TDC1_ORYSJ
ID TDC1_ORYSJ Reviewed; 514 AA.
AC Q6ZJK7;
DT 20-JUN-2018, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 03-AUG-2022, entry version 137.
DE RecName: Full=Tryptophan decarboxylase 1 {ECO:0000303|PubMed:17763868};
DE EC=4.1.1.28 {ECO:0000269|PubMed:17763868, ECO:0000269|PubMed:32595985};
DE AltName: Full=5-hydroxytryptophan decarboxylase TDC1 {ECO:0000305};
GN Name=TDC1 {ECO:0000303|PubMed:17763868};
GN OrderedLocusNames=Os08g0140300 {ECO:0000312|EMBL:BAF22882.1},
GN LOC_Os08g04540 {ECO:0000305};
GN ORFNames=OJ1368_G08.14 {ECO:0000312|EMBL:BAD11581.1},
GN OsJ_25993 {ECO:0000312|EMBL:EAZ41470.1};
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT "The genomes of Oryza sativa: a history of duplications.";
RL PLoS Biol. 3:266-281(2005).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12869764; DOI=10.1126/science.1081288;
RG The rice full-length cDNA consortium;
RT "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT japonica rice.";
RL Science 301:376-379(2003).
RN [6]
RP FUNCTION, CATALYTIC ACTIVITY, AND BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=17763868; DOI=10.1007/s00425-007-0614-z;
RA Kang S., Kang K., Lee K., Back K.;
RT "Characterization of rice tryptophan decarboxylases and their direct
RT involvement in serotonin biosynthesis in transgenic rice.";
RL Planta 227:263-272(2007).
RN [7]
RP FUNCTION, AND INDUCTION.
RX PubMed=19439571; DOI=10.1104/pp.109.138552;
RA Kang K., Kim Y.S., Park S., Back K.;
RT "Senescence-induced serotonin biosynthesis and its role in delaying
RT senescence in rice leaves.";
RL Plant Physiol. 150:1380-1393(2009).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (1.97 ANGSTROMS) IN COMPLEX WITH PYRIDOXAL PHOSPHATE;
RP TRYPTAMINE AND SEROTONIN, FUNCTION, CATALYTIC ACTIVITY, ACTIVE SITE,
RP SUBUNIT, N6-(PYRIDOXAL PHOSPHATE)LYSINE, AND MUTAGENESIS OF TRP-95;
RP SER-106; PHE-127; HIS-214; ASP-298; ALA-300; LYS-330; LEU-336; GLU-358;
RP TYR-359; LEU-360; LYS-361 AND VAL-380.
RX PubMed=32595985; DOI=10.1016/j.jare.2020.06.004;
RA Zhou Y., Liao L., Liu X., Liu B., Chen X., Guo Y., Huang C., Zhao Y.,
RA Zeng Z.;
RT "Crystal structure of Oryza sativa TDC reveals the substrate specificity
RT for TDC-mediated melatonin biosynthesis.";
RL J. Adv. Res. 24:501-511(2020).
CC -!- FUNCTION: Involved in serotonin biosynthesis (PubMed:17763868,
CC PubMed:32595985, PubMed:19439571). Catalyzes the decarboxylation of L-
CC tryptophan to produce tryptamine, which is converted to serotonin by
CC tryptamine 5-hydroxylase (PubMed:17763868, PubMed:32595985). May play a
CC major role in serotonin biosynthesis during senescence
CC (PubMed:19439571). Accumulation of serotonin attenuates leaf senescence
CC (PubMed:19439571). Catalyzes the decarboxylation of 5-hydroxy-L-
CC tryptophan to produce serotonin (PubMed:32595985).
CC {ECO:0000269|PubMed:17763868, ECO:0000269|PubMed:19439571,
CC ECO:0000269|PubMed:32595985}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H(+) + L-tryptophan = CO2 + tryptamine; Xref=Rhea:RHEA:30339,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:16526, ChEBI:CHEBI:57887,
CC ChEBI:CHEBI:57912; EC=4.1.1.28;
CC Evidence={ECO:0000269|PubMed:17763868, ECO:0000269|PubMed:32595985};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:30340;
CC Evidence={ECO:0000269|PubMed:17763868, ECO:0000269|PubMed:32595985};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=5-hydroxy-L-tryptophan + H(+) = CO2 + serotonin;
CC Xref=Rhea:RHEA:18533, ChEBI:CHEBI:15378, ChEBI:CHEBI:16526,
CC ChEBI:CHEBI:58266, ChEBI:CHEBI:350546; EC=4.1.1.28;
CC Evidence={ECO:0000269|PubMed:32595985};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:18534;
CC Evidence={ECO:0000269|PubMed:32595985};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000269|PubMed:17763868, ECO:0000269|PubMed:32595985};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.69 mM for tryptophan {ECO:0000269|PubMed:17763868};
CC -!- SUBUNIT: Forms homodimers. {ECO:0000269|PubMed:32595985}.
