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Q8TVD2

- SYS2_METKA

UniProt

Q8TVD2 - SYS2_METKA

Protein

Type-2 serine--tRNA ligase

Gene

serS

Organism
Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 77 (01 Oct 2014)
      Sequence version 1 (01 Jun 2002)
      Previous versions | rss
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    Functioni

    Catalyzes the attachment of serine to tRNA(Ser). Is also 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).UniRule annotation

    Catalytic activityi

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

    Cofactori

    Binds 1 Zn2+ ion per subunit. This ion is coordinated with 2 cysteines, 1 glutamate and a water molecule that dissociates from the zinc ion to allow the coordination of the amino group of the serine substrate, which is essential for catalysis.UniRule annotation

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei317 – 3171Serine; via carbonyl oxygenUniRule annotation
    Metal bindingi319 – 3191Zinc; catalyticUniRule annotation
    Binding sitei349 – 3491SerineUniRule annotation
    Metal bindingi368 – 3681Zinc; catalyticUniRule annotation
    Metal bindingi478 – 4781Zinc; catalyticUniRule annotation
    Binding sitei485 – 4851ATPUniRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi349 – 3513ATPUniRule annotation
    Nucleotide bindingi360 – 3612ATPUniRule annotation

    GO - Molecular functioni

    1. ATP binding Source: UniProtKB-HAMAP
    2. serine-tRNA ligase activity Source: UniProtKB-HAMAP
    3. zinc ion binding 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, Metal-binding, Nucleotide-binding, Zinc

    Enzyme and pathway databases

    UniPathwayiUPA00906; UER00895.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Type-2 serine--tRNA ligaseUniRule annotation (EC:6.1.1.11UniRule annotation)
    Alternative name(s):
    Seryl-tRNA synthetaseUniRule annotation
    Short name:
    SerRSUniRule annotation
    Seryl-tRNA(Ser/Sec) synthetaseUniRule annotation
    Gene namesi
    Name:serSUniRule annotation
    Ordered Locus Names:MK1460
    OrganismiMethanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938)
    Taxonomic identifieri190192 [NCBI]
    Taxonomic lineageiArchaeaEuryarchaeotaMethanopyriMethanopyralesMethanopyraceaeMethanopyrus
    ProteomesiUP000001826: Chromosome

    Subcellular locationi

    Cytoplasm UniRule annotation

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 527527Type-2 serine--tRNA ligasePRO_0000286169Add
    BLAST

    Interactioni

    Subunit structurei

    Homodimer.UniRule annotation

    Protein-protein interaction databases

    STRINGi190192.MK1460.

    Structurei

    Secondary structure

    1
    527
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi2 – 1514
    Helixi19 – 3517
    Helixi37 – 393
    Beta strandi50 – 567
    Beta strandi58 – 7114
    Helixi73 – 9220
    Beta strandi96 – 10914
    Helixi116 – 1194
    Beta strandi126 – 1305
    Beta strandi132 – 14110
    Helixi144 – 1485
    Helixi151 – 16313
    Turni164 – 1674
    Helixi169 – 1713
    Beta strandi181 – 1844
    Helixi196 – 2027
    Beta strandi205 – 2084
    Beta strandi215 – 2173
    Helixi219 – 23517
    Turni236 – 2416
    Beta strandi249 – 2524
    Helixi253 – 2586
    Helixi261 – 2644
    Helixi266 – 2683
    Helixi279 – 29214
    Helixi297 – 3059
    Beta strandi312 – 3143
    Beta strandi316 – 3183
    Helixi321 – 3266
    Turni333 – 3353
    Beta strandi338 – 3425
    Beta strandi345 – 3484
    Beta strandi358 – 3603
    Beta strandi362 – 37312
    Helixi375 – 39521
    Beta strandi400 – 4045
    Beta strandi412 – 4143
    Helixi415 – 4184
    Beta strandi428 – 4347
    Helixi436 – 4383
    Helixi444 – 4463
    Beta strandi447 – 45711
    Helixi459 – 4635
    Beta strandi467 – 4704
    Beta strandi475 – 4828
    Helixi483 – 49412
    Helixi498 – 5003
    Helixi503 – 51311
    Beta strandi523 – 5253

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3W3SX-ray3.10A1-527[»]
    ProteinModelPortaliQ8TVD2.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni366 – 3683Serine bindingUniRule annotation

    Domaini

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

    Sequence similaritiesi

    Belongs to the class-II aminoacyl-tRNA synthetase family. Type-2 seryl-tRNA synthetase subfamily.UniRule annotation

    Phylogenomic databases

    eggNOGiCOG0172.
    HOGENOMiHOG000254149.
    KOiK01875.
    OMAiAQCEPFY.

