PAL2_ARATH
ID PAL2_ARATH Reviewed; 717 AA.
AC P45724; Q53ZM9; Q8RWP4; Q94KC9; Q9SCN5;
DT 01-NOV-1995, integrated into UniProtKB/Swiss-Prot.
DT 27-MAY-2002, sequence version 2.
DT 03-AUG-2022, entry version 171.
DE RecName: Full=Phenylalanine ammonia-lyase 2;
DE EC=4.3.1.24 {ECO:0000269|PubMed:15276452};
GN Name=PAL2; OrderedLocusNames=At3g53260; ORFNames=T4D2.190;
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=11130713; DOI=10.1038/35048706;
RA Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL Nature 408:820-822(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).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [6]
RP REVIEW, AND NOMENCLATURE.
RX PubMed=23473981; DOI=10.1016/j.plaphy.2013.02.001;
RA Saito K., Yonekura-Sakakibara K., Nakabayashi R., Higashi Y., Yamazaki M.,
RA Tohge T., Fernie A.R.;
RT "The flavonoid biosynthetic pathway in Arabidopsis: Structural and genetic
RT diversity.";
RL Plant Physiol. Biochem. 72:21-34(2013).
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=64 uM for L-phenylalanine {ECO:0000269|PubMed:15276452};
CC Vmax=10.5 umol/sec/mg enzyme {ECO:0000269|PubMed:15276452};
CC pH dependence:
CC Optimum pH is 8.4-8.9. {ECO:0000269|PubMed:15276452};
CC Temperature dependence:
CC Optimum temperature is 48 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 -!- 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}.
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DR EMBL; L33678; AAC18871.1; -; Genomic_DNA.
DR EMBL; AY303129; AAP59439.1; -; mRNA.
DR EMBL; AL132958; CAB64229.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE79055.1; -; Genomic_DNA.
DR EMBL; AF367308; AAK32895.1; -; mRNA.
DR EMBL; AY092957; AAM12956.1; -; mRNA.
DR EMBL; AY133595; AAM91425.1; -; mRNA.
DR EMBL; BT000035; AAN15354.1; -; mRNA.
DR PIR; T46172; T46172.
DR RefSeq; NP_190894.1; NM_115186.4.
DR AlphaFoldDB; P45724; -.
DR SMR; P45724; -.
DR BioGRID; 9810; 9.
DR IntAct; P45724; 5.
DR STRING; 3702.AT3G53260.1; -.
DR PaxDb; P45724; -.
DR PRIDE; P45724; -.
DR ProteomicsDB; 248654; -.
DR EnsemblPlants; AT3G53260.1; AT3G53260.1; AT3G53260.
DR GeneID; 824493; -.
DR Gramene; AT3G53260.1; AT3G53260.1; AT3G53260.
DR KEGG; ath:AT3G53260; -.
DR Araport; AT3G53260; -.
DR TAIR; locus:2101958; AT3G53260.
DR eggNOG; KOG0222; Eukaryota.
DR HOGENOM; CLU_014801_3_0_1; -.
DR InParanoid; P45724; -.
DR OMA; MYVHSIP; -.
DR OrthoDB; 923557at2759; -.
DR PhylomeDB; P45724; -.
DR BRENDA; 4.3.1.24; 399.
DR SABIO-RK; P45724; -.
DR UniPathway; UPA00713; UER00725.
DR PRO; PR:P45724; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; P45724; baseline and differential.
DR Genevisible; P45724; 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; IGI:TAIR.
DR GO; GO:0009699; P:phenylpropanoid biosynthetic process; TAS:TAIR.
DR GO; GO:0006979; P:response to oxidative stress; IEP:TAIR.
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; Lyase; Phenylalanine catabolism; Phenylpropanoid metabolism;
KW Reference proteome.
FT CHAIN 1..717
FT /note="Phenylalanine ammonia-lyase 2"
FT /id="PRO_0000215383"
FT ACT_SITE 109
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000250|UniProtKB:Q68G84"
FT BINDING 261
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q68G84"
FT BINDING 349
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q68G84"
FT BINDING 355
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q68G84"
FT BINDING 385
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q68G84"
FT BINDING 488
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q68G84"
FT MOD_RES 204
FT /note="2,3-didehydroalanine (Ser)"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10122"
FT CROSSLNK 203..205
FT /note="5-imidazolinone (Ala-Gly)"
FT /evidence="ECO:0000250|UniProtKB:Q68G84"
FT CONFLICT 50
FT /note="E -> A (in Ref. 5; AAM12956/AAN15354)"
FT /evidence="ECO:0000305"
FT CONFLICT 206
FT /note="D -> H (in Ref. 1; AAC18871)"
FT /evidence="ECO:0000305"
FT CONFLICT 235
FT /note="A -> E (in Ref. 1; AAC18871)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 717 AA; 77860 MW; 360A206295AF787D CRC64;
MDQIEAMLCG GGEKTKVAVT TKTLADPLNW GLAADQMKGS HLDEVKKMVE EYRRPVVNLG
GETLTIGQVA AISTVGGSVK VELAETSRAG VKASSDWVME SMNKGTDSYG VTTGFGATSH
RRTKNGTALQ TELIRFLNAG IFGNTKETCH TLPQSATRAA MLVRVNTLLQ GYSGIRFEIL
EAITSLLNHN ISPSLPLRGT ITASGDLVPL SYIAGLLTGR PNSKATGPDG ESLTAKEAFE
KAGISTGFFD LQPKEGLALV NGTAVGSGMA SMVLFEANVQ AVLAEVLSAI FAEVMSGKPE
FTDHLTHRLK HHPGQIEAAA IMEHILDGSS YMKLAQKVHE MDPLQKPKQD RYALRTSPQW
LGPQIEVIRQ ATKSIEREIN SVNDNPLIDV SRNKAIHGGN FQGTPIGVSM DNTRLAIAAI
GKLMFAQFSE LVNDFYNNGL PSNLTASSNP SLDYGFKGAE IAMASYCSEL QYLANPVTSH
VQSAEQHNQD VNSLGLISSR KTSEAVDILK LMSTTFLVGI CQAVDLRHLE ENLRQTVKNT
VSQVAKKVLT TGINGELHPS RFCEKDLLKV VDREQVFTYV DDPCSATYPL MQRLRQVIVD
HALSNGETEK NAVTSIFQKI GAFEEELKAV LPKEVEAARA AYGNGTAPIP NRIKECRSYP
LYRFVREELG TKLLTGEKVV SPGEEFDKVF TAMCEGKLID PLMDCLKEWN GAPIPIC
