ODC_NICGU
ID ODC_NICGU Reviewed; 432 AA.
AC Q9FPK5;
DT 03-AUG-2022, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2001, sequence version 1.
DT 03-AUG-2022, entry version 72.
DE RecName: Full=Ornithine decarboxylase, chloroplastic {ECO:0000303|PubMed:11736657};
DE EC=4.1.1.17 {ECO:0000250|UniProtKB:P11926};
DE AltName: Full=Lysine decarboxylase {ECO:0000303|PubMed:11736657};
DE EC=4.1.1.18 {ECO:0000250|UniProtKB:P11926};
DE Flags: Precursor;
GN Name=ODC {ECO:0000303|PubMed:11736657};
OS Nicotiana glutinosa (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=35889;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, MUTAGENESIS OF LYS-95; CYS-96;
RP CYS-338 AND CYS-377, CATALYTIC ACTIVITY, PATHWAY, SUBUNIT,
RP BIOPHYSICOCHEMICAL PROPERTIES, AND ACTIVITY REGULATION.
RX PubMed=11736657; DOI=10.1042/0264-6021:3600657;
RA Lee Y.-S., Cho Y.-D.;
RT "Identification of essential active-site residues in ornithine
RT decarboxylase of Nicotiana glutinosa decarboxylating both L-ornithine and
RT L-lysine.";
RL Biochem. J. 360:657-665(2001).
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) (By similarity). Catalyzes the first and rate-
CC limiting step of polyamine biosynthesis that converts ornithine into
CC putrescine, which is the precursor for the polyamines, spermidine and
CC spermine (PubMed:11736657). Can also use, with a lower efficiency, L-
CC lysine as substrate to produce cadaverine (PubMed:11736657). Polyamines
CC are 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:0000250|UniProtKB:P93351,
CC ECO:0000269|PubMed:11736657}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H(+) + L-lysine = cadaverine + CO2; Xref=Rhea:RHEA:22352,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:16526, ChEBI:CHEBI:32551,
CC ChEBI:CHEBI:58384; EC=4.1.1.18;
CC Evidence={ECO:0000269|PubMed:11736657};
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:0000269|PubMed:11736657};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000250|UniProtKB:P11926};
CC -!- ACTIVITY REGULATION: Repressed by alpha-difluoromethylornithine (DFMO),
CC 5,5'-dithiobis-(2-nitrobenzoic acid) (DTNB) and salicylaldehyde.
CC {ECO:0000269|PubMed:11736657}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=562 uM for L-ornithine (at pH 8.0) {ECO:0000269|PubMed:11736657};
CC KM=1592 uM for L-lysine (at pH 6.8) {ECO:0000269|PubMed:11736657};
CC Vmax=12.54 nmol/min/mg enzyme with L-ornithine as substrate (at pH
CC 8.0) {ECO:0000269|PubMed:11736657};
CC Vmax=0.152 nmol/min/mg enzyme with L-lysine as substrate (at pH 6.8)
CC {ECO:0000269|PubMed:11736657};
CC Note=kcat is 77.78 sec(-1) with L-ornithine as substrate (at pH 8.0)
CC (PubMed:11736657). kcat is 0.236 sec(-1) with L-lysine as substrate
CC (at pH 6.8) (PubMed:11736657). {ECO:0000269|PubMed:11736657};
CC pH dependence:
CC Optimum pH is 8.0 with L-ornithine as substrate (PubMed:11736657).
CC Optimum pH is 6.8 with L-lysine as substrate (PubMed:11736657).
CC {ECO:0000269|PubMed:11736657};
CC -!- PATHWAY: Alkaloid biosynthesis; nicotine biosynthesis.
CC {ECO:0000250|UniProtKB:A0A1S4AUX8}.
CC -!- PATHWAY: Amine and polyamine biosynthesis; putrescine biosynthesis via
CC L-ornithine pathway; putrescine from L-ornithine: step 1/1.
CC {ECO:0000269|PubMed:11736657}.
CC -!- SUBUNIT: Homodimer (PubMed:11736657). 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 ECO:0000269|PubMed:11736657}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast {ECO:0000255}.
CC -!- SIMILARITY: Belongs to the Orn/Lys/Arg decarboxylase class-II family.
CC {ECO:0000305}.
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DR EMBL; AF323910; AAG45222.1; -; mRNA.
DR SMR; Q9FPK5; -.
DR BRENDA; 4.1.1.17; 3636.
DR SABIO-RK; Q9FPK5; -.
DR UniPathway; UPA00107; -.
DR UniPathway; UPA00535; UER00288.
DR GO; GO:0042802; F:identical protein binding; IDA:UniProtKB.
DR GO; GO:0008923; F:lysine decarboxylase activity; IDA:UniProtKB.
DR GO; GO:0004586; F:ornithine decarboxylase activity; IDA:UniProtKB.
DR GO; GO:0042803; F:protein homodimerization activity; IDA:UniProtKB.
DR GO; GO:0033387; P:putrescine biosynthetic process from ornithine; IDA: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 1: Evidence at protein level;
KW Alkaloid metabolism; Chloroplast; Lyase; Plastid; Pyridoxal phosphate;
KW Transit peptide.
FT TRANSIT 1..?
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN ?..432
FT /note="Ornithine decarboxylase, chloroplastic"
FT /id="PRO_0000455778"
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 MUTAGEN 95
FT /note="K->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:11736657"
FT MUTAGEN 96
FT /note="C->A: Almost unchanged activity."
FT /evidence="ECO:0000269|PubMed:11736657"
FT MUTAGEN 338
FT /note="C->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:11736657"
FT MUTAGEN 377
FT /note="C->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:11736657"
SQ SEQUENCE 432 AA; 46559 MW; 65E8160F2691AB79 CRC64;
MAGQTIIVSG LNPAAILQST IGGGASPTAA AAENGTRKVI PLSRDALQDF MLSIITQKLQ
DEKQPFYVLD LGEVVSLMDQ WKSSLPNIRP FYAVKCNPEP SFLSILSAMG SNFDCASRAE
IEYVLALGIS PDRIVFANPC KPESDIIFAA KVGVNLTTYD SEDEVYKIRK HHPKSELLPR
IKPMFDGNAR CPMGPKYGAL PEEVEPLLRA AQAARLTVSG VSFHIGSGDA DSNAYLGAIA
AAKEVFETAA KLGMSKMTVL DVGGGFTSGH QFTTAAVAVK SALKQHFDDE PELTIIAEPG
RFFAETAFTL ATTVIGKRVR GELREYWIND GLYGSMNCVL YDHATVNATP LAVLSNRTNV
TCGGSKTFPT TVFGPTCDAL DTVLRDYQLP ELQVNDWLVF PNMGAYTKAA GSNFNGFNTS
TIVTHLAYTY PS
