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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.

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.

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)DescriptionActionsGraphical viewLength
    Active sitei323Proton donor; shared with dimeric partnerBy similarity1

    GO - Molecular functioni

    GO - Biological processi

    Keywordsi

    Molecular functionDecarboxylase, Lyase
    Biological processPolyamine biosynthesis, Putrescine biosynthesis, Spermidine biosynthesis
    LigandPyridoxal phosphate

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-12423.
    BRENDAi4.1.1.18. 5668.
    SABIO-RKiO50657.
    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)DescriptionActionsGraphical viewLength
    Mutagenesisi44 – 46AGV → 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 Publication3
    Mutagenesisi52A → C: No change in substrate specificity. 1
    Mutagenesisi54P → 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 Publication1
    Mutagenesisi319G → W: 7-fold increase in substrate specificity towards ornithine. 1 Publication1
    Mutagenesisi322S → 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 Publication1
    Mutagenesisi322S → 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 Publication1
    Mutagenesisi326I → 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 Publication1
    Mutagenesisi350G → D: Loss of dimer formation and decarboxylase activity. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001499101 – 393Lysine/ornithine decarboxylaseAdd BLAST393

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Modified residuei51N6-(pyridoxal phosphate)lysineBy similarity1

    Interactioni

    Subunit structurei

    Homodimer.

    Structurei

    Secondary structure

    1393
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi8 – 17Combined sources10
    Beta strandi20 – 25Combined sources6
    Helixi27 – 40Combined sources14
    Beta strandi44 – 49Combined sources6
    Helixi56 – 65Combined sources10
    Beta strandi68 – 71Combined sources4
    Helixi74 – 82Combined sources9
    Helixi87 – 89Combined sources3
    Beta strandi90 – 92Combined sources3
    Helixi99 – 107Combined sources9
    Beta strandi112 – 115Combined sources4
    Helixi118 – 120Combined sources3
    Helixi121 – 127Combined sources7
    Beta strandi128 – 130Combined sources3
    Beta strandi132 – 138Combined sources7
    Beta strandi149 – 152Combined sources4
    Helixi156 – 158Combined sources3
    Helixi159 – 168Combined sources10
    Beta strandi172 – 177Combined sources6
    Helixi188 – 206Combined sources19
    Beta strandi213 – 215Combined sources3
    Helixi230 – 246Combined sources17
    Beta strandi250 – 254Combined sources5
    Helixi258 – 261Combined sources4
    Helixi262 – 264Combined sources3
    Beta strandi265 – 275Combined sources11
    Beta strandi277 – 280Combined sources4
    Beta strandi282 – 287Combined sources6
    Turni289 – 293Combined sources5
    Helixi294 – 298Combined sources5
    Beta strandi305 – 307Combined sources3
    Beta strandi314 – 319Combined sources6
    Beta strandi321 – 323Combined sources3
    Beta strandi328 – 335Combined sources8
    Beta strandi343 – 346Combined sources4
    Beta strandi350 – 353Combined sources4
    Helixi354 – 356Combined sources3
    Helixi360 – 362Combined sources3
    Beta strandi368 – 370Combined sources3
    Helixi371 – 373Combined sources3
    Helixi375 – 379Combined sources5

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    5GJMX-ray2.91A/B1-393[»]
    5GJNX-ray2.00A1-393[»]
    5GJOX-ray1.80A/B1-393[»]
    5GJPX-ray2.50A1-393[»]
    ProteinModelPortaliO50657.
    SMRiO50657.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Family and domain databases

    Gene3Di2.40.37.10. 1 hit.
    3.20.20.10. 1 hit.
    InterProiView protein in InterPro
    IPR009006. 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.
    PfamiView protein in Pfam
    PF02784. Orn_Arg_deC_N. 1 hit.
    PF00278. Orn_DAP_Arg_deC. 1 hit.
    PRINTSiPR01179. ODADCRBXLASE.
    PR01182. ORNDCRBXLASE.
    SUPFAMiSSF50621. SSF50621. 1 hit.
    SSF51419. SSF51419. 1 hit.
    PROSITEiView protein in PROSITE
    PS00878. ODR_DC_2_1. 1 hit.
    PS00879. ODR_DC_2_2. 1 hit.

    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.

    Genome annotation databases

    GeneIDi31522868.

    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.

    Entry informationi

    Entry nameiDCLO_SELRU
    AccessioniPrimary (citable) accession number: O50657
    Secondary accession number(s): Q7DFY1
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 21, 2001
    Last sequence update: June 1, 1998
    Last modified: July 5, 2017
    This is version 80 of the entry and version 1 of the sequence. See complete history.
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Direct protein sequencing

    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