CC -!- INDUCTION: Induced by senescence and abscisic acid (ABA).
CC {ECO:0000269|PubMed:19439571}.
CC -!- SIMILARITY: Belongs to the group II decarboxylase family.
CC {ECO:0000305}.
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DR EMBL; AP003911; BAD11581.1; -; Genomic_DNA.
DR EMBL; AP008214; BAF22882.1; -; Genomic_DNA.
DR EMBL; AP014964; BAT03777.1; -; Genomic_DNA.
DR EMBL; CM000145; EAZ41470.1; -; Genomic_DNA.
DR EMBL; AK069031; BAG91223.1; -; mRNA.
DR RefSeq; XP_015648701.1; XM_015793215.1.
DR PDB; 6KHN; X-ray; 2.29 A; A/B=1-514.
DR PDB; 6KHO; X-ray; 1.97 A; A/B=1-514.
DR PDB; 6KHP; X-ray; 2.30 A; A/B=1-514.
DR PDBsum; 6KHN; -.
DR PDBsum; 6KHO; -.
DR PDBsum; 6KHP; -.
DR AlphaFoldDB; Q6ZJK7; -.
DR SMR; Q6ZJK7; -.
DR STRING; 4530.OS08T0140300-01; -.
DR PaxDb; Q6ZJK7; -.
DR PRIDE; Q6ZJK7; -.
DR EnsemblPlants; Os08t0140300-01; Os08t0140300-01; Os08g0140300.
DR GeneID; 4344636; -.
DR Gramene; Os08t0140300-01; Os08t0140300-01; Os08g0140300.
DR KEGG; osa:4344636; -.
DR eggNOG; KOG0628; Eukaryota.
DR HOGENOM; CLU_011856_3_1_1; -.
DR InParanoid; Q6ZJK7; -.
DR OMA; FICPEMR; -.
DR OrthoDB; 856958at2759; -.
DR PlantReactome; R-OSA-1119344; Hydroxycinnamic acid serotonin amides biosynthesis.
DR PlantReactome; R-OSA-1119438; Secologanin and strictosidine biosynthesis.
DR PlantReactome; R-OSA-1119486; IAA biosynthesis I.
DR Proteomes; UP000000763; Chromosome 8.
DR Proteomes; UP000007752; Chromosome 8.
DR Proteomes; UP000059680; Chromosome 8.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0036467; F:5-hydroxy-L-tryptophan decarboxylase activity; IEA:RHEA.
DR GO; GO:0016831; F:carboxy-lyase activity; IBA:GO_Central.
DR GO; GO:0036469; F:L-tryptophan decarboxylase activity; IDA:UniProtKB.
DR GO; GO:0030170; F:pyridoxal phosphate binding; IDA:UniProtKB.
DR GO; GO:0006587; P:serotonin biosynthetic process from tryptophan; IDA:UniProtKB.
DR Gene3D; 3.40.640.10; -; 1.
DR Gene3D; 3.90.1150.10; -; 1.
DR InterPro; IPR010977; Aromatic_deC.
DR InterPro; IPR002129; PyrdxlP-dep_de-COase.
DR InterPro; IPR015424; PyrdxlP-dep_Trfase.
DR InterPro; IPR015421; PyrdxlP-dep_Trfase_major.
DR InterPro; IPR015422; PyrdxlP-dep_Trfase_small.
DR InterPro; IPR021115; Pyridoxal-P_BS.
DR Pfam; PF00282; Pyridoxal_deC; 1.
DR PRINTS; PR00800; YHDCRBOXLASE.
DR SUPFAM; SSF53383; SSF53383; 1.
DR PROSITE; PS00392; DDC_GAD_HDC_YDC; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Decarboxylase; Lyase; Pyridoxal phosphate;
KW Reference proteome; Serotonin biosynthesis.
