ODC1B_TOBAC
ID ODC1B_TOBAC Reviewed; 433 AA.
AC P93351; Q40594; Q71S27;
DT 03-AUG-2022, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-1997, sequence version 1.
DT 03-AUG-2022, entry version 111.
DE RecName: Full=Ornithine decarboxylase 1B, chloroplastic {ECO:0000303|PubMed:32242247};
DE Short=Nt-ODC {ECO:0000303|Ref.6};
DE EC=4.1.1.17 {ECO:0000250|UniProtKB:P11926};
DE Flags: Precursor;
GN Name=ODC1B {ECO:0000303|PubMed:32242247};
GN Synonyms=C308 {ECO:0000303|PubMed:18001808},
GN ODC {ECO:0000303|PubMed:9869416, ECO:0000303|Ref.2, ECO:0000303|Ref.4,
GN ECO:0000303|Ref.6}, ODC2;
GN ORFNames=LOC107815922 {ECO:0000312|RefSeq:XP_016497060.1};
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 [MRNA], AND INDUCTION BY JASMONATE.
RC STRAIN=cv. Bright Yellow 2;
RX PubMed=9869416; DOI=10.1023/a:1006058700949;
RA Imanishi S., Hashizume K., Nakakita M., Kojima H., Matsubayashi Y.,
RA Hashimoto T., Sakagami Y., Yamada Y., Nakamura K.;
RT "Differential induction by methyl jasmonate of genes encoding ornithine
RT decarboxylase and other enzymes involved in nicotine biosynthesis in
RT tobacco cell cultures.";
RL Plant Mol. Biol. 38:1101-1111(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC STRAIN=cv. Burley 21; TISSUE=Root;
RA Wang J., Timko M.P.;
RT "Cloning and characterization of a cDNA encoding ornithine decarboxylase, a
RT key enzyme in polyamine and alkaloid biosynthesis in Nicotiana tabacum L.";
RL Submitted (FEB-1999) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC STRAIN=cv. SR1;
RA Cordeiro A.F.;
RT "Nicotiana tabacum cDNA for ornithine decarboxylase.";
RL Submitted (NOV-2000) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=cv. Burley 21;
RA Xu B., Sheehan M.J., Timko M.P.;
RT "Differential induction of ornithine decarboxylase (ODC) gene family
RT members in transgenic tobacco (Nicotiana tabacum L. cv. Bright Yellow 2)
RT cell suspensions by methyl-jasmonate treatment.";
RL Plant Growth Regul. 44:101-116(2004).
RN [5]
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 [6]
RP NUCLEOTIDE SEQUENCE [MRNA] OF 191-433.
RA Malik V., Watson M.G., Malmberg R.L.;
RT "A tobacco ornithine decarboxylase partial cDNA clone.";
RL J. Plant Biochem. Biotechnol. 5:109-112(1996).
RN [7]
RP REVIEW.
RC TISSUE=Protoplast;
RX PubMed=18001808; DOI=10.1016/j.phytochem.2007.09.010;
RA Haekkinen S.T., Tilleman S., Swiatek A., De Sutter V., Rischer H.,
RA Vanhoutte I., Van Onckelen H., Hilson P., Inze D., Oksman-Caldentey K.-M.,
RA Goossens A.;
RT "Functional characterisation of genes involved in pyridine alkaloid
RT biosynthesis in tobacco.";
RL Phytochemistry 68:2773-2785(2007).
RN [8]
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 [9]
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 [10]
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 [11]
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 -!- INDUCTION: Accumulates transiently in response to jasmonic acid (MeJA).
CC {ECO:0000269|PubMed:9869416}.
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; D89984; BAA14049.1; -; mRNA.
DR EMBL; AF127242; AAF42973.1; -; mRNA.
DR EMBL; AF321138; AAQ14852.1; -; mRNA.
DR EMBL; AF233849; AAK13622.1; -; Genomic_DNA.
DR EMBL; U59812; AAB65826.1; -; mRNA.
DR PIR; T03035; T03035.
DR RefSeq; NP_001312894.1; NM_001325965.1.
DR RefSeq; XP_016497060.1; XM_016641574.1.
DR SMR; P93351; -.
DR GeneID; 107815922; -.
DR KEGG; nta:107815922; -.
DR OMA; WRTHMAQ; -.
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:0033387; P:putrescine biosynthetic process from ornithine; IBA:GO_Central.
DR GO; GO:0009753; P:response to jasmonic acid; IEP: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 ?..433
FT /note="Ornithine decarboxylase 1B, chloroplastic"
FT /id="PRO_0000455776"
FT ACT_SITE 378
FT /note="Proton donor; shared with dimeric partner"
FT /evidence="ECO:0000250|UniProtKB:P11926"
FT BINDING 228
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250|UniProtKB:P11926"
FT BINDING 266
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250|UniProtKB:P11926"
FT BINDING 299..302
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250|UniProtKB:P11926"
FT BINDING 342..343
FT /ligand="substrate"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000250|UniProtKB:P07805"
FT BINDING 379
FT /ligand="substrate"
FT /ligand_note="ligand shared between dimeric partners"
FT /evidence="ECO:0000250|UniProtKB:P07805"
FT BINDING 407
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250|UniProtKB:P11926"
FT SITE 225
FT /note="Stacks against the aromatic ring of pyridoxal
FT phosphate and stabilizes reaction intermediates"
FT /evidence="ECO:0000250|UniProtKB:P00860"
FT MOD_RES 96
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000250|UniProtKB:P11926"
FT CONFLICT 179..180
FT /note="LL -> SV (in Ref. 3; AAQ14852)"
FT /evidence="ECO:0000305"
FT CONFLICT 192..193
FT /note="CP -> SA (in Ref. 3; AAQ14852)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 433 AA; 46554 MW; B391D68A3CDEDACB CRC64;
MAGQTIIVSG LNPAAILQST IGGGASPTAA AAAENGTRKV IPLSRDALQD FMLSIITQKL
QDEKQPFYVL DLGEVVSLMD QWKSALPNIR PFYAVKCNPE PSFLSILSAM GSNFDCASRA
EIEYVLSLGI SPDRIVFANP CKPESDIIFA AKVGVNLTTY DSEDEVYKIR KHHPKSELLL
RIKPMLDGNA RCPMGPKYGA LPEEVDPLLR AAQAARLTVS GVSFHIGSGD ADSNAYLGAI
AAAKEVFETA AKLGMSKMTV LDVGGGFTSG HQFTTAAVAV KSALKQHFDD EPELTIIAEP
GRFFAETAFT LATTIIGKRV RGELREYWIN DGLYGSMNCV LYDHATVNAT PLAVLSNRSN
VTCGGSKTFP TTVFGPTCDA LDTVLRDYQL PELQVNDWLV FPNMGAYTKA AGSNFNGFNT
SAIVTHLAYS YPS
