PAL1_ORYSJ
ID PAL1_ORYSJ Reviewed; 701 AA.
AC P14717; Q0DZE3; Q6K1Q8;
DT 01-APR-1990, integrated into UniProtKB/Swiss-Prot.
DT 30-MAY-2006, sequence version 2.
DT 03-AUG-2022, entry version 151.
DE RecName: Full=Phenylalanine ammonia-lyase;
DE EC=4.3.1.24 {ECO:0000250|UniProtKB:P24481};
GN Name=PAL; OrderedLocusNames=Os02g0626100, LOC_Os02g41630;
GN ORFNames=B1215B07.42, OsJ_07592 {ECO:0000312|EMBL:EAZ23873.1}, P0042D01.1;
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 [GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=2806257; DOI=10.1111/j.1432-1033.1989.tb15075.x;
RA Minami E., Ozeki Y., Matsuoka M., Koizuka N., Tanaka Y.;
RT "Structure and some characterization of the gene for phenylalanine ammonia-
RT lyase from rice plants.";
RL Eur. J. Biochem. 185:19-25(1989).
RN [2]
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 [3]
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 [4]
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 [5]
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 [6]
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 [7]
RP PROTEIN SEQUENCE OF 327-332.
RC STRAIN=cv. Nipponbare; TISSUE=Stem;
RX PubMed=14681440; DOI=10.1093/nar/gkh020;
RA Komatsu S., Kojima K., Suzuki K., Ozaki K., Higo K.;
RT "Rice proteome database based on two-dimensional polyacrylamide gel
RT electrophoresis: its status in 2003.";
RL Nucleic Acids Res. 32:D388-D392(2004).
CC -!- FUNCTION: This is a key enzyme of plant metabolism catalyzing the first
CC reaction in the biosynthesis from L-phenylalanine of a wide variety of
CC natural products based on the phenylpropane skeleton.
CC {ECO:0000250|UniProtKB:P24481}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-phenylalanine = (E)-cinnamate + NH4(+);
CC Xref=Rhea:RHEA:21384, ChEBI:CHEBI:15669, ChEBI:CHEBI:28938,
CC ChEBI:CHEBI:58095; EC=4.3.1.24;
CC Evidence={ECO:0000250|UniProtKB:P24481};
CC -!- PATHWAY: Phenylpropanoid metabolism; trans-cinnamate biosynthesis;
CC trans-cinnamate from L-phenylalanine: step 1/1. {ECO:0000305}.
CC -!- SUBUNIT: Homotetramer. {ECO:0000250|UniProtKB:P24481}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC -!- PTM: Contains an active site 4-methylidene-imidazol-5-one (MIO), which
CC is formed autocatalytically by cyclization and dehydration of residues
CC Ala-Ser-Gly. {ECO:0000250|UniProtKB:Q68G84}.
CC -!- SIMILARITY: Belongs to the PAL/histidase family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAA34226.1; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; X16099; CAA34226.1; ALT_FRAME; Genomic_DNA.
DR EMBL; AP005000; BAD23149.1; -; Genomic_DNA.
DR EMBL; AP006523; BAD23794.1; -; Genomic_DNA.
DR EMBL; AP008208; BAF09395.1; -; Genomic_DNA.
DR EMBL; AP014958; BAS79861.1; -; Genomic_DNA.
DR EMBL; CM000139; EAZ23873.1; -; Genomic_DNA.
DR EMBL; AK102817; BAG95732.1; -; mRNA.
DR RefSeq; XP_015625120.1; XM_015769634.1.
DR AlphaFoldDB; P14717; -.
DR SMR; P14717; -.
DR STRING; 4530.OS02T0626100-01; -.
DR CarbonylDB; P14717; -.
DR PaxDb; P14717; -.
DR PRIDE; P14717; -.
DR EnsemblPlants; Os02t0626100-01; Os02t0626100-01; Os02g0626100.
DR GeneID; 4330034; -.
DR Gramene; Os02t0626100-01; Os02t0626100-01; Os02g0626100.
DR KEGG; osa:4330034; -.
DR eggNOG; KOG0222; Eukaryota.
DR InParanoid; P14717; -.
DR OMA; RTNQGVA; -.
DR OrthoDB; 923557at2759; -.
DR PlantReactome; R-OSA-1119261; Salicylate biosynthesis.
DR PlantReactome; R-OSA-1119418; Suberin biosynthesis.
DR PlantReactome; R-OSA-1119582; Phenylpropanoid biosynthesis, initial reactions.
DR UniPathway; UPA00713; UER00725.
DR Proteomes; UP000000763; Chromosome 2.
DR Proteomes; UP000007752; Chromosome 2.
DR Proteomes; UP000059680; Chromosome 2.
DR ExpressionAtlas; P14717; baseline and differential.