FT CHAIN 1..514
FT /note="Tryptophan decarboxylase 1"
FT /id="PRO_0000444622"
FT ACT_SITE 359
FT /note="Proton donor"
FT /evidence="ECO:0000269|PubMed:32595985"
FT BINDING 104
FT /ligand="serotonin"
FT /ligand_id="ChEBI:CHEBI:350546"
FT /evidence="ECO:0000269|PubMed:32595985,
FT ECO:0007744|PDB:6KHN"
FT BINDING 175
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000269|PubMed:32595985,
FT ECO:0007744|PDB:6KHN, ECO:0007744|PDB:6KHO,
FT ECO:0007744|PDB:6KHP"
FT BINDING 176
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000269|PubMed:32595985,
FT ECO:0007744|PDB:6KHN, ECO:0007744|PDB:6KHO,
FT ECO:0007744|PDB:6KHP"
FT BINDING 214
FT /ligand="serotonin"
FT /ligand_id="ChEBI:CHEBI:350546"
FT /evidence="ECO:0000269|PubMed:32595985,
FT ECO:0007744|PDB:6KHN"
FT BINDING 273
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250|UniProtKB:P20711"
FT BINDING 380
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000269|PubMed:32595985,
FT ECO:0007744|PDB:6KHP"
FT BINDING 381
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000269|PubMed:32595985,
FT ECO:0007744|PDB:6KHO"
FT MOD_RES 330
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000269|PubMed:32595985,
FT ECO:0007744|PDB:6KHN, ECO:0007744|PDB:6KHP"
FT MUTAGEN 95
FT /note="W->A: Abolishes enzymatic activity."
FT /evidence="ECO:0000269|PubMed:32595985"
FT MUTAGEN 106
FT /note="S->A: Slightly increases enzymatic activity."
FT /evidence="ECO:0000269|PubMed:32595985"
FT MUTAGEN 127
FT /note="F->A: Reduces enzymatic activity 5-fold."
FT /evidence="ECO:0000269|PubMed:32595985"
FT MUTAGEN 214
FT /note="H->A,F,Q: Reduces enzymatic activity 50-fold."
FT /evidence="ECO:0000269|PubMed:32595985"
FT MUTAGEN 214
FT /note="H->Q: Reduces enzymatic activity 20-fold."
FT /evidence="ECO:0000269|PubMed:32595985"
FT MUTAGEN 214
FT /note="H->Y: Abolishes enzymatic activity."
FT /evidence="ECO:0000269|PubMed:32595985"
FT MUTAGEN 298
FT /note="D->A: Abolishes enzymatic activity."
FT /evidence="ECO:0000269|PubMed:32595985"
FT MUTAGEN 300
FT /note="A->G: Reduces enzymatic activity 7-fold."
FT /evidence="ECO:0000269|PubMed:32595985"
FT MUTAGEN 330
FT /note="K->A: Abolishes enzymatic activity."
FT /evidence="ECO:0000269|PubMed:32595985"
FT MUTAGEN 336
FT /note="L->A: Reduces enzymatic activity 40-fold."
FT /evidence="ECO:0000269|PubMed:32595985"
FT MUTAGEN 358
FT /note="E->A: Slightly decreases enzymatic activity."
FT /evidence="ECO:0000269|PubMed:32595985"
FT MUTAGEN 359
FT /note="Y->A,F,H: Abolishes enzymatic activity."
FT /evidence="ECO:0000269|PubMed:32595985"
FT MUTAGEN 359
FT /note="Y->Q: Reduces enzymatic activity 20-fold."
FT /evidence="ECO:0000269|PubMed:32595985"
FT MUTAGEN 360
FT /note="L->A: Abolishes enzymatic activity."
FT /evidence="ECO:0000269|PubMed:32595985"
FT MUTAGEN 361
FT /note="K->A: No effect on enzymatic activity."
FT /evidence="ECO:0000269|PubMed:32595985"
FT MUTAGEN 380
FT /note="V->A: Reduces enzymatic activity 5-fold."
