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P34945

- SYS_THET2

UniProt

P34945 - SYS_THET2

Protein

Serine--tRNA ligase

Gene

serS

Organism
Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 111 (01 Oct 2014)
      Sequence version 2 (24 May 2004)
      Previous versions | rss
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    Functioni

    Catalyzes the attachment of serine to tRNA(Ser). Is also probably able to aminoacylate tRNA(Sec) with serine, to form the misacylated tRNA L-seryl-tRNA(Sec), which will be further converted into selenocysteinyl-tRNA(Sec).

    Catalytic activityi

    ATP + L-serine + tRNA(Ser) = AMP + diphosphate + L-seryl-tRNA(Ser).
    ATP + L-serine + tRNA(Sec) = AMP + diphosphate + L-seryl-tRNA(Sec).

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei272 – 2721ATP; via amide nitrogen and carbonyl oxygen
    Binding sitei279 – 2791Serine
    Binding sitei380 – 3801Serine

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi256 – 2583ATP
    Nucleotide bindingi345 – 3484ATP

    GO - Molecular functioni

    1. ATP binding Source: UniProtKB-HAMAP
    2. serine-tRNA ligase activity Source: UniProtKB-HAMAP

    GO - Biological processi

    1. selenocysteine biosynthetic process Source: UniProtKB-HAMAP
    2. selenocysteinyl-tRNA(Sec) biosynthetic process Source: UniProtKB-UniPathway
    3. seryl-tRNA aminoacylation Source: UniProtKB-HAMAP

    Keywords - Molecular functioni

    Aminoacyl-tRNA synthetase, Ligase

    Keywords - Biological processi

    Protein biosynthesis

    Keywords - Ligandi

    ATP-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciTTHE262724:GCAT-532-MONOMER.
    UniPathwayiUPA00906; UER00895.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Serine--tRNA ligase (EC:6.1.1.11)
    Alternative name(s):
    Seryl-tRNA synthetase
    Short name:
    SerRS
    Seryl-tRNA(Ser/Sec) synthetase
    Gene namesi
    Name:serS
    Ordered Locus Names:TT_C0520
    OrganismiThermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
    Taxonomic identifieri262724 [NCBI]
    Taxonomic lineageiBacteriaDeinococcus-ThermusDeinococciThermalesThermaceaeThermus
    ProteomesiUP000000592: Chromosome

    Subcellular locationi

    Cytoplasm By similarity

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 421421Serine--tRNA ligasePRO_0000122145Add
    BLAST

    Interactioni

    Subunit structurei

    Homodimer. A single tRNA molecule binds across the dimer.3 Publications

    Protein-protein interaction databases

    STRINGi262724.TTC0520.

    Structurei

    Secondary structure

    1
    421
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi4 – 96
    Helixi11 – 2111
    Helixi27 – 5731
    Beta strandi58 – 614
    Helixi63 – 653
    Helixi94 – 985
    Beta strandi111 – 1133
    Helixi114 – 1163
    Beta strandi118 – 1247
    Helixi136 – 1438
    Helixi150 – 1545
    Helixi163 – 18220
    Beta strandi186 – 1894
    Beta strandi192 – 1954
    Helixi196 – 2027
    Turni205 – 2084
    Helixi209 – 2113
    Turni216 – 2194
    Beta strandi220 – 2223
    Helixi227 – 2326
    Turni233 – 2364
    Beta strandi238 – 2403
    Helixi241 – 2433
    Beta strandi245 – 25511
    Beta strandi268 – 2714
    Beta strandi273 – 28412
    Helixi288 – 30821
    Beta strandi313 – 3175
    Turni320 – 3223
    Beta strandi328 – 33710
    Helixi338 – 3403
    Beta strandi342 – 35312
    Helixi355 – 3606
    Beta strandi363 – 3653
    Beta strandi371 – 3733
    Beta strandi375 – 38410
    Helixi386 – 39510
    Helixi406 – 4083
    Helixi409 – 4124
    Beta strandi413 – 4175

