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Phenylalanine ammonia-lyase 1 (EC 4.3.1.24)

 PAL1_ARATH              Reviewed;         725 AA.
P35510; Q94AN1; Q9ZQD6;
01-JUN-1994, integrated into UniProtKB/Swiss-Prot.
27-SEP-2005, sequence version 3.
07-JUN-2017, entry version 142.
RecName: Full=Phenylalanine ammonia-lyase 1;
EC=4.3.1.24;
Name=PAL1; OrderedLocusNames=At2g37040; ORFNames=T1J8.22;
Arabidopsis thaliana (Mouse-ear cress).
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;
Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae;
Arabidopsis.
NCBI_TaxID=3702;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=cv. Landsberg erecta;
PubMed=7888622; DOI=10.1007/BF00020187;
Wanner L.A., Li G., Ware D., Somssich I.E., Davis K.R.;
"The phenylalanine ammonia-lyase gene family in Arabidopsis
thaliana.";
Plant Mol. Biol. 27:327-338(1995).
[2]
NUCLEOTIDE SEQUENCE [MRNA], AND BIOPHYSICOCHEMICAL PROPERTIES.
STRAIN=cv. Columbia;
PubMed=15276452; DOI=10.1016/j.phytochem.2004.05.006;
Cochrane F.C., Davin L.B., Lewis N.G.;
"The Arabidopsis phenylalanine ammonia lyase gene family: kinetic
characterization of the four PAL isoforms.";
Phytochemistry 65:1557-1564(2004).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Columbia;
PubMed=10617197; DOI=10.1038/45471;
Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L.,
Moffat K.S., Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L.,
Tallon L.J., Gill J.E., Adams M.D., Carrera A.J., Creasy T.H.,
Goodman H.M., Somerville C.R., Copenhaver G.P., Preuss D.,
Nierman W.C., White O., Eisen J.A., Salzberg S.L., Fraser C.M.,
Venter J.C.;
"Sequence and analysis of chromosome 2 of the plant Arabidopsis
thaliana.";
Nature 402:761-768(1999).
[4]
GENOME REANNOTATION.
STRAIN=cv. Columbia;
The Arabidopsis Information Portal (Araport);
Submitted (MAY-2016) to the EMBL/GenBank/DDBJ databases.
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
STRAIN=cv. Columbia;
PubMed=14593172; DOI=10.1126/science.1088305;
Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J.,
Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F.,
Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.,
Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J.,
Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y.,
Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P.,
Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F.,
Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M.,
Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J.,
Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T.,
Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y.,
Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.;
"Empirical analysis of transcriptional activity in the Arabidopsis
genome.";
Science 302:842-846(2003).
[6]
NUCLEOTIDE SEQUENCE OF 1-240.
STRAIN=cv. Columbia;
PubMed=2152131; DOI=10.1105/tpc.2.9.837;
Ohl S., Hedrick S.A., Chory J., Lamb C.J.;
"Functional properties of a phenylalanine ammonia-lyase promoter from
Arabidopsis.";
Plant Cell 2:837-848(1990).
[7]
REVIEW, AND NOMENCLATURE.
PubMed=23473981; DOI=10.1016/j.plaphy.2013.02.001;
Saito K., Yonekura-Sakakibara K., Nakabayashi R., Higashi Y.,
Yamazaki M., Tohge T., Fernie A.R.;
"The flavonoid biosynthetic pathway in Arabidopsis: Structural and
genetic diversity.";
Plant Physiol. Biochem. 72:21-34(2013).
-!- FUNCTION: This is a key enzyme of plant metabolism catalyzing the
first reaction in the biosynthesis from L-phenylalanine of a wide
variety of natural products based on the phenylpropane skeleton.
-!- CATALYTIC ACTIVITY: L-phenylalanine = trans-cinnamate + ammonia.
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=68 uM for L-phenylalanine {ECO:0000269|PubMed:15276452};
Vmax=5.5 umol/sec/mg enzyme {ECO:0000269|PubMed:15276452};
pH dependence:
Optimum pH is 8.4-9.2. {ECO:0000269|PubMed:15276452};
Temperature dependence:
Optimum temperature is 46-48 degrees Celsius.
{ECO:0000269|PubMed:15276452};
-!- PATHWAY: Phenylpropanoid metabolism; trans-cinnamate biosynthesis;
trans-cinnamate from L-phenylalanine: step 1/1.
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
-!- PTM: Contains an active site 4-methylidene-imidazol-5-one (MIO),
which is formed autocatalytically by cyclization and dehydration
of residues Ala-Ser-Gly. {ECO:0000250}.
-!- SIMILARITY: Belongs to the PAL/histidase family. {ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; L33677; AAC18870.1; -; Genomic_DNA.
EMBL; AY303128; AAP59438.1; -; mRNA.
EMBL; AC006922; AAM15324.1; -; Genomic_DNA.
EMBL; CP002685; AEC09341.1; -; Genomic_DNA.
EMBL; AY045919; AAK76593.1; -; mRNA.
EMBL; AY079363; AAL85094.1; -; mRNA.
EMBL; BT003330; AAO29949.1; -; mRNA.
EMBL; X62747; CAA44609.1; -; Genomic_DNA.
PIR; G84787; G84787.
PIR; S52990; S52990.
RefSeq; NP_181241.1; NM_129260.3.
UniGene; At.21614; -.
UniGene; At.22705; -.
ProteinModelPortal; P35510; -.
SMR; P35510; -.
BioGrid; 3624; 9.
IntAct; P35510; 4.
