Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Alpha-aminoadipate--LysW ligase LysX

Gene

lysX

Organism
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the ATP-dependent formation of a covalent bond between the amino group of alpha-aminoadipate (AAA) and the gamma-carboxyl group of the C-terminal glutamate residue in LysW.1 Publication

Catalytic activityi

ATP + [lysine-biosynthesis-protein LysW]-C-terminal-L-glutamate + L-2-aminoadipate = ADP + phosphate + [lysine-biosynthesis-protein LysW]-C-terminal-gamma-(L-2-aminoadip-2-yl)-L-glutamate.1 Publication

Cofactori

Mg2+By similarityNote: Binds 2 magnesium ions per subunit.By similarity

Kineticsi

  1. KM=2.1 mM for alpha-aminoadipate1 Publication
  2. KM=2.6 mM for ATP1 Publication

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei89 – 891ATPBy similarity
    Binding sitei129 – 1291ATP
    Binding sitei194 – 1941ATP
    Binding sitei202 – 2021ATPBy similarity
    Metal bindingi237 – 2371Magnesium 1By similarity
    Metal bindingi249 – 2491Magnesium 1By similarity
    Metal bindingi249 – 2491Magnesium 2By similarity
    Metal bindingi251 – 2511Magnesium 2By similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi133 – 1397ATP
    Nucleotide bindingi169 – 18012ATPAdd
    BLAST

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Ligase

    Keywords - Biological processi

    Amino-acid biosynthesis, Lysine biosynthesis

    Keywords - Ligandi

    ATP-binding, Magnesium, Metal-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-6728.
    TTHE300852:GH8R-1953-MONOMER.
    BRENDAi6.3.2.B13. 2305.
    UniPathwayiUPA00033; UER00035.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Alpha-aminoadipate--LysW ligase LysX (EC:6.3.2.431 Publication)
    Short name:
    AAA--LysW ligase LysX
    Gene namesi
    Name:lysX
    Ordered Locus Names:TTHA1907
    OrganismiThermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
    Taxonomic identifieri300852 [NCBI]
    Taxonomic lineageiBacteriaDeinococcus-ThermusDeinococciThermalesThermaceaeThermus
    ProteomesiUP000000532 Componenti: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 280280Alpha-aminoadipate--LysW ligase LysXPRO_0000391001Add
    BLAST

    Interactioni

    Subunit structurei

    Homodimer.2 Publications

    Protein-protein interaction databases

    STRINGi300852.TTHA1907.

    Structurei

    Secondary structure

    1
    280
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi2 – 87Combined sources
    Helixi11 – 2212Combined sources
    Beta strandi27 – 315Combined sources
    Helixi32 – 343Combined sources
    Helixi44 – 463Combined sources
    Beta strandi51 – 544Combined sources
    Helixi59 – 7113Combined sources
    Beta strandi76 – 783Combined sources
    Helixi80 – 878Combined sources
    Helixi89 – 9911Combined sources
    Beta strandi106 – 1116Combined sources
    Helixi112 – 12211Combined sources
    Beta strandi124 – 1296Combined sources
    Beta strandi140 – 1423Combined sources
    Helixi145 – 15814Combined sources
    Helixi161 – 1644Combined sources
    Beta strandi165 – 1706Combined sources
    Beta strandi175 – 18410Combined sources
    Beta strandi187 – 1959Combined sources
    Beta strandi197 – 2004Combined sources
    Helixi203 – 2053Combined sources
    Beta strandi208 – 2114Combined sources
    Helixi216 – 22813Combined sources
    Beta strandi232 – 24110Combined sources
    Beta strandi244 – 25310Combined sources
    Helixi259 – 2635Combined sources
    Helixi267 – 27711Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1UC8X-ray2.00A/B1-280[»]
    1UC9X-ray2.38A/B1-280[»]
    3VPDX-ray1.95A/B1-279[»]
    ProteinModelPortaliQ5SH23.
    SMRiQ5SH23. Positions 1-280.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ5SH23.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini93 – 276184ATP-graspPROSITE-ProRule annotationAdd
    BLAST

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi258 – 2592N-[TS] motif that is essential for LysX substrate specificity

    Sequence similaritiesi

    Belongs to the RimK family. LysX subfamily.Curated
    Contains 1 ATP-grasp domain.PROSITE-ProRule annotation

    Phylogenomic databases

    eggNOGiCOG0189.
    HOGENOMiHOG000228553.
    KOiK05827.
    OMAiHTMEFKN.
    OrthoDBiEOG6DZDX8.
    PhylomeDBiQ5SH23.

