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Protein

Lysine/ornithine decarboxylase

Gene

ldc

Organism
Selenomonas ruminantium
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Decarboxylates both L-lysine and L-ornithine with similar catalytic efficiency.

Catalytic activityi

L-lysine = cadaverine + CO2.
L-ornithine = putrescine + CO2.

Cofactori

Enzyme regulationi

Inhibited competitively by both alpha-difluoromethyllysine and alpha-difluoromethylornithine.

Kineticsi

  1. KM=1.5 mM for L-lysine
  2. KM=0.96 mM for L-ornithine

    Pathwayi: putrescine biosynthesis via L-ornithine pathway

    This protein is involved in step 1 of the subpathway that synthesizes putrescine from L-ornithine.
    Proteins known to be involved in this subpathway in this organism are:
    1. Lysine/ornithine decarboxylase (ldc)
    This subpathway is part of the pathway putrescine biosynthesis via L-ornithine pathway, which is itself part of Amine and polyamine biosynthesis.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes putrescine from L-ornithine, the pathway putrescine biosynthesis via L-ornithine pathway and in Amine and polyamine biosynthesis.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei323 – 3231Proton donor; shared with dimeric partnerBy similarity

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Decarboxylase, Lyase

    Keywords - Biological processi

    Polyamine biosynthesis, Putrescine biosynthesis, Spermidine biosynthesis

    Keywords - Ligandi

    Pyridoxal phosphate

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-12423.
    RETL1328306-WGS:GSTH-3702-MONOMER.
    BRENDAi4.1.1.18. 5668.
    SABIO-RKO50657.
    UniPathwayiUPA00535; UER00288.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Lysine/ornithine decarboxylase (EC:4.1.1.17, EC:4.1.1.18)
    Short name:
    LDC
    Gene namesi
    Name:ldc
    OrganismiSelenomonas ruminantium
    Taxonomic identifieri971 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesNegativicutesSelenomonadalesSelenomonadaceaeSelenomonas

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi44 – 463AGV → VTP: 2-fold increase in substrate specificity towards ornithine. 5-fold increase in substrate specificity towards ornithine; when associated with D-54. 70-fold increase in substrate specificity towards ornithine; when associated with D-54 and A-322. 16-fold increase in substrate specificity towards ornithine; when associated with D-54; T-322 and L-326. 1 Publication
    Mutagenesisi52 – 521A → C: No change in substrate specificity.
    Mutagenesisi54 – 541P → D: 3-fold increase in substrate specificity towards ornithine. 5-fold increase in substrate specificity towards ornithine; when associated with 44-V--P-46. 70-fold increase in substrate specificity towards ornithine; when associated with 44-V--P-46 and A-322. 16-fold increase in substrate specificity towards ornithine; when associated with 44-V--P-46; T-322 and L-326. 1 Publication
    Mutagenesisi319 – 3191G → W: 7-fold increase in substrate specificity towards ornithine. 1 Publication
    Mutagenesisi322 – 3221S → A: 29-fold increase in substrate specificity towards ornithine. 70-fold increase in substrate specificity towards ornithine; when associated with 44-V--P-46 and D-54. 1 Publication
    Mutagenesisi322 – 3221S → T: 16-fold increase in substrate specificity towards ornithine; when associated with L-326. 16-fold increase in substrate specificity towards ornithine; when associated with 44-V--P-46; D-54 and L-326. 1 Publication
    Mutagenesisi326 – 3261I → L: 16-fold increase in substrate specificity towards ornithine; when associated with T-322. 16-fold increase in substrate specificity towards ornithine; when associated with 44-V--P-46; D-54 and T-322. 1 Publication
    Mutagenesisi350 – 3501G → D: Loss of dimer formation and decarboxylase activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 393393Lysine/ornithine decarboxylasePRO_0000149910Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei51 – 511N6-(pyridoxal phosphate)lysineBy similarity

    Interactioni

    Subunit structurei

    Homodimer.

    Structurei

    3D structure databases

    ProteinModelPortaliO50657.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Family and domain databases

