477.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi300852.TTHA0115.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiBAD69938; BAD69938; BAD69938.
    GeneIDi3169620.
    KEGGittj:TTHA0115.
    PATRICi23955165. VBITheThe93045_0113.

    Phylogenomic databases

    eggNOGiENOG4107R1M. Bacteria.
    COG0442. LUCA.
    HOGENOMiHOG000167538.
    KOiK01881.
    OMAiVYWGKAY.
    OrthoDBiEOG6G7R2R.
    PhylomeDBiQ5SM28.

    Enzyme and pathway databases

    BioCyciTTHE300852:GH8R-121-MONOMER.
    BRENDAi6.1.1.15. 2305.
    SABIO-RKQ5SM28.

    Miscellaneous databases

    EvolutionaryTraceiQ5SM28.

    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.
    [Graphical view]
    PANTHERiPTHR11451:SF6. PTHR11451:SF6. 1 hit.
    PfamiPF03129. HGTP_anticodon. 1 hit.
    PF09180. ProRS-C_1. 1 hit.
    PF00587. tRNA-synt_2b. 1 hit.
    [Graphical view]
    PRINTSiPR01046. TRNASYNTHPRO.
    SMARTiSM00946. ProRS-C_1. 1 hit.
    [Graphical view]
    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. "Aminoacyl-tRNA formation in the hyperthermophile Thermus thermophilus."
      Ahel I., Stathopoulos C., Hartsch T., Soell D.
      Submitted (MAY-2001) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "Complete genome sequence of Thermus thermophilus HB8."
      Masui R., Kurokawa K., Nakagawa N., Tokunaga F., Koyama Y., Shibata T., Oshima T., Yokoyama S., Yasunaga T., Kuramitsu S.
      Submitted (NOV-2004) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: HB8 / ATCC 27634 / DSM 579.
    3. "Aminoacyl-tRNA formation in the extreme thermophile Thermus thermophilus."
      Feng L., Stathopoulos C., Ahel I., Mitra A., Tumbula-Hansen D., Hartsch T., Soell D.
      Extremophiles 6:167-174(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROLINE AND CYSTEINE ACTIVATION, FUNCTION, CATALYTIC ACTIVITY.
    4. "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: PROLINE AND CYSTEINE ACTIVATION, FUNCTION, CATALYTIC ACTIVITY, KINETIC PARAMETERS.
    5. "Crystal structure of a eukaryote/archaeon-like prolyl-tRNA synthetase and its complex with tRNAPro(CGG)."
      Yaremchuk A., Cusack S., Tukalo M.
      EMBO J. 19:4745-4758(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.43 ANGSTROMS) OF APOENZYME AND IN COMPLEX WITH ZINC IONS AND TRNA, MUTAGENESIS OF TYR-477, SUBUNIT.
    6. "A succession of substrate induced conformational changes ensures the amino acid specificity of Thermus thermophilus prolyl-tRNA synthetase: comparison with histidyl-tRNA synthetase."
      Yaremchuk A., Tukalo M., Groetli M., Cusack S.
      J. Mol. Biol. 309:989-1002(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.85 ANGSTROMS) IN COMPLEX WITH PROLINE; ZINC IONS, TRNA AND PRO-AMP ANALOGS, SUBUNIT.

    Entry informationi

    Entry nameiSYP_THET8
    AccessioniPrimary (citable) accession number: Q5SM28
    Secondary accession number(s): Q93N97
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: September 5, 2006
    Last sequence update: December 21, 2004
    Last modified: January 20, 2016
    This is version 92 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Aminoacyl-tRNA synthetases
      List of aminoacyl-tRNA synthetase entries
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. 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.