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1SERX-ray2.90A/B1-421[»]
    1SESX-ray2.50A/B1-421[»]
    1SETX-ray2.55A/B1-421[»]
    1SRYX-ray2.50A/B1-421[»]
    3ERRX-ray2.27A/B94-419[»]
    DisProtiDP00514.
    ProteinModelPortaliP34945.
    SMRiP34945. Positions 1-421.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP34945.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni225 – 2273Serine binding

    Domaini

    Consists of two distinct domains, a catalytic core and a N-terminal extension that is involved in tRNA binding.

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG0172.
    KOiK01875.
    OMAiNEGHNES.
    OrthoDBiEOG61KBH9.

    Family and domain databases

    Gene3Di1.10.287.40. 1 hit.
    HAMAPiMF_00176. Ser_tRNA_synth_type1.
    InterProiIPR002314. aa-tRNA-synt_IIb_cons-dom.
    IPR006195. aa-tRNA-synth_II.
    IPR002317. Ser-tRNA-ligase_type_1.
    IPR015866. Ser-tRNA-synth_1_N.
    IPR010978. tRNA-bd_arm.
    [Graphical view]
    PANTHERiPTHR11778. PTHR11778. 1 hit.
    PfamiPF02403. Seryl_tRNA_N. 1 hit.
    PF00587. tRNA-synt_2b. 1 hit.
    [Graphical view]
    PIRSFiPIRSF001529. Ser-tRNA-synth_IIa. 1 hit.
    PRINTSiPR00981. TRNASYNTHSER.
    SUPFAMiSSF46589. SSF46589. 1 hit.
    TIGRFAMsiTIGR00414. serS. 1 hit.
    PROSITEiPS50862. AA_TRNA_LIGASE_II. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P34945-1 [UniParc]FASTAAdd to Basket

    « Hide

    MVDLKRLRQE PEVFHRAIRE KGVALDLEAL LALDREVQEL KKRLQEVQTE    50
    RNQVAKRVPK APPEEKEALI ARGKALGEEA KRLEEALREK EARLEALLLQ 100
    VPLPPWPGAP VGGEEANREI KRVGGPPEFS FPPLDHVALM EKNGWWEPRI 150
    SQVSGSRSYA LKGDLALYEL ALLRFAMDFM ARRGFLPMTL PSYAREKAFL 200
    GTGHFPAYRD QVWAIAETDL YLTGTAEVVL NALHSGEILP YEALPLRYAG 250
    YAPAFRSEAG SFGKDVRGLM RVHQFHKVEQ YVLTEASLEA SDRAFQELLE 300
    NAEEILRLLE LPYRLVEVAT GDMGPGKWRQ VDIEVYLPSE GRYRETHSCS 350
    ALLDWQARRA NLRYRDPEGR VRYAYTLNNT ALATPRILAM LLENHQLQDG 400
    RVRVPQALIP YMGKEVLEPC G 421
    Length:421
    Mass (Da):47,813
    Last modified:May 24, 2004 - v2
    Checksum:i5E89B0D131EFC209
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AE017221 Genomic DNA. Translation: AAS80868.1.
    RefSeqiWP_011172965.1. NC_005835.1.
    YP_004495.1. NC_005835.1.

    Genome annotation databases

    EnsemblBacteriaiAAS80868; AAS80868; TT_C0520.
    GeneIDi2775083.
    KEGGitth:TTC0520.
    PATRICi23951447. VBITheThe54392_0520.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AE017221 Genomic DNA. Translation: AAS80868.1 .
    RefSeqi WP_011172965.1. NC_005835.1.
    YP_004495.1. NC_005835.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1SER X-ray 2.90 A/B 1-421 [» ]
    1SES X-ray 2.50 A/B 1-421 [» ]
    1SET X-ray 2.55 A/B 1-421 [» ]
    1SRY X-ray 2.50 A/B 1-421 [» ]
    3ERR X-ray 2.27 A/B 94-419 [» ]
    DisProti DP00514.
    ProteinModelPortali P34945.
    SMRi P34945. Positions 1-421.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 262724.TTC0520.

