ODC1A_TOBAC
ID ODC1A_TOBAC Reviewed; 432 AA.
AC A0A1S4AUX8; A0A0M4URG0; Q9SXF3;
DT 03-AUG-2022, integrated into UniProtKB/Swiss-Prot.
DT 12-APR-2017, sequence version 1.
DT 03-AUG-2022, entry version 22.
DE RecName: Full=Ornithine decarboxylase 1A, chloroplastic {ECO:0000303|PubMed:32242247};
DE EC=4.1.1.17 {ECO:0000250|UniProtKB:P11926};
DE Flags: Precursor;
GN Name=ODC1A {ECO:0000303|PubMed:32242247};
GN Synonyms=ODC {ECO:0000303|Ref.1, ECO:0000303|Ref.2}, ODC1;
GN ORFNames=LOC107801491 {ECO:0000312|RefSeq:XP_016480308.1};
OS Nicotiana tabacum (Common tobacco).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC asterids; lamiids; Solanales; Solanaceae; Nicotianoideae; Nicotianeae;
OC Nicotiana.
OX NCBI_TaxID=4097;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=cv. NK 326;
RA Imanishi S., Nakakita M., Yamashita K., Furuta A., Utsuno K., Muramoto N.,
RA Kojima H., Nakamura K.;
RT "Aspirin and Salicylic Acid Do not Inhibit Methyl Jasmonate-inducible
RT Expression of a Gene for Ornithine Decarboxylase in Tabacco BY-2 Cells.";
RL Submitted (AUG-1999) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC STRAIN=cv. Petit Havana SR1;
RA Bunsupa S., Yamazaki M., Saito K.;
RT "Plant lysine decarboxylase independently evolved from ornithine
RT decarboxylase to produce alkaloids.";
RL Submitted (FEB-2015) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. TN90;
RX PubMed=24807620; DOI=10.1038/ncomms4833;
RA Sierro N., Battey J.N., Ouadi S., Bakaher N., Bovet L., Willig A.,
RA Goepfert S., Peitsch M.C., Ivanov N.V.;
RT "The tobacco genome sequence and its comparison with those of tomato and
RT potato.";
RL Nat. Commun. 5:3833-3833(2014).
RN [4]
RP REVIEW ON ALKALOID BIOSYNTHESIS IN NICOTIANA TABACUM.
RX PubMed=23953973; DOI=10.1016/j.phytochem.2013.06.002;
RA Dewey R.E., Xie J.;
RT "Molecular genetics of alkaloid biosynthesis in Nicotiana tabacum.";
RL Phytochemistry 94:10-27(2013).
RN [5]
RP REVIEW ON NICOTINE BIOSYNTHESIS.
RX PubMed=25582664; DOI=10.1007/s00438-015-0989-7;
RA Wang X., Bennetzen J.L.;
RT "Current status and prospects for the study of Nicotiana genomics,
RT genetics, and nicotine biosynthesis genes.";
RL Mol. Genet. Genomics 290:11-21(2015).
RN [6]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. SC58;
RX PubMed=27126795; DOI=10.1093/jxb/erw166;
RA Dalton H.L., Blomstedt C.K., Neale A.D., Gleadow R., DeBoer K.D.,
RA Hamill J.D.;
RT "Effects of down-regulating ornithine decarboxylase upon putrescine-
RT associated metabolism and growth in Nicotiana tabacum L.";
RL J. Exp. Bot. 67:3367-3381(2016).
RN [7]
RP FUNCTION, DISRUPTION PHENOTYPE, AND PATHWAY.
RC STRAIN=cv. K326-ALCS3;
RX PubMed=32242247; DOI=10.1007/s00425-020-03387-1;
RA Hidalgo Martinez D., Payyavula R.S., Kudithipudi C., Shen Y., Xu D.,
RA Warek U., Strickland J.A., Melis A.;
RT "Genetic attenuation of alkaloids and nicotine content in tobacco
RT (Nicotiana tabacum).";
RL Planta 251:92-92(2020).
