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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: L-lysine biosynthesis via AAA pathway

    This protein is involved in step 1 of the subpathway that synthesizes L-lysine from L-alpha-aminoadipate (Thermus route).
    Proteins known to be involved in the 5 steps of the subpathway in this organism are:
    1. Alpha-aminoadipate--LysW ligase LysX (lysX)
    2. Acetylglutamate/acetylaminoadipate kinase (argB)
    3. N-acetyl-gamma-glutamyl-phosphate/N-acetyl-gamma-aminoadipyl-phosphate reductase (argC), N-acetyl-gamma-glutamyl-phosphate/N-acetyl-gamma-aminoadipyl-phosphate reductase (argC)
    4. Acetylornithine/acetyl-lysine aminotransferase (argD), Acetylornithine/acetyl-lysine aminotransferase (argD)
    5. N-acetyl-lysine deacetylase (lysK)
    This subpathway is part of the pathway L-lysine biosynthesis via AAA pathway, which is itself part of Amino-acid biosynthesis.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes L-lysine from L-alpha-aminoadipate (Thermus route), the pathway L-lysine biosynthesis via AAA pathway and in Amino-acid biosynthesis.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei89ATPBy similarity1
    Binding sitei129ATP1
    Binding sitei194ATP1
    Binding sitei202ATPBy similarity1
    Metal bindingi237Magnesium 1By similarity1
    Metal bindingi249Magnesium 1By similarity1
    Metal bindingi249Magnesium 2By similarity1
    Metal bindingi251Magnesium 2By similarity1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi133 – 139ATP7
    Nucleotide bindingi169 – 180ATPAdd BLAST12

    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.
    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
    Proteomesi
    • UP000000532 Componenti: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00003910011 – 280Alpha-aminoadipate--LysW ligase LysXAdd BLAST280

    Interactioni

    Subunit structurei

    Homodimer.2 Publications

    Protein-protein interaction databases

    DIPiDIP-61749N.
    STRINGi300852.TTHA1907.

    Structurei

    Secondary structure

    1280
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi2 – 8Combined sources7
    Helixi11 – 22Combined sources12
    Beta strandi27 – 31Combined sources5
    Helixi32 – 34Combined sources3
    Helixi44 – 46Combined sources3
    Beta strandi51 – 54Combined sources4
    Helixi59 – 71Combined sources13
    Beta strandi76 – 78Combined sources3
    Helixi80 – 87Combined sources8
    Helixi89 – 99Combined sources11
    Beta strandi106 – 111Combined sources6
    Helixi112 – 122Combined sources11
    Beta strandi124 – 129Combined sources6
    Beta strandi140 – 142Combined sources3
    Helixi145 – 158Combined sources14
    Helixi161 – 164Combined sources4
    Beta strandi165 – 170Combined sources6
    Beta strandi175 – 184Combined sources10
    Beta strandi187 – 195Combined sources9
    Beta strandi197 – 200Combined sources4
    Helixi203 – 205Combined sources3
    Beta strandi208 – 211Combined sources4
    Helixi216 – 228Combined sources13
    Beta strandi232 – 241Combined sources10
    Beta strandi244 – 253Combined sources10
    Helixi259 – 263Combined sources5
    Helixi267 – 277Combined sources11

    3D structure databases

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

    Miscellaneous databases

    EvolutionaryTraceiQ5SH23.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Domaini93 – 276ATP-graspPROSITE-ProRule annotationAdd BLAST184

    Motif

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Motifi258 – 259N-[TS] motif that is essential for LysX substrate specificity2

    Sequence similaritiesi

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

    Phylogenomic databases

    eggNOGiENOG4105D9I. Bacteria.
    COG0189. LUCA.
    HOGENOMiHOG000228553.
    KOiK05827.
    OMAiGDKWATS.
    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
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1UC8X-ray2.00A/B1-280[»]
    1UC9X-ray2.38A/B1-280[»]
    3VPDX-ray1.95A/B1-279[»]
    ProteinModelPortaliQ5SH23.
    SMRiQ5SH23.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    DIPiDIP-61749N.
    STRINGi300852.TTHA1907.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

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

    Phylogenomic databases

    eggNOGiENOG4105D9I. Bacteria.
    COG0189. LUCA.
    HOGENOMiHOG000228553.
    KOiK05827.
    OMAiGDKWATS.
    PhylomeDBiQ5SH23.

    Enzyme and pathway databases

    UniPathwayiUPA00033; UER00035.
    BioCyciMetaCyc:MONOMER-6728.
    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...

    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: November 2, 2016
    This is version 82 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

    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.