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Protein

Ornithine decarboxylase

Gene

ODC1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Catalyzes the first and rate-limiting step of polyamine biosynthesis that converts ornithine into putrescine, which is the precursor for the polyamines, spermidine and spermine. Polyamines are essential for cell proliferation and are implicated in cellular processes, ranging from DNA replication to apoptosis.1 Publication

Catalytic activityi

L-ornithine = putrescine + CO2.1 Publication

Cofactori

pyridoxal 5'-phosphate2 Publications

Enzyme regulationi

Inhibited by S-nitrosylation (PubMed:10462479, PubMed:11461922). Inhibited by antizymes (AZs) OAZ1, OAZ2 and OAZ3 in response to polyamine levels. AZs inhibit the assembly of the functional homodimer by binding to ODC monomers. Additionally, OAZ1 targets ODC monomers for ubiquitin-independent proteolytic destruction by the 26S proteasome (PubMed:17900240). Inhibited by 1-amino-oxy-3-aminopropane (APA, an isosteric analog of putrescine) (PubMed:17407445). Irreversibly inhibited by alpha-difluoromethylornithine (DFMO) (PubMed:17407445).4 Publications

Kineticsi

kcat is 3.3 sec(-1) with L-ornithine as substrate.1 Publication
  1. KM=0.08 mM for L-ornithine1 Publication

    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. Ornithine decarboxylase (ODC1)
    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
    Sitei197Stacks against the aromatic ring of pyridoxal phosphate and stabilizes reaction intermediatesBy similarity1
    Binding sitei200Pyridoxal phosphateCombined sources1 Publication1
    Binding sitei237Pyridoxal phosphate; via amino nitrogenCombined sources1 Publication1
    Active sitei360Proton donor; shared with dimeric partner1 Publication1
    Binding sitei361Substrate; shared with dimeric partnerBy similarity1
    Binding sitei389Pyridoxal phosphateCombined sources3 Publications1

    GO - Molecular functioni

    • ornithine decarboxylase activity Source: UniProtKB
    • protein homodimerization activity Source: UniProtKB

    GO - Biological processi

    Keywordsi

    Molecular functionDecarboxylase, Lyase
    Biological processPolyamine biosynthesis
    LigandPyridoxal phosphate

    Enzyme and pathway databases

    BioCyciMetaCyc:HS03935-MONOMER
    BRENDAi4.1.1.17 2681
    ReactomeiR-HSA-350562 Regulation of ornithine decarboxylase (ODC)
    R-HSA-351202 Metabolism of polyamines
    SABIO-RKiP11926
    SIGNORiP11926
    UniPathwayiUPA00535; UER00288

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ornithine decarboxylase (EC:4.1.1.171 Publication)
    Short name:
    ODC
    Gene namesi
    Name:ODC1
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    Proteomesi
    • UP000005640 Componenti: Chromosome 2

    Organism-specific databases

    EuPathDBiHostDB:ENSG00000115758.12
    HGNCiHGNC:8109 ODC1
    MIMi165640 gene
    neXtProtiNX_P11926

    Subcellular locationi

    Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi360C → A: 25% decrease of in vitro nitrosylation level. 1 Publication1

    Organism-specific databases

    DisGeNETi4953
    MalaCardsiODC1
    OpenTargetsiENSG00000115758
    PharmGKBiPA31897

    Chemistry databases

    ChEMBLiCHEMBL1869
    DrugBankiDB03856 Alpha-Difluoromethylornithine
    DB06243 Eflornithine
    DB04263 Geneticin
    DB04083 N'-Pyridoxyl-Lysine-5'-Monophosphate
    DB02824 N-Pyridoxyl-Glycine-5-Monophosphate
    DB01917 Putrescine
    DB00114 Pyridoxal Phosphate
    DB02209 Pyridoxine-5'-Phosphate
    DB00127 Spermine
    GuidetoPHARMACOLOGYi1276

    Polymorphism and mutation databases

    BioMutaiODC1
    DMDMi118377

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001498911 – 461Ornithine decarboxylaseAdd BLAST461