FT /evidence="ECO:0000269|PubMed:32595985"
FT HELIX 27..47
FT /evidence="ECO:0007829|PDB:6KHO"
FT HELIX 48..50
FT /evidence="ECO:0007829|PDB:6KHO"
FT HELIX 61..65
FT /evidence="ECO:0007829|PDB:6KHO"
FT HELIX 77..87
FT /evidence="ECO:0007829|PDB:6KHO"
FT HELIX 89..91
FT /evidence="ECO:0007829|PDB:6KHO"
FT STRAND 102..104
FT /evidence="ECO:0007829|PDB:6KHO"
FT HELIX 110..122
FT /evidence="ECO:0007829|PDB:6KHO"
FT STRAND 127..129
FT /evidence="ECO:0007829|PDB:6KHO"
FT HELIX 133..149
FT /evidence="ECO:0007829|PDB:6KHO"
FT HELIX 154..156
FT /evidence="ECO:0007829|PDB:6KHO"
FT STRAND 168..173
FT /evidence="ECO:0007829|PDB:6KHO"
FT HELIX 175..194
FT /evidence="ECO:0007829|PDB:6KHO"
FT HELIX 200..204
FT /evidence="ECO:0007829|PDB:6KHO"
FT STRAND 205..210
FT /evidence="ECO:0007829|PDB:6KHO"
FT HELIX 215..223
FT /evidence="ECO:0007829|PDB:6KHO"
FT HELIX 228..230
FT /evidence="ECO:0007829|PDB:6KHO"
FT STRAND 231..234
FT /evidence="ECO:0007829|PDB:6KHO"
FT HELIX 238..240
FT /evidence="ECO:0007829|PDB:6KHO"
FT HELIX 246..258
FT /evidence="ECO:0007829|PDB:6KHO"
FT STRAND 262..271
FT /evidence="ECO:0007829|PDB:6KHO"
FT TURN 273..275
FT /evidence="ECO:0007829|PDB:6KHO"
FT HELIX 281..289
FT /evidence="ECO:0007829|PDB:6KHO"
FT TURN 290..292
FT /evidence="ECO:0007829|PDB:6KHO"
FT STRAND 294..298
FT /evidence="ECO:0007829|PDB:6KHO"
FT HELIX 302..307
FT /evidence="ECO:0007829|PDB:6KHO"
FT TURN 309..311
FT /evidence="ECO:0007829|PDB:6KHO"
FT HELIX 312..315
FT /evidence="ECO:0007829|PDB:6KHO"
FT HELIX 318..320
FT /evidence="ECO:0007829|PDB:6KHO"
FT STRAND 321..326
FT /evidence="ECO:0007829|PDB:6KHO"
FT HELIX 328..331
FT /evidence="ECO:0007829|PDB:6KHO"
FT STRAND 339..344
FT /evidence="ECO:0007829|PDB:6KHO"
FT HELIX 346..353
FT /evidence="ECO:0007829|PDB:6KHO"
FT HELIX 358..360
FT /evidence="ECO:0007829|PDB:6KHO"
FT HELIX 363..366
FT /evidence="ECO:0007829|PDB:6KHO"
FT HELIX 373..376
FT /evidence="ECO:0007829|PDB:6KHO"
FT STRAND 377..380
FT /evidence="ECO:0007829|PDB:6KHO"
FT HELIX 386..420
FT /evidence="ECO:0007829|PDB:6KHO"
FT STRAND 425..427
FT /evidence="ECO:0007829|PDB:6KHO"
FT STRAND 433..440
FT /evidence="ECO:0007829|PDB:6KHO"
FT STRAND 444..446
FT /evidence="ECO:0007829|PDB:6KHN"
FT HELIX 451..468
FT /evidence="ECO:0007829|PDB:6KHO"
FT STRAND 474..478
FT /evidence="ECO:0007829|PDB:6KHO"
FT STRAND 481..487
FT /evidence="ECO:0007829|PDB:6KHO"
FT HELIX 495..513
FT /evidence="ECO:0007829|PDB:6KHO"
SQ SEQUENCE 514 AA; 55702 MW; C72C94D1A5485FE9 CRC64;
MGSLDTNPTA FSAFPAGEGE TFQPLNADDV RSYLHKAVDF ISDYYKSVES MPVLPNVKPG
YLQDELRASP PTYSAPFDVT MKELRSSVVP GMTHWASPNF FAFFPSTNSA AAIAGDLIAS
AMNTVGFTWQ ASPAATEMEV LALDWLAQML NLPTSFMNRT GEGRGTGGGV ILGTTSEAML
VTLVAARDAA LRRSGSDGVA GLHRLAVYAA DQTHSTFFKA CRLAGFDPAN IRSIPTGAET
DYGLDPARLL EAMQADADAG LVPTYVCATV GTTSSNAVDP VGAVADVAAR FAAWVHVDAA
YAGSACICPE FRHHLDGVER VDSISMSPHK WLMTCLDCTC LYVRDTHRLT GSLETNPEYL
KNHASDSGEV TDLKDMQVGV GRRFRGLKLW MVMRTYGVAK LQEHIRSDVA MAKVFEDLVR
GDDRFEVVVP RNFALVCFRI RAGAGAAAAT EEDADEANRE LMERLNKTGK AYVAHTVVGG
RFVLRFAVGS SLQEEHHVRS AWELIKKTTT EMMN
