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Protein

Ornithine decarboxylase

Gene
N/A
Organism
Trypanosoma brucei brucei
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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.By similarity

Catalytic activityi

L-ornithine = putrescine + CO2.1 Publication

Cofactori

pyridoxal 5'-phosphate3 Publications

Enzyme regulationi

Inhibited by antizyme (AZ) in response to polyamine levels. AZ inhibits the assembly of the functional homodimer by binding to ODC monomers and targeting them for ubiquitin-independent proteolytic destruction by the 26S proteasome.By similarity

Kineticsi

kcat is 15 sec(-1) with L-ornithine as substrate.1 Publication
  1. KM=400 µM 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.1 Publication
    Proteins known to be involved in this subpathway in this organism are:
    1. Ornithine decarboxylase
    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
    Sitei195Stacks against the aromatic ring of pyridoxal phosphate and stabilizes reaction intermediates1 Publication1
    Binding sitei198Pyridoxal phosphate3 Publications1
    Binding sitei235Pyridoxal phosphate; via amino nitrogen3 Publications1
    Active sitei358Proton donor; shared with dimeric partner2 Publications1
    Binding sitei359Substrate; shared with dimeric partner2 Publications1
    Binding sitei387Pyridoxal phosphate3 Publications1

    GO - Molecular functioni

    • ornithine decarboxylase activity Source: GeneDB

    GO - Biological processi

    • polyamine biosynthetic process Source: GeneDB
    • putrescine biosynthetic process from ornithine Source: UniProtKB-UniPathway

    Keywordsi

    Molecular functionDecarboxylase, Lyase
    Biological processPolyamine biosynthesis
    LigandPyridoxal phosphate

    Enzyme and pathway databases

    BRENDAi4.1.1.17. 6519.
    SABIO-RKiP07805.
    UniPathwayiUPA00535; UER00288.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ornithine decarboxylase (EC:4.1.1.171 Publication)
    Short name:
    ODC
    OrganismiTrypanosoma brucei brucei
    Taxonomic identifieri5702 [NCBI]
    Taxonomic lineageiEukaryotaEuglenozoaKinetoplastidaTrypanosomatidaeTrypanosoma

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi358C → S or A: Converts the enzyme into a decarboxylation-dependent transaminase, producing gamma-aminobutyaldehyde (gamma-ABA) and pyridoxamine 5-phosphate (PMP) instead of putrescine. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001499031 – 423Ornithine decarboxylaseAdd BLAST423

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Modified residuei67N6-(pyridoxal phosphate)lysineCombined sources2 Publications1

    Proteomic databases

    PRIDEiP07805.

    Interactioni

    Subunit structurei

    Homodimer. Only the dimer is catalytically active, as the active sites are constructed of residues from both monomers.By similarity

    Structurei

    Secondary structure

    1423
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi19 – 26Combined sources8
    Beta strandi38 – 42Combined sources5
    Helixi43 – 56Combined sources14
    Beta strandi60 – 65Combined sources6
    Helixi66 – 68Combined sources3
    Helixi72 – 80Combined sources9
    Beta strandi84 – 87Combined sources4
    Helixi90 – 98Combined sources9
    Helixi103 – 105Combined sources3
    Beta strandi106 – 108Combined sources3
    Helixi115 – 123Combined sources9
    Beta strandi128 – 131Combined sources4
    Helixi134 – 143Combined sources10
    Beta strandi148 – 153Combined sources6
    Beta strandi166 – 168Combined sources3
    Helixi172 – 184Combined sources13
    Beta strandi188 – 193Combined sources6
    Helixi204 – 222Combined sources19
    Beta strandi229 – 231Combined sources3
    Beta strandi239 – 241Combined sources3
    Beta strandi242 – 244Combined sources3
    Helixi246 – 260Combined sources15
    Beta strandi268 – 271Combined sources4
    Helixi275 – 278Combined sources4
    Helixi279 – 281Combined sources3
    Beta strandi282 – 293Combined sources12
    Beta strandi312 – 317Combined sources6
    Turni320 – 322Combined sources3
    Helixi323 – 325Combined sources3
    Helixi326 – 329Combined sources4
    Beta strandi337 – 340Combined sources4
    Beta strandi348 – 354Combined sources7
    Beta strandi356 – 358Combined sources3
    Beta strandi363 – 371Combined sources9
    Beta strandi378 – 381Combined sources4
    Beta strandi386 – 388Combined sources3
    Helixi389 – 391Combined sources3
    Helixi395 – 397Combined sources3
    Beta strandi402 – 406Combined sources5
    Helixi414 – 418Combined sources5