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Modified residuei69N6-(pyridoxal phosphate)lysine1 Publication1 Publication1
    Modified residuei303Phosphoserine; by CK2By similarity1
    Modified residuei360S-nitrosocysteine; in inhibited form1 Publication1

    Post-translational modificationi

    S-Nitrosylation inhibits the enzyme. S-Nitrosylated in vitro on 4 cysteine residues.2 Publications

    Keywords - PTMi

    Phosphoprotein, S-nitrosylation

    Proteomic databases

    PaxDbiP11926
    PeptideAtlasiP11926
    PRIDEiP11926

    PTM databases

    iPTMnetiP11926
    PhosphoSitePlusiP11926

    Expressioni

    Inductioni

    Down-regulated in response to enterovirus 71 (EV71) infection (at protein level).1 Publication

    Gene expression databases

    BgeeiENSG00000115758
    CleanExiHS_ODC1
    ExpressionAtlasiP11926 baseline and differential
    GenevisibleiP11926 HS

    Organism-specific databases

    HPAiCAB035996
    HPA001536

    Interactioni

    Subunit structurei

    Homodimer. Only the dimer is catalytically active, as the active sites are constructed of residues from both monomers (Probable). Does not form a heterodimer with AZIN2 (By similarity).By similarity1 Publication

    Binary interactionsi

    Show more details

    GO - Molecular functioni

    Protein-protein interaction databases

    BioGridi111007, 10 interactors
    CORUMiP11926
    IntActiP11926, 16 interactors
    MINTiP11926
    STRINGi9606.ENSP00000234111

    Chemistry databases

    BindingDBiP11926

    Structurei

    Secondary structure

    1461
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi1 – 5Combined sources5
    Turni6 – 8Combined sources3
    Beta strandi11 – 14Combined sources4
    Helixi20 – 30Combined sources11
    Turni31 – 33Combined sources3
    Beta strandi40 – 44Combined sources5
    Helixi45 – 58Combined sources14
    Beta strandi62 – 67Combined sources6
    Helixi68 – 70Combined sources3
    Helixi74 – 83Combined sources10
    Beta strandi86 – 89Combined sources4
    Helixi92 – 100Combined sources9
    Helixi105 – 107Combined sources3
    Beta strandi108 – 110Combined sources3
    Helixi117 – 125Combined sources9
    Beta strandi130 – 133Combined sources4
    Helixi136 – 145Combined sources10
    Beta strandi150 – 155Combined sources6
    Beta strandi162 – 164Combined sources3
    Turni167 – 169Combined sources3
    Helixi174 – 186Combined sources13
    Beta strandi190 – 195Combined sources6
    Helixi206 – 225Combined sources20
    Beta strandi231 – 233Combined sources3
    Beta strandi240 – 246Combined sources7
    Helixi248 – 262Combined sources15
    Helixi265 – 267Combined sources3
    Beta strandi270 – 273Combined sources4
    Helixi277 – 280Combined sources4
    Helixi281 – 283Combined sources3
    Beta strandi284 – 296Combined sources13
    Beta strandi313 – 319Combined sources7
    Turni322 – 324Combined sources3
    Helixi325 – 327Combined sources3
    Helixi328 – 331Combined sources4
    Beta strandi339 – 342Combined sources4
    Beta strandi350 – 356Combined sources7
    Beta strandi358 – 360Combined sources3
    Beta strandi365 – 373Combined sources9
    Beta strandi380 – 383Combined sources4
    Beta strandi388 – 390Combined sources3
    Helixi391 – 393Combined sources3
    Helixi397 – 399Combined sources3
    Beta strandi404 – 410Combined sources7
    Helixi411 – 420Combined sources10

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1D7KX-ray2.10A/B7-427[»]
    2ON3X-ray3.00A/B1-461[»]
    2OO0X-ray1.90A/B1-461[»]
    4ZGYX-ray2.63A2-421[»]
    5BWAX-ray3.20A1-461[»]
    ProteinModelPortaliP11926
    SMRiP11926
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP11926

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni274 – 277Pyridoxal phosphate bindingCombined sources3 Publications4
    Regioni331 – 332Substrate bindingBy similarity2

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiKOG0622 Eukaryota
    COG0019 LUCA
    GeneTreeiENSGT00390000011560
    HOGENOMiHOG000274133
    HOVERGENiHBG005456
    InParanoidiP11926
    KOiK01581
    OMAiVVGYICE
    OrthoDBiEOG091G0AJV
    PhylomeDBiP11926
    TreeFamiTF300760

    Family and domain databases

    Gene3Di2.40.37.10, 2 hits
    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.