    Chemistry

    DrugBanki DB00131. Adenosine monophosphate.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAS80868 ; AAS80868 ; TT_C0520 .
    GeneIDi 2775083.
    KEGGi tth:TTC0520.
    PATRICi 23951447. VBITheThe54392_0520.

    Phylogenomic databases

    eggNOGi COG0172.
    KOi K01875.
    OMAi NEGHNES.
    OrthoDBi EOG61KBH9.

    Enzyme and pathway databases

    UniPathwayi UPA00906 ; UER00895 .
    BioCyci TTHE262724:GCAT-532-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P34945.

    Family and domain databases

    Gene3Di 1.10.287.40. 1 hit.
    HAMAPi MF_00176. Ser_tRNA_synth_type1.
    InterProi IPR002314. aa-tRNA-synt_IIb_cons-dom.
    IPR006195. aa-tRNA-synth_II.
    IPR002317. Ser-tRNA-ligase_type_1.
    IPR015866. Ser-tRNA-synth_1_N.
    IPR010978. tRNA-bd_arm.
    [Graphical view ]
    PANTHERi PTHR11778. PTHR11778. 1 hit.
    Pfami PF02403. Seryl_tRNA_N. 1 hit.
    PF00587. tRNA-synt_2b. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF001529. Ser-tRNA-synth_IIa. 1 hit.
    PRINTSi PR00981. TRNASYNTHSER.
    SUPFAMi SSF46589. SSF46589. 1 hit.
    TIGRFAMsi TIGR00414. serS. 1 hit.
    PROSITEi PS50862. AA_TRNA_LIGASE_II. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: HB27 / ATCC BAA-163 / DSM 7039.
    2. "Refined crystal structure of the seryl-tRNA synthetase from Thermus thermophilus at 2.5-A resolution."
      Fujinaga M., Berthet-Colominas C., Yaremchuk A.D., Tukalo M.A., Cusack S.
      J. Mol. Biol. 234:222-233(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS), SUBUNIT.
    3. "Crystal structures at 2.5 angstrom resolution of seryl-tRNA synthetase complexed with two analogs of seryl adenylate."
      Belrhali H., Yaremchuk A.D., Tukalo M.A., Larsen K., Berthet-Colominas C., Leberman R., Beijer B., Sproat B., Als-Nielsen J., Gruebel G., Legrand J.-F., Lehmann M., Cusack S.
      Science 263:1432-1436(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) IN COMPLEXES WITH SUBSTRATE ANALOGS.
    4. "The 2.9 A crystal structure of T. thermophilus seryl-tRNA synthetase complexed with tRNA(Ser)."
      Biou V., Yaremchuk A.D., Tukalo M.A., Cusack S.
      Science 263:1404-1410(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS) IN COMPLEX WITH TRNA(SER), SUBUNIT.
    5. "The crystal structure of the ternary complex of T.thermophilus seryl-tRNA synthetase with tRNA(Ser) and a seryl-adenylate analogue reveals a conformational switch in the active site."
      Cusack S., Yaremchuk A.D., Tukalo M.A.
      EMBO J. 15:2834-2842(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) IN COMPLEX WITH TRNA(SER) AND SUBSTRATE ANALOG, SUBUNIT.

    Entry informationi

    Entry nameiSYS_THET2
    AccessioniPrimary (citable) accession number: P34945
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1994
    Last sequence update: May 24, 2004
    Last modified: October 1, 2014
    This is version 111 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome

    Documents

    1. Aminoacyl-tRNA synthetases
      List of aminoacyl-tRNA synthetase entries
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3