PAL3_ARATH
ID PAL3_ARATH Reviewed; 694 AA.
AC P45725; Q53YP2; Q9FYD8;
DT 01-NOV-1995, integrated into UniProtKB/Swiss-Prot.
DT 27-SEP-2005, sequence version 3.
DT 03-AUG-2022, entry version 156.
DE RecName: Full=Phenylalanine ammonia-lyase 3;
DE EC=4.3.1.24 {ECO:0000269|PubMed:15276452};
GN Name=PAL3; OrderedLocusNames=At5g04230; ORFNames=F21E1_150;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=7888622; DOI=10.1007/bf00020187;
RA Wanner L.A., Li G., Ware D., Somssich I.E., Davis K.R.;
RT "The phenylalanine ammonia-lyase gene family in Arabidopsis thaliana.";
RL Plant Mol. Biol. 27:327-338(1995).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, CATALYTIC ACTIVITY, AND
RP BIOPHYSICOCHEMICAL PROPERTIES.
RC STRAIN=cv. Columbia;
RX PubMed=15276452; DOI=10.1016/j.phytochem.2004.05.006;
RA Cochrane F.C., Davin L.B., Lewis N.G.;
RT "The Arabidopsis phenylalanine ammonia lyase gene family: kinetic
RT characterization of the four PAL isoforms.";
RL Phytochemistry 65:1557-1564(2004).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130714; DOI=10.1038/35048507;
RA Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E.,
RA Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M.,
RA Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K.,
RA Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M.,
RA Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L.,
RA O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D.,
RA Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M.,
RA Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L.,
RA Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B.,
RA Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P.,
RA Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M.,
RA Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D.,
RA Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A.,
RA Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I.,
RA Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T.,
RA Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A.,
RA McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U.,
RA Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W.,
RA Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M.,
RA Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S.,
RA Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G.,
RA Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W.,
RA Bevan M., Fransz P.F.;
RT "Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana.";
RL Nature 408:823-826(2000).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
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:0000269|PubMed:15276452}.
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:0000269|PubMed:15276452};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=2.56 mM for L-phenylalanine {ECO:0000269|PubMed:15276452};
CC Vmax=0.4 umol/sec/mg enzyme {ECO:0000269|PubMed:15276452};
CC pH dependence:
CC Optimum pH is 8.7-8.9. {ECO:0000269|PubMed:15276452};
CC Temperature dependence:
CC Optimum temperature is 31 degrees Celsius.
CC {ECO:0000269|PubMed:15276452};
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 -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=1;
CC Comment=A number of isoforms are produced. According to EST
CC sequences.;
CC Name=1;
CC IsoId=P45725-1; Sequence=Displayed;
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=CAC05505.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; L33679; AAA69905.1; -; Genomic_DNA.
DR EMBL; AY528562; AAS18574.1; -; mRNA.
DR EMBL; AL391716; CAC05505.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002688; AED90714.1; -; Genomic_DNA.
DR PIR; S52992; S52992.
DR RefSeq; NP_001190223.1; NM_001203294.1.
DR RefSeq; NP_196043.2; NM_120505.4. [P45725-1]
DR AlphaFoldDB; P45725; -.
DR SMR; P45725; -.
DR BioGRID; 15582; 2.
DR STRING; 3702.AT5G04230.2; -.
DR PaxDb; P45725; -.
DR PRIDE; P45725; -.
DR ProteomicsDB; 248745; -. [P45725-1]
DR EnsemblPlants; AT5G04230.1; AT5G04230.1; AT5G04230. [P45725-1]
DR GeneID; 830302; -.
DR Gramene; AT5G04230.1; AT5G04230.1; AT5G04230. [P45725-1]
DR KEGG; ath:AT5G04230; -.
DR Araport; AT5G04230; -.
DR eggNOG; KOG0222; Eukaryota.
DR InParanoid; P45725; -.
DR OrthoDB; 923557at2759; -.
DR PhylomeDB; P45725; -.
DR BRENDA; 4.3.1.24; 399.
DR SABIO-RK; P45725; -.
DR UniPathway; UPA00713; UER00725.
DR PRO; PR:P45725; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; P45725; baseline and differential.
DR Genevisible; P45725; AT.
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; IBA:GO_Central.
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 Alternative splicing; Cytoplasm; Lyase; Phenylalanine catabolism;
KW Phenylpropanoid metabolism; Reference proteome.
FT CHAIN 1..694
FT /note="Phenylalanine ammonia-lyase 3"
FT /id="PRO_0000215384"
FT ACT_SITE 94
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000250|UniProtKB:Q68G84"
FT BINDING 248
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q68G84"
FT BINDING 336
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q68G84"
FT BINDING 342
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q68G84"
FT BINDING 372
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q68G84"
FT BINDING 475
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q68G84"
FT MOD_RES 192
FT /note="2,3-didehydroalanine (Ser)"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10122"
FT CROSSLNK 191..193
FT /note="5-imidazolinone (Ala-Gly)"
FT /evidence="ECO:0000250|UniProtKB:Q68G84"
FT CONFLICT 63
FT /note="G -> GG (in Ref. 1; AAA69905)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 694 AA; 76241 MW; 44C2179F17CE479E CRC64;
MEFRQPNATA LSDPLNWNVA AEALKGSHLE EVKKMVKDYR KGTVQLGGET LTIGQVAAVA
SGGPTVELSE EARGGVKASS DWVMESMNRD TDTYGITTGF GSSSRRRTDQ GAALQKELIR
YLNAGIFATG NEDDDRSNTL PRPATRAAML IRVNTLLQGY SGIRFEILEA ITTLLNCKIT
PLLPLRGTIT ASGDLVPLSY IAGFLIGRPN SRSVGPSGEI LTALEAFKLA GVSSFFELRP
KEGLALVNGT AVGSALASTV LYDANILVVF SEVASAMFAE VMQGKPEFTD HLTHKLKHHP
GQIEAAAIME HILDGSSYVK EALHLHKIDP LQKPKQDRYA LRTSPQWLGP QIEVIRAATK
MIEREINSVN DNPLIDVSRN KAIHGGNFQG TPIGVAMDNT RLALASIGKL MFAQFTELVN
DFYNNGLPSN LSGGRNPSLD YGLKGAEVAM ASYCSELQFL ANPVTNHVES ASQHNQDVNS
LGLISSRTTA EAVVILKLMS TTYLVALCQA FDLRHLEEIL KKAVNEVVSH TAKSVLAIEP
FRKHDDILGV VNREYVFSYV DDPSSLTNPL MQKLRHVLFD KALAEPEGET DTVFRKIGAF
EAELKFLLPK EVERVRTEYE NGTFNVANRI KKCRSYPLYR FVRNELETRL LTGEDVRSPG
EDFDKVFRAI SQGKLIDPLF ECLKEWNGAP ISIC