    P11926-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MNNFGNEEFD CHFLDEGFTA KDILDQKINE VSSSDDKDAF YVADLGDILK
    60 70 80 90 100
    KHLRWLKALP RVTPFYAVKC NDSKAIVKTL AATGTGFDCA SKTEIQLVQS
    110 120 130 140 150
    LGVPPERIIY ANPCKQVSQI KYAANNGVQM MTFDSEVELM KVARAHPKAK
    160 170 180 190 200
    LVLRIATDDS KAVCRLSVKF GATLRTSRLL LERAKELNID VVGVSFHVGS
    210 220 230 240 250
    GCTDPETFVQ AISDARCVFD MGAEVGFSMY LLDIGGGFPG SEDVKLKFEE
    260 270 280 290 300
    ITGVINPALD KYFPSDSGVR IIAEPGRYYV ASAFTLAVNI IAKKIVLKEQ
    310 320 330 340 350
    TGSDDEDESS EQTFMYYVND GVYGSFNCIL YDHAHVKPLL QKRPKPDEKY
    360 370 380 390 400
    YSSSIWGPTC DGLDRIVERC DLPEMHVGDW MLFENMGAYT VAAASTFNGF
    410 420 430 440 450
    QRPTIYYVMS GPAWQLMQQF QNPDFPPEVE EQDASTLPVS CAWESGMKRH
    460
    RAACASASIN V
    Length:461
    Mass (Da):51,148
    Last modified:April 1, 1990 - v2
    Checksum:i8CCB88CE80E823C5
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M16650 mRNA Translation: AAA59966.2
    M31061 Genomic DNA Translation: AAA60563.1
    X16277 Genomic DNA Translation: CAA34353.1
    M33764 Genomic DNA Translation: AAA60564.1
    M34158 Genomic DNA Translation: AAA59969.1
    M81740 Genomic DNA Translation: AAA59967.1
    X55362 mRNA Translation: CAA39047.1
    AK292352 mRNA Translation: BAF85041.1
    AK312766 mRNA Translation: BAG35632.1
    AY841870 Genomic DNA Translation: AAV88093.1
    AC007249 Genomic DNA Translation: AAY15034.1
    CH471053 Genomic DNA Translation: EAX00958.1
    CH471053 Genomic DNA Translation: EAX00959.1
    BC025296 mRNA Translation: AAH25296.1
    X53271 mRNA Translation: CAA37369.1
    M20372 mRNA Translation: AAA59968.1
    CCDSiCCDS1672.1
    PIRiS06900 DCHUO
    RefSeqiNP_001274118.1, NM_001287189.1
    NP_001274119.1, NM_001287190.1
    NP_002530.1, NM_002539.2
    UniGeneiHs.467701

    Genome annotation databases

    EnsembliENST00000234111; ENSP00000234111; ENSG00000115758
    ENST00000405333; ENSP00000385333; ENSG00000115758
    GeneIDi4953
    KEGGihsa:4953
    UCSCiuc002rao.3 human

    Similar proteinsi

    Entry informationi

    Entry nameiDCOR_HUMAN
    AccessioniPrimary (citable) accession number: P11926
    Secondary accession number(s): Q53TU3, Q6LDS9
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 1, 1989
    Last sequence update: April 1, 1990
    Last modified: May 23, 2018
    This is version 197 of the entry and version 2 of the sequence. See complete history.
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program
    DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Human chromosome 2
      Human chromosome 2: entries, gene names and cross-references to MIM
    2. MIM cross-references
      Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
    3. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    4. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    5. SIMILARITY comments
      Index of protein domains and families

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