    Family and domain databases

    HAMAPiMF_01278. Ser_tRNA_synth_type2.
    InterProiIPR002314. aa-tRNA-synt_IIb_cons-dom.
    IPR006195. aa-tRNA-synth_II.
    IPR004503. Ser-tRNA-ligase_IIa_arc.
    [Graphical view]
    PfamiPF00587. tRNA-synt_2b. 1 hit.
    [Graphical view]
    TIGRFAMsiTIGR00415. serS_MJ. 1 hit.
    PROSITEiPS50862. AA_TRNA_LIGASE_II. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q8TVD2-1 [UniParc]FASTAAdd to Basket

    « Hide

    MELKFSAEVE LTLSREVDPA EIEPTVEEFV KEANEDLLQR GVPTGKEGAK    50
    IESYRVLEDT IEMEITGTRY LRPHEAAMRV RKRLAERLGR KHRVGVRDLK 100
    IPRYEVVLRF DREVTRDDVG YVPVADDVVV EDGTVRLTFQ DVDEEMLRRH 150
    VIDRVIRLVA WAVEERSELV ERVTKVEPGT VVDESGPREI RFDGDVTEEA 200
    RRRGWVKEFP GRGQWIYTPP MAALFEVLRD FLLERVTRKL GFEPALFPKL 250
    IPLETMFRMR YLHGLPDGMY YVCPPKRDPE LFDDFKRELY VWGELNERTL 300
    GSLKEKLRDP GYVLAPAQCE PFYELLRDEV VDPERLPIKL YDCSGWTYRW 350
    EGGAAKGLER VNEFQRIEHV WIAEPEEAER IREELLEATK RVAEELELEW 400
    KVVVSDDPFY LEGRLLEDRD IELPDVPSYE FEVYLPFKGE RSSEEAWISV 450
    GSFNVHGEHF VDGFNVKEKS GRTLFTGCAG LGVTRWVVGL LAQHGFEPEE 500
    WPEPILERID EKFGGLPEVP KTLTWPE 527
    Length:527
    Mass (Da):61,368
    Last modified:June 1, 2002 - v1
    Checksum:i7526147D81EFC5CD
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AE009439 Genomic DNA. Translation: AAM02673.1.
    RefSeqiNP_614743.1. NC_003551.1.

    Genome annotation databases

    EnsemblBacteriaiAAM02673; AAM02673; MK1460.
    GeneIDi1478055.
    KEGGimka:MK1460.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AE009439 Genomic DNA. Translation: AAM02673.1 .
    RefSeqi NP_614743.1. NC_003551.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    3W3S X-ray 3.10 A 1-527 [» ]
    ProteinModelPortali Q8TVD2.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 190192.MK1460.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAM02673 ; AAM02673 ; MK1460 .
    GeneIDi 1478055.
    KEGGi mka:MK1460.

    Phylogenomic databases

    eggNOGi COG0172.
    HOGENOMi HOG000254149.
    KOi K01875.
    OMAi AQCEPFY.

    Enzyme and pathway databases

    UniPathwayi UPA00906 ; UER00895 .

    Family and domain databases

    HAMAPi MF_01278. Ser_tRNA_synth_type2.
    InterProi IPR002314. aa-tRNA-synt_IIb_cons-dom.
    IPR006195. aa-tRNA-synth_II.
    IPR004503. Ser-tRNA-ligase_IIa_arc.
    [Graphical view ]
    Pfami PF00587. tRNA-synt_2b. 1 hit.
    [Graphical view ]
    TIGRFAMsi TIGR00415. serS_MJ. 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: AV19 / DSM 6324 / JCM 9639 / NBRC 100938.

    Entry informationi

    Entry nameiSYS2_METKA
    AccessioniPrimary (citable) accession number: Q8TVD2
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 1, 2007
    Last sequence update: June 1, 2002
    Last modified: October 1, 2014
    This is version 77 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. 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