ID PAL4_ARATH Reviewed; 707 AA.
AC Q9SS45; Q53ZM8;
DT 01-JUN-2001, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 27-MAR-2024, entry version 159.
DE RecName: Full=Phenylalanine ammonia-lyase 4;
DE EC=4.3.1.24 {ECO:0000269|PubMed:15276452};
GN Name=PAL4; OrderedLocusNames=At3g10340; ORFNames=F14P13.6;
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 [MRNA], AND 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 [2]
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 [3]
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 [4]
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).
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=71 uM for L-phenylalanine {ECO:0000269|PubMed:15276452};
CC Vmax=9.9 umol/sec/mg enzyme {ECO:0000269|PubMed:15276452};
CC pH dependence:
CC Optimum pH is 8.4-8.8. {ECO:0000269|PubMed:15276452};
CC Temperature dependence:
CC Optimum temperature is 46-48 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; AY303130; AAP59440.1; -; mRNA.
DR EMBL; AC009400; AAF02809.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE74893.1; -; Genomic_DNA.
DR EMBL; AY099657; AAM20508.1; -; mRNA.
DR EMBL; BT000252; AAN15571.1; -; mRNA.
DR RefSeq; NP_187645.1; NM_111869.4.
DR AlphaFoldDB; Q9SS45; -.
DR SMR; Q9SS45; -.
DR BioGRID; 5530; 8.
DR IntAct; Q9SS45; 4.
DR STRING; 3702.Q9SS45; -.
DR PaxDb; 3702-AT3G10340-1; -.
DR ProteomicsDB; 226051; -.
DR EnsemblPlants; AT3G10340.1; AT3G10340.1; AT3G10340.
DR GeneID; 820196; -.
DR Gramene; AT3G10340.1; AT3G10340.1; AT3G10340.
DR KEGG; ath:AT3G10340; -.
DR Araport; AT3G10340; -.
DR TAIR; AT3G10340; PAL4.
DR eggNOG; KOG0222; Eukaryota.
DR HOGENOM; CLU_014801_3_0_1; -.
DR InParanoid; Q9SS45; -.
DR OMA; MMIVQYV; -.
DR OrthoDB; 1030318at2759; -.
DR PhylomeDB; Q9SS45; -.
DR BRENDA; 4.3.1.24; 399.
DR SABIO-RK; Q9SS45; -.
DR UniPathway; UPA00713; UER00725.
DR PRO; PR:Q9SS45; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9SS45; baseline and differential.
DR Genevisible; Q9SS45; AT.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
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; 1.20.200.10; Fumarase/aspartase (Central domain); 1.
DR Gene3D; 1.10.275.10; Fumarase/aspartase (N-terminal domain); 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 NCBIfam; TIGR01226; phe_am_lyase; 1.
DR PANTHER; PTHR10362; HISTIDINE AMMONIA-LYASE; 1.
DR PANTHER; PTHR10362:SF65; PHENYLALANINE AMMONIA-LYASE 4; 1.
DR Pfam; PF00221; Lyase_aromatic; 1.
DR SUPFAM; SSF48557; L-aspartase-like; 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..707
FT /note="Phenylalanine ammonia-lyase 4"
FT /id="PRO_0000215385"
FT ACT_SITE 99
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000250|UniProtKB:Q68G84"
FT BINDING 251
FT /ligand="(E)-cinnamate"
FT /ligand_id="ChEBI:CHEBI:15669"
FT /evidence="ECO:0000250|UniProtKB:Q68G84"
FT BINDING 339
FT /ligand="(E)-cinnamate"
FT /ligand_id="ChEBI:CHEBI:15669"
FT /evidence="ECO:0000250|UniProtKB:Q68G84"
FT BINDING 345
FT /ligand="(E)-cinnamate"
FT /ligand_id="ChEBI:CHEBI:15669"
FT /evidence="ECO:0000250|UniProtKB:Q68G84"
FT BINDING 375
FT /ligand="(E)-cinnamate"
FT /ligand_id="ChEBI:CHEBI:15669"
FT /evidence="ECO:0000250|UniProtKB:Q68G84"
FT BINDING 447
FT /ligand="(E)-cinnamate"
FT /ligand_id="ChEBI:CHEBI:15669"
FT /evidence="ECO:0000250|UniProtKB:P11544"
FT BINDING 475
FT /ligand="(E)-cinnamate"
FT /ligand_id="ChEBI:CHEBI:15669"
FT /evidence="ECO:0000250|UniProtKB:P11544"
FT BINDING 478
FT /ligand="(E)-cinnamate"
FT /ligand_id="ChEBI:CHEBI:15669"
FT /evidence="ECO:0000250|UniProtKB:Q68G84"
FT MOD_RES 195
FT /note="2,3-didehydroalanine (Ser)"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10122"
FT CROSSLNK 194..196
FT /note="5-imidazolinone (Ala-Gly)"
FT /evidence="ECO:0000250|UniProtKB:Q68G84"
SQ SEQUENCE 707 AA; 76920 MW; B67743C941B50B9B CRC64;
MELCNQNNHI TAVSGDPLNW NATAEALKGS HLDEVKRMVK EYRKEAVKLG GETLTIGQVA
AVARGGGGST VELAEEARAG VKASSEWVME SMNRGTDSYG VTTGFGATSH RRTKQGGALQ
NELIRFLNAG IFGPGAGDTS HTLPKPTTRA AMLVRVNTLL QGYSGIRFEI LEAITKLLNH
EITPCLPLRG TITASGDLVP LSYIAGLLTG RPNSKAVGPS GETLTASEAF KLAGVSSFFE
LQPKEGLALV NGTAVGSGLA STVLFDANIL AVLSEVMSAM FAEVMQGKPE FTDHLTHKLK
HHPGQIEAAA IMEHILDGSS YVKEAQLLHE MDPLQKPKQD RYALRTSPQW LGPQIEVIRA
ATKMIEREIN SVNDNPLIDV SRNKALHGGN FQGTPIGVAM DNSRLAIASI GKLMFAQFSE
LVNDFYNNGL PSNLSGGRNP SLDYGFKGAE IAMASYCSEL QFLANPVTNH VQSAEQHNQD
VNSLGLISSR KTAEAVDILK LMSTTYLVAL CQAVDLRHLE ENLKKAVKSA VSQVAKRVLT
VGANGELHPS RFTERDVLQV VDREYVFSYA DDPCSLTYPL MQKLRHILVD HALADPEREA
NSATSVFHKI GAFEAELKLL LPKEVERVRV EYEEGTSAIA NRIKECRSYP LYRFVRDELN
TELLTGENVR SPGEEFDKVF LAISDGKLID PLLECLKEWN GAPVSIC
//
