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Protein

Phenylalanine ammonia-lyase 2

Gene

PAL2

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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 activityi

L-phenylalanine = trans-cinnamate + ammonia.

Kineticsi

  1. KM=64 µM for L-phenylalanine1 Publication
  1. Vmax=10.5 µmol/sec/mg enzyme1 Publication

pH dependencei

Optimum pH is 8.4-8.9.1 Publication

Temperature dependencei

Optimum temperature is 48 degrees Celsius.1 Publication

Pathwayi: trans-cinnamate biosynthesis

This protein is involved in step 1 of the subpathway that synthesizes trans-cinnamate from L-phenylalanine.
Proteins known to be involved in this subpathway in this organism are:
  1. Phenylalanine ammonia-lyase 3 (PAL3), Phenylalanine ammonia-lyase 2 (PAL2), Phenylalanine ammonia-lyase (At3g53260), Phenylalanine ammonia-lyase 1 (PAL1), Phenylalanine ammonia-lyase 4 (PAL4), Phenylalanine ammonia-lyase (PAL3)
This subpathway is part of the pathway trans-cinnamate biosynthesis, which is itself part of Phenylpropanoid metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes trans-cinnamate from L-phenylalanine, the pathway trans-cinnamate biosynthesis and in Phenylpropanoid metabolism.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei109 – 1091Proton donor/acceptorBy similarity
Binding sitei355 – 3551SubstrateBy similarity

GO - Molecular functioni

  • phenylalanine ammonia-lyase activity Source: TAIR

GO - Biological processi

  • cinnamic acid biosynthetic process Source: UniProtKB-UniPathway
  • L-phenylalanine catabolic process Source: InterPro
  • phenylpropanoid biosynthetic process Source: TAIR
  • response to karrikin Source: TAIR
  • response to oxidative stress Source: TAIR
Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Biological processi

Phenylpropanoid metabolism

Enzyme and pathway databases

BRENDAi4.3.1.24. 399.
ReactomeiR-ATH-70921. Histidine catabolism.
SABIO-RKP45724.
UniPathwayiUPA00713; UER00725.

Names & Taxonomyi

Protein namesi
Recommended name:
Phenylalanine ammonia-lyase 2 (EC:4.3.1.24)
Gene namesi
Name:PAL2
Ordered Locus Names:At3g53260
ORF Names:T4D2.190
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 3

Organism-specific databases

TAIRiAT3G53260.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 717717Phenylalanine ammonia-lyase 2PRO_0000215383Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Cross-linki203 ↔ 2055-imidazolinone (Ala-Gly)By similarity
Modified residuei204 – 20412,3-didehydroalanine (Ser)PROSITE-ProRule annotation

Post-translational modificationi

Contains an active site 4-methylidene-imidazol-5-one (MIO), which is formed autocatalytically by cyclization and dehydration of residues Ala-Ser-Gly.By similarity
Ubiquitinated.1 Publication

Keywords - PTMi

Ubl conjugation

Proteomic databases

PaxDbiP45724.
PRIDEiP45724.

Expressioni

Gene expression databases

GenevisibleiP45724. AT.

Interactioni

Protein-protein interaction databases

BioGridi9810. 9 interactions.
IntActiP45724. 5 interactions.
MINTiMINT-8060879.
STRINGi3702.AT3G53260.1.

Structurei

3D structure databases

ProteinModelPortaliP45724.
SMRiP45724. Positions 26-717.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the PAL/histidase family.Curated

Phylogenomic databases

eggNOGiKOG0222. Eukaryota.
COG2986. LUCA.
HOGENOMiHOG000214384.
InParanoidiP45724.
KOiK10775.
OMAiAGEMEDR.
PhylomeDBiP45724.