CC -!- FUNCTION: Involved in the biosynthesis of pyridine alkaloid natural
CC products, leading mainly to the production of anabasine, anatabine,
CC nicotine and nornicotine, effective deterrents against herbivores with
CC antiparasitic and pesticide properties (neurotoxins); nornicotine
CC serves as the precursor in the synthesis of the carcinogen compound N'-
CC nitrosonornicotine (NNN) (PubMed:32242247, PubMed:27126795). Catalyzes
CC the first and rate-limiting step of polyamine biosynthesis that
CC converts ornithine into putrescine, which is the precursor for the
CC polyamines, spermidine and spermine (By similarity). Polyamines are
CC essential for cell proliferation and are implicated in cellular
CC processes, ranging from DNA replication to apoptosis (By similarity).
CC {ECO:0000250|UniProtKB:P11926, ECO:0000269|PubMed:27126795,
CC ECO:0000269|PubMed:32242247}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H(+) + L-ornithine = CO2 + putrescine; Xref=Rhea:RHEA:22964,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:16526, ChEBI:CHEBI:46911,
CC ChEBI:CHEBI:326268; EC=4.1.1.17;
CC Evidence={ECO:0000250|UniProtKB:P11926};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000250|UniProtKB:P11926};
CC -!- PATHWAY: Alkaloid biosynthesis; nicotine biosynthesis.
CC {ECO:0000269|PubMed:32242247}.
CC -!- PATHWAY: Amine and polyamine biosynthesis; putrescine biosynthesis via
CC L-ornithine pathway; putrescine from L-ornithine: step 1/1.
CC {ECO:0000250|UniProtKB:O22616}.
CC -!- SUBUNIT: Homodimer (By similarity). Only the dimer is catalytically
CC active, as the active sites are constructed of residues from both
CC monomers (By similarity). {ECO:0000250|UniProtKB:P11926}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast {ECO:0000255}.
CC -!- DISRUPTION PHENOTYPE: Reduced alkaloids and nicotin levels associated
CC with a lower putrescine production (PubMed:32242247). Occasionally, an
CC early senescence and a lower viability of the older leaves is observed
CC (PubMed:32242247). Plants lacking both ODC1A and ODC1B have lower
CC concentrations of nicotine and nornicotine as well as of polyamines
CC (putrescine, spermidine and spermine), tyramine and phenolamides
CC (caffeoylputrescine and dicaffeoylspermidine), but significantly higher
CC levels of anatabine and of amino acids ornithine, arginine, aspartate,
CC glutamate and glutamine; these phenotypes are associated with reduced
CC plant growth and vigor, and are exacerbated by wounding and shoot apex
CC removal (PubMed:27126795). {ECO:0000269|PubMed:27126795,
CC ECO:0000269|PubMed:32242247}.
CC -!- SIMILARITY: Belongs to the Orn/Lys/Arg decarboxylase class-II family.
CC {ECO:0000305}.
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DR EMBL; AB031066; BAA83427.1; -; Genomic_DNA.
DR EMBL; LC030209; BAS29588.1; -; mRNA.
DR RefSeq; NP_001312626.1; NM_001325697.1.
DR RefSeq; XP_016480308.1; XM_016624822.1.
DR SMR; A0A1S4AUX8; -.
DR GeneID; 107801491; -.
DR KEGG; nta:107801491; -.
DR OMA; SFFVCDL; -.
DR OrthoDB; 725914at2759; -.
DR UniPathway; UPA00107; -.
DR UniPathway; UPA00535; UER00288.
DR Proteomes; UP000084051; Unplaced.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0004586; F:ornithine decarboxylase activity; IBA:GO_Central.
DR GO; GO:0042179; P:nicotine biosynthetic process; IMP:UniProtKB.
DR GO; GO:0006596; P:polyamine biosynthetic process; IMP:UniProtKB.
DR GO; GO:0033387; P:putrescine biosynthetic process from ornithine; IBA:GO_Central.
DR GO; GO:0009611; P:response to wounding; IMP:UniProtKB.
DR GO; GO:1901695; P:tyramine biosynthetic process; IMP:UniProtKB.