    Gene3Di2.40.37.10. 1 hit.
    3.20.20.10. 1 hit.
    InterProiIPR009006. Ala_racemase/Decarboxylase_C.
    IPR022643. De-COase2_C.
    IPR022657. De-COase2_CS.
    IPR022644. De-COase2_N.
    IPR022653. De-COase2_pyr-phos_BS.
    IPR000183. Orn/DAP/Arg_de-COase.
    IPR002433. Orn_de-COase.
    IPR029066. PLP-binding_barrel.
    [Graphical view]
    PfamiPF02784. Orn_Arg_deC_N. 1 hit.
    PF00278. Orn_DAP_Arg_deC. 1 hit.
    [Graphical view]
    PRINTSiPR01179. ODADCRBXLASE.
    PR01182. ORNDCRBXLASE.
    SUPFAMiSSF50621. SSF50621. 1 hit.
    SSF51419. SSF51419. 1 hit.
    PROSITEiPS00878. ODR_DC_2_1. 1 hit.
    PS00879. ODR_DC_2_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    O50657-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MKNFRLSEKE VKTLAKRIPT PFLVASLDKV EENYQFMRRH LPRAGVFYAM
    60 70 80 90 100
    KANPTPEILS LLAGLGSHFD VASAGEMEIL HELGVDGSQM IYANPVKDAR
    110 120 130 140 150
    GLKAAADYNV RRFTFDDPSE IDKMAKAVPG ADVLVRIAVR NNKALVDLNT
    160 170 180 190 200
    KFGAPVEEAL DLLKAAQDAG LHAMGICFHV GSQSLSTAAY EEALLVARRL
    210 220 230 240 250
    FDEAEEMGMH LTDLDIGGGF PVPDAKGLNV DLAAMMEAIN KQIDRLFPDT
    260 270 280 290 300
    AVWTEPGRYM CGTAVNLVTS VIGTKTRGEQ PWYILDEGIY GCFSGIMYDH
    310 320 330 340 350
    WTYPLHCFGK GNKKPSTFGG PSCDGIDVLY RDFMAPELKI GDKVLVTEMG
    360 370 380 390
    SYTSVSATRF NGFYLAPTII FEDQPEYAAR LTEDDDVKKK AAV
    Length:393
    Mass (Da):43,214
    Last modified:June 1, 1998 - v1
    Checksum:i66249907E2061167
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AB011029 Genomic DNA. Translation: BAA24923.1.
    AB104737 Genomic DNA. Translation: BAC57940.1.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AB011029 Genomic DNA. Translation: BAA24923.1.
    AB104737 Genomic DNA. Translation: BAC57940.1.

    3D structure databases

    ProteinModelPortaliO50657.
    ModBaseiSearch...
    MobiDBiSearch...

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Enzyme and pathway databases

    UniPathwayiUPA00535; UER00288.
    BioCyciMetaCyc:MONOMER-12423.
    RETL1328306-WGS:GSTH-3702-MONOMER.
    BRENDAi4.1.1.18. 5668.
    SABIO-RKO50657.

    Family and domain databases

    Gene3Di2.40.37.10. 1 hit.
    3.20.20.10. 1 hit.
    InterProiIPR009006. Ala_racemase/Decarboxylase_C.
    IPR022643. De-COase2_C.
    IPR022657. De-COase2_CS.
    IPR022644. De-COase2_N.
    IPR022653. De-COase2_pyr-phos_BS.
    IPR000183. Orn/DAP/Arg_de-COase.
    IPR002433. Orn_de-COase.
    IPR029066. PLP-binding_barrel.
    [Graphical view]
    PfamiPF02784. Orn_Arg_deC_N. 1 hit.
    PF00278. Orn_DAP_Arg_deC. 1 hit.
    [Graphical view]
    PRINTSiPR01179. ODADCRBXLASE.
    PR01182. ORNDCRBXLASE.
    SUPFAMiSSF50621. SSF50621. 1 hit.
    SSF51419. SSF51419. 1 hit.
    PROSITEiPS00878. ODR_DC_2_1. 1 hit.
    PS00879. ODR_DC_2_2. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    1. "Gene cloning and molecular characterization of lysine decarboxylase from Selenomonas ruminantium delineate its evolutionary relationship to ornithine decarboxylases from eukaryotes."
      Takatsuka Y., Yamaguchi Y., Ono M., Kamio Y.
      J. Bacteriol. 182:6732-6741(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-28; 30-37; 52-64; 153-163; 276-288 AND 344-352, MUTAGENESIS OF 44-ALA--VAL-46; PRO-54; GLY-319; SER-322; ILE-326 AND GLY-350.
      Strain: Subsp. lactilytica.

    Entry informationi

    Entry nameiDCLO_SELRU
    AccessioniPrimary (citable) accession number: O50657
    Secondary accession number(s): Q7DFY1
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 21, 2001
    Last sequence update: June 1, 1998
    Last modified: July 6, 2016
    This is version 75 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Mutagen studies showed that it is possible to convert S.ruminantium LDC to an enzyme with a preference for decarboxylating L-ornithine when five amino acid residues (Ala-44, Gly-45, Val-46, Pro-54 and Ser-322) were replaced with the corresponding ones found in mouse ODC.

    Keywords - Technical termi

    Direct protein sequencing

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. 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.