Family and domain databases

Gene3Di1.10.274.20. 1 hit.
1.10.275.10. 1 hit.
InterProiIPR001106. Aromatic_Lyase.
IPR024083. Fumarase/histidase_N.
IPR008948. L-Aspartase-like.
IPR022313. Phe/His_NH3-lyase_AS.
IPR005922. Phe_NH3-lyase.
IPR023144. Phe_NH3-lyase_shielding_dom.
[Graphical view]
PfamiPF00221. Lyase_aromatic. 1 hit.
[Graphical view]
SUPFAMiSSF48557. SSF48557. 1 hit.
TIGRFAMsiTIGR01226. phe_am_lyase. 1 hit.
PROSITEiPS00488. PAL_HISTIDASE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P45724-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDQIEAMLCG GGEKTKVAVT TKTLADPLNW GLAADQMKGS HLDEVKKMVE
60 70 80 90 100
EYRRPVVNLG GETLTIGQVA AISTVGGSVK VELAETSRAG VKASSDWVME
110 120 130 140 150
SMNKGTDSYG VTTGFGATSH RRTKNGTALQ TELIRFLNAG IFGNTKETCH
160 170 180 190 200
TLPQSATRAA MLVRVNTLLQ GYSGIRFEIL EAITSLLNHN ISPSLPLRGT
210 220 230 240 250
ITASGDLVPL SYIAGLLTGR PNSKATGPDG ESLTAKEAFE KAGISTGFFD
260 270 280 290 300
LQPKEGLALV NGTAVGSGMA SMVLFEANVQ AVLAEVLSAI FAEVMSGKPE
310 320 330 340 350
FTDHLTHRLK HHPGQIEAAA IMEHILDGSS YMKLAQKVHE MDPLQKPKQD
360 370 380 390 400
RYALRTSPQW LGPQIEVIRQ ATKSIEREIN SVNDNPLIDV SRNKAIHGGN
410 420 430 440 450
FQGTPIGVSM DNTRLAIAAI GKLMFAQFSE LVNDFYNNGL PSNLTASSNP
460 470 480 490 500
SLDYGFKGAE IAMASYCSEL QYLANPVTSH VQSAEQHNQD VNSLGLISSR
510 520 530 540 550
KTSEAVDILK LMSTTFLVGI CQAVDLRHLE ENLRQTVKNT VSQVAKKVLT
560 570 580 590 600
TGINGELHPS RFCEKDLLKV VDREQVFTYV DDPCSATYPL MQRLRQVIVD
610 620 630 640 650
HALSNGETEK NAVTSIFQKI GAFEEELKAV LPKEVEAARA AYGNGTAPIP
660 670 680 690 700
NRIKECRSYP LYRFVREELG TKLLTGEKVV SPGEEFDKVF TAMCEGKLID
710
PLMDCLKEWN GAPIPIC
Length:717
Mass (Da):77,860
Last modified:May 27, 2002 - v2
Checksum:i360A206295AF787D
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti50 – 501E → A in AAM12956 (PubMed:14593172).Curated
Sequence conflicti50 – 501E → A in AAN15354 (PubMed:14593172).Curated
Sequence conflicti206 – 2061D → H in AAC18871 (PubMed:7888622).Curated
Sequence conflicti235 – 2351A → E in AAC18871 (PubMed:7888622).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L33678 Genomic DNA. Translation: AAC18871.1.
AY303129 mRNA. Translation: AAP59439.1.
AL132958 Genomic DNA. Translation: CAB64229.1.
CP002686 Genomic DNA. Translation: AEE79055.1.
AF367308 mRNA. Translation: AAK32895.1.
AY092957 mRNA. Translation: AAM12956.1.
AY133595 mRNA. Translation: AAM91425.1.
BT000035 mRNA. Translation: AAN15354.1.
PIRiT46172.
RefSeqiNP_190894.1. NM_115186.3.
UniGeneiAt.21614.

Genome annotation databases

EnsemblPlantsiAT3G53260.1; AT3G53260.1; AT3G53260.
GeneIDi824493.
GrameneiAT3G53260.1; AT3G53260.1; AT3G53260.
KEGGiath:AT3G53260.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L33678 Genomic DNA. Translation: AAC18871.1.
AY303129 mRNA. Translation: AAP59439.1.
AL132958 Genomic DNA. Translation: CAB64229.1.
CP002686 Genomic DNA. Translation: AEE79055.1.
AF367308 mRNA. Translation: AAK32895.1.
AY092957 mRNA. Translation: AAM12956.1.
AY133595 mRNA. Translation: AAM91425.1.
BT000035 mRNA. Translation: AAN15354.1.
PIRiT46172.
RefSeqiNP_190894.1. NM_115186.3.
UniGeneiAt.21614.