STRING; 3702.AT2G37040.1; -.
iPTMnet; P35510; -.
PaxDb; P35510; -.
PRIDE; P35510; -.
EnsemblPlants; AT2G37040.1; AT2G37040.1; AT2G37040.
GeneID; 818280; -.
Gramene; AT2G37040.1; AT2G37040.1; AT2G37040.
KEGG; ath:AT2G37040; -.
Araport; AT2G37040; -.
TAIR; locus:2057981; AT2G37040.
eggNOG; KOG0222; Eukaryota.
eggNOG; COG2986; LUCA.
HOGENOM; HOG000214384; -.
InParanoid; P35510; -.
KO; K10775; -.
OMA; RCVPQIL; -.
OrthoDB; EOG093603B9; -.
PhylomeDB; P35510; -.
BRENDA; 4.3.1.24; 399.
Reactome; R-ATH-70921; Histidine catabolism.
SABIO-RK; P35510; -.
UniPathway; UPA00713; UER00725.
PRO; PR:P35510; -.
Proteomes; UP000006548; Chromosome 2.
ExpressionAtlas; P35510; baseline and differential.
Genevisible; P35510; AT.
GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
GO; GO:0045548; F:phenylalanine ammonia-lyase activity; IDA:TAIR.
GO; GO:0009800; P:cinnamic acid biosynthetic process; IEA:UniProtKB-UniPathway.
GO; GO:0009819; P:drought recovery; IMP:TAIR.
GO; GO:0006559; P:L-phenylalanine catabolic process; IEA:InterPro.
GO; GO:0046274; P:lignin catabolic process; IMP:TAIR.
GO; GO:0009555; P:pollen development; IMP:TAIR.
GO; GO:0080167; P:response to karrikin; IEP:TAIR.
GO; GO:0006979; P:response to oxidative stress; IEP:TAIR.
GO; GO:0010224; P:response to UV-B; IMP:TAIR.
GO; GO:0046244; P:salicylic acid catabolic process; IMP:TAIR.
CDD; cd00332; PAL-HAL; 1.
Gene3D; 1.10.275.10; -; 1.
InterPro; IPR001106; Aromatic_Lyase.
InterPro; IPR024083; Fumarase/histidase_N.
InterPro; IPR008948; L-Aspartase-like.
InterPro; IPR022313; Phe/His_NH3-lyase_AS.
InterPro; IPR005922; Phe_NH3-lyase.
Pfam; PF00221; Lyase_aromatic; 1.
SUPFAM; SSF48557; SSF48557; 1.
TIGRFAMs; TIGR01226; phe_am_lyase; 1.
PROSITE; PS00488; PAL_HISTIDASE; 1.
1: Evidence at protein level;
Complete proteome; Cytoplasm; Lyase; Phenylpropanoid metabolism;
Reference proteome.
CHAIN 1 725 Phenylalanine ammonia-lyase 1.
/FTId=PRO_0000215382.
ACT_SITE 117 117 Proton donor/acceptor. {ECO:0000250}.
BINDING 363 363 Substrate. {ECO:0000250}.
MOD_RES 212 212 2,3-didehydroalanine (Ser).
{ECO:0000255|PROSITE-ProRule:PRU10122}.
CROSSLNK 211 213 5-imidazolinone (Ala-Gly). {ECO:0000250}.
CONFLICT 329 329 I -> V (in Ref. 1; AAC18870).
{ECO:0000305}.
CONFLICT 426 426 A -> R (in Ref. 1; AAC18870).
{ECO:0000305}.
CONFLICT 612 612 I -> V (in Ref. 1; AAC18870).
{ECO:0000305}.
SEQUENCE 725 AA; 78726 MW; 02626B3B2DEFE9CE CRC64;
MEINGAHKSN GGGVDAMLCG GDIKTKNMVI NAEDPLNWGA AAEQMKGSHL DEVKRMVAEF
RKPVVNLGGE TLTIGQVAAI STIGNSVKVE LSETARAGVN ASSDWVMESM NKGTDSYGVT
TGFGATSHRR TKNGVALQKE LIRFLNAGIF GSTKETSHTL PHSATRAAML VRINTLLQGF
SGIRFEILEA ITSFLNNNIT PSLPLRGTIT ASGDLVPLSY IAGLLTGRPN SKATGPNGEA
LTAEEAFKLA GISSGFFDLQ PKEGLALVNG TAVGSGMASM VLFETNVLSV LAEILSAVFA
EVMSGKPEFT DHLTHRLKHH PGQIEAAAIM EHILDGSSYM KLAQKLHEMD PLQKPKQDRY
ALRTSPQWLG PQIEVIRYAT KSIEREINSV NDNPLIDVSR NKAIHGGNFQ GTPIGVSMDN
TRLAIAAIGK LMFAQFSELV NDFYNNGLPS NLTASRNPSL DYGFKGAEIA MASYCSELQY
LANPVTSHVQ SAEQHNQDVN SLGLISSRKT SEAVDILKLM STTFLVAICQ AVDLRHLEEN
LRQTVKNTVS QVAKKVLTTG VNGELHPSRF CEKDLLKVVD REQVYTYADD PCSATYPLIQ
KLRQVIVDHA LINGESEKNA VTSIFHKIGA FEEELKAVLP KEVEAARAAY DNGTSAIPNR
IKECRSYPLY RFVREELGTE LLTGEKVTSP GEEFDKVFTA ICEGKIIDPM MECLNEWNGA
PIPIC


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