    Family and domain databases

    Gene3Di3.30.1490.20. 1 hit.
    3.30.470.20. 1 hit.
    3.40.50.20. 1 hit.
    InterProiIPR011761. ATP-grasp.
    IPR013651. ATP-grasp_RimK-type.
    IPR013815. ATP_grasp_subdomain_1.
    IPR013816. ATP_grasp_subdomain_2.
    IPR011870. LysX_arch.
    IPR016185. PreATP-grasp_dom.
    IPR004666. RpS6_RimK/Lys_biosynth_LsyX.
    [Graphical view]
    PfamiPF08443. RimK. 1 hit.
    [Graphical view]
    SUPFAMiSSF52440. SSF52440. 1 hit.
    TIGRFAMsiTIGR02144. LysX_arch. 1 hit.
    TIGR00768. rimK_fam. 1 hit.
    PROSITEiPS50975. ATP_GRASP. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q5SH23-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MLAILYDRIR PDERMLFERA EALGLPYKKV YVPALPMVLG ERPKELEGVT
    60 70 80 90 100
    VALERCVSQS RGLAAARYLT ALGIPVVNRP EVIEACGDKW ATSVALAKAG
    110 120 130 140 150
    LPQPKTALAT DREEALRLME AFGYPVVLKP VIGSWGRLLA KVTDRAAAEA
    160 170 180 190 200
    LLEHKEVLGG FQHQLFYIQE YVEKPGRDIR VFVVGERAIA AIYRRSAHWI
    210 220 230 240 250
    TNTARGGQAE NCPLTEEVAR LSVKAAEAVG GGVVAVDLFE SERGLLVNEV
    260 270 280
    NHTMEFKNSV HTTGVDIPGE ILKYAWSLAS
    Length:280
    Mass (Da):30,718
    Last modified:December 21, 2004 - v1
    Checksum:iB168629146AF1344
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AB103032 Genomic DNA. Translation: BAC67243.1.
    AP008226 Genomic DNA. Translation: BAD71730.1.
    RefSeqiWP_011229004.1. NC_006461.1.
    YP_145173.1. NC_006461.1.

    Genome annotation databases

    EnsemblBacteriaiBAD71730; BAD71730; BAD71730.
    GeneIDi3167971.
    KEGGittj:TTHA1907.
    PATRICi23958779. VBITheThe93045_1875.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AB103032 Genomic DNA. Translation: BAC67243.1.
    AP008226 Genomic DNA. Translation: BAD71730.1.
    RefSeqiWP_011229004.1. NC_006461.1.
    YP_145173.1. NC_006461.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1UC8X-ray2.00A/B1-280[»]
    1UC9X-ray2.38A/B1-280[»]
    3VPDX-ray1.95A/B1-279[»]
    ProteinModelPortaliQ5SH23.
    SMRiQ5SH23. Positions 1-280.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi300852.TTHA1907.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiBAD71730; BAD71730; BAD71730.
    GeneIDi3167971.
    KEGGittj:TTHA1907.
    PATRICi23958779. VBITheThe93045_1875.

    Phylogenomic databases

    eggNOGiCOG0189.
    HOGENOMiHOG000228553.
    KOiK05827.
    OMAiHTMEFKN.
    OrthoDBiEOG6DZDX8.
    PhylomeDBiQ5SH23.

    Enzyme and pathway databases

    UniPathwayiUPA00033; UER00035.
    BioCyciMetaCyc:MONOMER-6728.
    TTHE300852:GH8R-1953-MONOMER.
    BRENDAi6.3.2.B13. 2305.

    Miscellaneous databases

    EvolutionaryTraceiQ5SH23.

    Family and domain databases

    Gene3Di3.30.1490.20. 1 hit.
    3.30.470.20. 1 hit.
    3.40.50.20. 1 hit.
    InterProiIPR011761. ATP-grasp.
    IPR013651. ATP-grasp_RimK-type.
    IPR013815. ATP_grasp_subdomain_1.
    IPR013816. ATP_grasp_subdomain_2.
    IPR011870. LysX_arch.
    IPR016185. PreATP-grasp_dom.
    IPR004666. RpS6_RimK/Lys_biosynth_LsyX.
    [Graphical view]
    PfamiPF08443. RimK. 1 hit.
    [Graphical view]
    SUPFAMiSSF52440. SSF52440. 1 hit.
    TIGRFAMsiTIGR02144. LysX_arch. 1 hit.
    TIGR00768. rimK_fam. 1 hit.
    PROSITEiPS50975. ATP_GRASP. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "Crystal structure of a lysine biosynthesis enzyme, LysX, from Thermus thermophilus HB8."
      Sakai H., Vassylyeva M.N., Matsuura T., Sekine S., Gotoh K., Nishiyama M., Terada T., Shirouzu M., Kuramitsu S., Vassylyev D.G., Yokoyama S.
      J. Mol. Biol. 332:729-740(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEX WITH ADP, SUBUNIT.
      Strain: HB8 / ATCC 27634 / DSM 579.
    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. "Discovery of proteinaceous N-modification in lysine biosynthesis of Thermus thermophilus."
      Horie A., Tomita T., Saiki A., Kono H., Taka H., Mineki R., Fujimura T., Nishiyama C., Kuzuyama T., Nishiyama M.
      Nat. Chem. Biol. 5:673-679(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES.
    4. Cited for: X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) IN COMPLEX WITH ATP ANALOG.

    Entry informationi

    Entry nameiLYSX_THET8
    AccessioniPrimary (citable) accession number: Q5SH23
    Secondary accession number(s): Q84BR0
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: January 19, 2010
    Last sequence update: December 21, 2004
    Last modified: April 1, 2015
    This is version 74 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. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3

    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 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.