DR Genevisible; P14717; OS.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0016841; F:ammonia-lyase activity; IBA:GO_Central.
DR GO; GO:0045548; F:phenylalanine ammonia-lyase activity; IEA:UniProtKB-EC.
DR GO; GO:0009800; P:cinnamic acid biosynthetic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0006559; P:L-phenylalanine catabolic process; IEA:UniProtKB-KW.
DR CDD; cd00332; PAL-HAL; 1.
DR Gene3D; 1.10.274.20; -; 1.
DR Gene3D; 1.10.275.10; -; 1.
DR InterPro; IPR001106; Aromatic_Lyase.
DR InterPro; IPR024083; Fumarase/histidase_N.
DR InterPro; IPR008948; L-Aspartase-like.
DR InterPro; IPR022313; Phe/His_NH3-lyase_AS.
DR InterPro; IPR005922; Phe_NH3-lyase.
DR InterPro; IPR023144; Phe_NH3-lyase_shielding_dom_sf.
DR PANTHER; PTHR10362; PTHR10362; 1.
DR Pfam; PF00221; Lyase_aromatic; 1.
DR SUPFAM; SSF48557; SSF48557; 1.
DR TIGRFAMs; TIGR01226; phe_am_lyase; 1.
DR PROSITE; PS00488; PAL_HISTIDASE; 1.
PE 1: Evidence at protein level;
KW Cytoplasm; Direct protein sequencing; Lyase; Phenylalanine catabolism;
KW Phenylpropanoid metabolism; Reference proteome.
FT CHAIN 1..701
FT /note="Phenylalanine ammonia-lyase"
FT /id="PRO_0000215401"
FT ACT_SITE 96
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000250|UniProtKB:Q68G84"
FT BINDING 247
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q68G84"
FT BINDING 335
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q68G84"
FT BINDING 341
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q68G84"
FT BINDING 371
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q68G84"
FT BINDING 474
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q68G84"
FT MOD_RES 190
FT /note="2,3-didehydroalanine (Ser)"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10122"
FT CROSSLNK 189..191
FT /note="5-imidazolinone (Ala-Gly)"
FT /evidence="ECO:0000250|UniProtKB:Q68G84"
FT CONFLICT 65
FT /note="G -> R (in Ref. 1; CAA34226)"
FT /evidence="ECO:0000305"
FT CONFLICT 87
FT /note="N -> T (in Ref. 1; CAA34226)"
FT /evidence="ECO:0000305"
FT CONFLICT 123
FT /note="H -> Y (in Ref. 1; CAA34226)"
FT /evidence="ECO:0000305"
FT CONFLICT 303
FT /note="E -> D (in Ref. 1; CAA34226)"
FT /evidence="ECO:0000305"
FT CONFLICT 352
FT /note="E -> Q (in Ref. 1; CAA34226)"
FT /evidence="ECO:0000305"
FT CONFLICT 453
FT /note="C -> S (in Ref. 1; CAA34226)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 701 AA; 75498 MW; C6AA7CB8DB4F8EE0 CRC64;
MAGNGPINKE DPLNWGAAAA EMAGSHLDEV KRMVAQFREP LVKIQGATLR VGQVAAVAQA
KDAAGVAVEL DEEARPRVKA SSEWILNCIA HGGDIYGVTT GFGGTSHRRT KDGPALQVEL
LRHLNAGIFG TGSDGHTLPS ETVRAAMLVR INTLLQGYSG IRFEILEAIT KLLNTGVTPC
LPLRGTITAS GDLVPLSYIA GLITGRPNAQ AISPDGRKVD AAEAFKLAGI EGGFFTLNPK
EGLAIVNGTS VGSALAATVM FDANILAVLS EVLSAVFCEV MNGKPEYTDH LTHKLKHHPG
SIEAAAIMEH ILAGSSFMSH AKKVNEMDPL LKPKQDRYAL RTSPQWLGPQ IEVIRAATKS
IEREVNSVND NPVIDVHRGK ALHGGNFQGT PIGVSMDNAR LAIANIGKLM FAQFSELVNE
FYNNGLTSNL AGSRNPSLDY GFKGTEIAMA SYCSELQYLA NPITNHVQSA EQHNQDVNSL
GLVSARKTLE AVDILKLMTS TYIVALCQAV DLRHLEENIK SSVKNCVTQV AKKVLTMNPT
GDLSSARFSE KNLLTAIDRE AVFSYADDPC SANYPLMQKL RAVLVEHALT SGDAEPEASV
FSKITKFEEE LRSALPREIE AARVAVANGT APVANRIVES RSFPLYRFVR EELGCVFLTG
EKLKSPGEEC NKVFLGISQG KLIDPMLDCL KEWNGEPLPI N