DR Gene3D; 2.40.37.10; -; 1.
DR Gene3D; 3.20.20.10; -; 1.
DR InterPro; IPR009006; Ala_racemase/Decarboxylase_C.
DR InterPro; IPR022643; De-COase2_C.
DR InterPro; IPR022657; De-COase2_CS.
DR InterPro; IPR022644; De-COase2_N.
DR InterPro; IPR022653; De-COase2_pyr-phos_BS.
DR InterPro; IPR000183; Orn/DAP/Arg_de-COase.
DR InterPro; IPR002433; Orn_de-COase.
DR InterPro; IPR029066; PLP-binding_barrel.
DR PANTHER; PTHR11482; PTHR11482; 1.
DR Pfam; PF02784; Orn_Arg_deC_N; 1.
DR Pfam; PF00278; Orn_DAP_Arg_deC; 1.
DR PRINTS; PR01179; ODADCRBXLASE.
DR PRINTS; PR01182; ORNDCRBXLASE.
DR SUPFAM; SSF50621; SSF50621; 1.
DR SUPFAM; SSF51419; SSF51419; 1.
DR PROSITE; PS00878; ODR_DC_2_1; 1.
DR PROSITE; PS00879; ODR_DC_2_2; 1.
PE 2: Evidence at transcript level;
KW Alkaloid metabolism; Chloroplast; Lyase; Plastid; Pyridoxal phosphate;
KW Reference proteome; Transit peptide.
FT TRANSIT 1..?
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN ?..432
FT /note="Ornithine decarboxylase 1A, chloroplastic"
FT /id="PRO_0000455775"
FT ACT_SITE 377
FT /note="Proton donor; shared with dimeric partner"
FT /evidence="ECO:0000250|UniProtKB:P11926"
FT BINDING 227
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250|UniProtKB:P11926"
FT BINDING 265
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250|UniProtKB:P11926"
FT BINDING 298..301
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250|UniProtKB:P11926"
FT BINDING 341..342
FT /ligand="substrate"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000250|UniProtKB:P07805"
FT BINDING 378
FT /ligand="substrate"
FT /ligand_note="ligand shared between dimeric partners"
FT /evidence="ECO:0000250|UniProtKB:P07805"
FT BINDING 406
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250|UniProtKB:P11926"
FT SITE 224
FT /note="Stacks against the aromatic ring of pyridoxal
FT phosphate and stabilizes reaction intermediates"
FT /evidence="ECO:0000250|UniProtKB:P00860"
FT MOD_RES 95
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000250|UniProtKB:P11926"
FT CONFLICT 78
FT /note="I -> M (in Ref. 2; BAS29588 and 1; BAA83427)"
FT /evidence="ECO:0000305"
FT CONFLICT 420
FT /note="S -> C (in Ref. 1; BAA83427)"
FT /evidence="ECO:0000305"
FT CONFLICT 429
FT /note="A -> T (in Ref. 2; BAS29588 and 1; BAA83427)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 432 AA; 46538 MW; 4D3CEBC5369E6CEF CRC64;
MAGQTIIVSG LNPAAILQST IGGGASPTAA AAENGTRKVI PLSRDALQDF MLSIITQKLQ
DEKQPFYVLD LGEVVSLIDQ WKSALPNIRP FYAVKCNPEP SFLSILSAMG SNFDCASRAE
IEYVLSLGIS PDRIVFANPC KPESDIIFAA KVGVNLTTYD SEDEVYKIRK HHPKSELLLR
IKPMFDGNAR CPMGPKYGAL PEEVEPLLRA AQAARLTVSG VSFHIGSGDA DSNAYLGAIA
AAKEVFETAA KLGMSKMTVL DVGGGFTSGH QFTTAAVAVR SALKQHFDDQ PELTIIAEPG
RFFAETAFTL ATTIIGKRVR GELREYWIND GLYGSMNCVL YDHATVNATP LAVLSNRTNV
TCGGSKTFPT TVFGPTCDAL DTVLRDYQLP ELQVNDWLVF PNMGAYTKAA GSNFNGFNTS
AIVTHLAYAY PS