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1F3TX-ray2.00A/B/C/D1-423[»]
    1QU4X-ray2.90A/B/C/D21-423[»]
    1SZRX-ray2.15A/B/C/D1-423[»]
    2TODX-ray2.00A/B/C/D21-423[»]
    DisProtiDP00051.
    ProteinModelPortaliP07805.
    SMRiP07805.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP07805.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni272 – 275Pyridoxal phosphate binding3 Publications4
    Regioni329 – 330Substrate binding2 Publications2

    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.
    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.

    P07805-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MDIVVNDDLS CRFLEGFNTR DALCKKISMN TCDEGDPFFV ADLGDIVRKH
    60 70 80 90 100
    ETWKKCLPRV TPFYAVKCND DWRVLGTLAA LGTGFDCASN TEIQRVRGIG
    110 120 130 140 150
    VPPEKIIYAN PCKQISHIRY ARDSGVDVMT FDCVDELEKV AKTHPKAKMV
    160 170 180 190 200
    LRISTDDSLA RCRLSVKFGA KVEDCRFILE QAKKLNIDVT GVSFHVGSGS
    210 220 230 240 250
    TDASTFAQAI SDSRFVFDMG TELGFNMHIL DIGGGFPGTR DAPLKFEEIA
    260 270 280 290 300
    GVINNALEKH FPPDLKLTIV AEPGRYYVAS AFTLAVNVIA KKVTPGVQTD
    310 320 330 340 350
    VGAHAESNAQ SFMYYVNDGV YGSFNCILYD HAVVRPLPQR EPIPNEKLYP
    360 370 380 390 400
    SSVWGPTCDG LDQIVERYYL PEMQVGEWLL FEDMGAYTVV GTSSFNGFQS
    410 420
    PTIYYVVSGL PDHVVRELKS QKS
    Length:423
    Mass (Da):46,881
    Last modified:May 30, 2000 - v2
    Checksum:i924A5AA6C4CD2C36
    GO

    Sequence cautioni

    The sequence AAA30218 differs from that shown. Reason: Erroneous initiation.Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    J02771 Genomic DNA. Translation: AAA30218.1. Different initiation.
    J02771 Genomic DNA. Translation: AAA30219.1.

    Genome annotation databases

    GeneDBiTb927.11.13730:pep.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    J02771 Genomic DNA. Translation: AAA30218.1. Different initiation.
    J02771 Genomic DNA. Translation: AAA30219.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1F3TX-ray2.00A/B/C/D1-423[»]
    1QU4X-ray2.90A/B/C/D21-423[»]
    1SZRX-ray2.15A/B/C/D1-423[»]
    2TODX-ray2.00A/B/C/D21-423[»]
    DisProtiDP00051.
    ProteinModelPortaliP07805.
    SMRiP07805.
    ModBaseiSearch...
    MobiDBiSearch...

    Proteomic databases

    PRIDEiP07805.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    GeneDBiTb927.11.13730:pep.

    Enzyme and pathway databases

    UniPathwayiUPA00535; UER00288.
    BRENDAi4.1.1.17. 6519.
    SABIO-RKiP07805.

    Miscellaneous databases

    EvolutionaryTraceiP07805.

    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.
    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.
    ProtoNetiSearch...

    Entry informationi

    Entry nameiDCOR_TRYBB
    AccessioniPrimary (citable) accession number: P07805
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 1, 1988
    Last sequence update: May 30, 2000
    Last modified: February 15, 2017
    This is version 107 of the entry and version 2 of the sequence. See complete history.
    Entry statusiReviewed (UniProtKB/Swiss-Prot)

    Miscellaneousi

    Keywords - Technical termi

    3D-structure

    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.