3D structure databases

ProteinModelPortaliP45724.
SMRiP45724. Positions 26-717.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi9810. 9 interactions.
IntActiP45724. 5 interactions.
MINTiMINT-8060879.
STRINGi3702.AT3G53260.1.

Proteomic databases

PaxDbiP45724.
PRIDEiP45724.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT3G53260.1; AT3G53260.1; AT3G53260.
GeneIDi824493.
GrameneiAT3G53260.1; AT3G53260.1; AT3G53260.
KEGGiath:AT3G53260.

Organism-specific databases

TAIRiAT3G53260.

Phylogenomic databases

eggNOGiKOG0222. Eukaryota.
COG2986. LUCA.
HOGENOMiHOG000214384.
InParanoidiP45724.
KOiK10775.
OMAiAGEMEDR.
PhylomeDBiP45724.

Enzyme and pathway databases

UniPathwayiUPA00713; UER00725.
BRENDAi4.3.1.24. 399.
ReactomeiR-ATH-70921. Histidine catabolism.
SABIO-RKP45724.

Miscellaneous databases

PROiP45724.

Gene expression databases

GenevisibleiP45724. AT.

Family and domain databases

Gene3Di1.10.274.20. 1 hit.
1.10.275.10. 1 hit.
InterProiIPR001106. Aromatic_Lyase.
IPR024083. Fumarase/histidase_N.
IPR008948. L-Aspartase-like.
IPR022313. Phe/His_NH3-lyase_AS.
IPR005922. Phe_NH3-lyase.
IPR023144. Phe_NH3-lyase_shielding_dom.
[Graphical view]
PfamiPF00221. Lyase_aromatic. 1 hit.
[Graphical view]
SUPFAMiSSF48557. SSF48557. 1 hit.
TIGRFAMsiTIGR01226. phe_am_lyase. 1 hit.
PROSITEiPS00488. PAL_HISTIDASE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The phenylalanine ammonia-lyase gene family in Arabidopsis thaliana."
    Wanner L.A., Li G., Ware D., Somssich I.E., Davis K.R.
    Plant Mol. Biol. 27:327-338(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: cv. Columbia.
  2. "The Arabidopsis phenylalanine ammonia lyase gene family: kinetic characterization of the four PAL isoforms."
    Cochrane F.C., Davin L.B., Lewis N.G.
    Phytochemistry 65:1557-1564(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], BIOPHYSICOCHEMICAL PROPERTIES.
    Strain: cv. Columbia.
  3. "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana."
    Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B., Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M., Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V., Choisne N., Artiguenave F.
    , Robert C., Brottier P., Wincker P., Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H., Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H., Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A., Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H., Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J., Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B., Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D., de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E., Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G., Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X., Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M., Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B., Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J., Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C., Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y., Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K., Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M., Tabata S.
    Nature 408:820-822(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  4. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  5. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
    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.
    Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: cv. Columbia.
  6. "Tandem affinity purification and mass spectrometric analysis of ubiquitylated proteins in Arabidopsis."
    Saracco S.A., Hansson M., Scalf M., Walker J.M., Smith L.M., Vierstra R.D.
    Plant J. 59:344-358(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: UBIQUITINATION [LARGE SCALE ANALYSIS].
  7. "The flavonoid biosynthetic pathway in Arabidopsis: Structural and genetic diversity."
    Saito K., Yonekura-Sakakibara K., Nakabayashi R., Higashi Y., Yamazaki M., Tohge T., Fernie A.R.
    Plant Physiol. Biochem. 0:0-0(2013)
    Cited for: REVIEW, NOMENCLATURE.

Entry informationi

Entry nameiPAL2_ARATH
AccessioniPrimary (citable) accession number: P45724
Secondary accession number(s): Q53ZM9
, Q8RWP4, Q94KC9, Q9SCN5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: May 27, 2002
Last modified: February 17, 2016
This is version 137 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.