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Protein

Phenylalanine/tyrosine ammonia-lyase

Gene

PAL

Organism
Rhodosporidium toruloides (Yeast) (Rhodotorula gracilis)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the non-oxidative deamination of L-phenylalanine and L-tyrosine to form trans-cinnamic acid and p-coumaric acid respectively with similar efficiencies. Facilitates the commitment step in phenylpropanoid pathways that produce lignins, coumarins and flavonoids.1 Publication

Catalytic activityi

L-phenylalanine = trans-cinnamate + ammonia.1 Publication
L-tyrosine = trans-p-hydroxycinnamate + ammonia.1 Publication

Kineticsi

  1. KM=0.29 mM for L-phenylalanine2 Publications
  2. KM=0.18 mM for L-tyrosine2 Publications

    pH dependencei

    Optimum pH is 8.5.2 Publications

    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 (FGENESH: predicted gene_9.166), Phenylalanine/tyrosine ammonia-lyase (PAL), Phenylalanine ammonia-lyase (RHTO0S_04e04676g)
    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)DescriptionActionsGraphical viewLength
    Active sitei110Proton donor/acceptorBy similarity1
    Binding sitei366SubstrateBy similarity1
    Binding sitei468Substrate1 Publication1
    Binding sitei496Substrate1 Publication1

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Lyase

    Keywords - Biological processi

    Phenylpropanoid metabolism

    Enzyme and pathway databases

    BRENDAi4.3.1.24. 5424.
    UniPathwayiUPA00713; UER00725.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Phenylalanine/tyrosine ammonia-lyase (EC:4.3.1.25)
    Alternative name(s):
    Bifunctional phenylalanine ammonia-lyase
    Short name:
    Bifunctional PAL
    Gene namesi
    Name:PAL
    OrganismiRhodosporidium toruloides (Yeast) (Rhodotorula gracilis)
    Taxonomic identifieri5286 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaBasidiomycotaPucciniomycotinaMicrobotryomycetesSporidiobolalesSporidiobolaceaeRhodotorula

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00002154321 – 716Phenylalanine/tyrosine ammonia-lyaseAdd BLAST716

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Cross-linki211 ↔ 2135-imidazolinone (Ala-Gly)
    Modified residuei2122,3-didehydroalanine (Ser)1

    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.

    Proteomic databases

    PRIDEiP11544.

    Interactioni

    Subunit structurei

    Homotetramer. Dimer of dimers.2 Publications

    Structurei

    Secondary structure

    1716
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi30 – 33Combined sources4
    Helixi44 – 52Combined sources9
    Beta strandi56 – 58Combined sources3
    Beta strandi60 – 62Combined sources3
    Helixi69 – 77Combined sources9
    Beta strandi82 – 84Combined sources3
    Helixi88 – 101Combined sources14
    Helixi103 – 107Combined sources5
    Helixi125 – 138Combined sources14
    Helixi147 – 149Combined sources3
    Helixi162 – 176Combined sources15
    Beta strandi179 – 181Combined sources3
    Helixi185 – 196Combined sources12
    Beta strandi204 – 206Combined sources3
    Beta strandi209 – 213Combined sources5
    Helixi215 – 225Combined sources11
    Beta strandi232 – 237Combined sources6
    Beta strandi240 – 245Combined sources6
    Helixi246 – 252Combined sources7
    Helixi264 – 269Combined sources6
    Beta strandi270 – 272Combined sources3
    Helixi273 – 303Combined sources31
    Helixi308 – 311Combined sources4
    Helixi313 – 315Combined sources3
    Turni316 – 319Combined sources4
    Helixi323 – 336Combined sources14
    Beta strandi340 – 343Combined sources4
    Helixi345 – 348Combined sources4
    Helixi363 – 366Combined sources4
    Helixi368 – 391Combined sources24
    Beta strandi396 – 401Combined sources6
    Turni402 – 405Combined sources4
    Beta strandi406 – 408Combined sources3
    Helixi416 – 443Combined sources28
    Turni446 – 448Combined sources3
    Helixi454 – 456Combined sources3
    Helixi461 – 463Combined sources3
    Helixi468 – 484Combined sources17
    Helixi489 – 491Combined sources3
    Turni496 – 499Combined sources4
    Beta strandi500 – 502Combined sources3
    Helixi506 – 560Combined sources55
    Turni561 – 566Combined sources6
    Helixi569 – 585Combined sources17
    Helixi593 – 611Combined sources19
    Turni612 – 614Combined sources3
    Helixi619 – 646Combined sources28
    Helixi649 – 651Combined sources3
    Helixi653 – 656Combined sources4
    Helixi662 – 670Combined sources9
    Turni671 – 673Combined sources3
    Helixi681 – 684Combined sources4
    Helixi691 – 703Combined sources13
    Turni704 – 707Combined sources4
    Helixi708 – 714Combined sources7

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1T6JX-ray2.10A/B1-716[»]
    1T6PX-ray2.70A/B/C/D/E/F/G/H1-716[»]
    1Y2MX-ray1.60A/B/C/D1-716[»]
    ProteinModelPortaliP11544.
    SMRiP11544.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP11544.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the PAL/histidase family.Curated

    Family and domain databases

    CDDicd00332. PAL-HAL. 1 hit.
    Gene3Di1.10.275.10. 1 hit.
    InterProiIPR001106. Aromatic_Lyase.
    IPR024083. Fumarase/histidase_N.
    IPR008948. L-Aspartase-like.
    IPR022313. Phe/His_NH3-lyase_AS.
    IPR005922. Phe_NH3-lyase.
    [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.

    P11544-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MAPSLDSISH SFANGVASAK QAVNGASTNL AVAGSHLPTT QVTQVDIVEK
    60 70 80 90 100
    MLAAPTDSTL ELDGYSLNLG DVVSAARKGR PVRVKDSDEI RSKIDKSVEF
    110 120 130 140 150
    LRSQLSMSVY GVTTGFGGSA DTRTEDAISL QKALLEHQLC GVLPSSFDSF
    160 170 180 190 200
    RLGRGLENSL PLEVVRGAMT IRVNSLTRGH SAVRLVVLEA LTNFLNHGIT
    210 220 230 240 250
    PIVPLRGTIS ASGDLSPLSY IAAAISGHPD SKVHVVHEGK EKILYAREAM
    260 270 280 290 300
    ALFNLEPVVL GPKEGLGLVN GTAVSASMAT LALHDAHMLS LLSQSLTAMT
    310 320 330 340 350
    VEAMVGHAGS FHPFLHDVTR PHPTQIEVAG NIRKLLEGSR FAVHHEEEVK
    360 370 380 390 400
    VKDDEGILRQ DRYPLRTSPQ WLGPLVSDLI HAHAVLTIEA GQSTTDNPLI
    410 420 430 440 450
    DVENKTSHHG GNFQAAAVAN TMEKTRLGLA QIGKLNFTQL TEMLNAGMNR
    460 470 480 490 500
    GLPSCLAAED PSLSYHCKGL DIAAAAYTSE LGHLANPVTT HVQPAEMANQ
    510 520 530 540 550
    AVNSLALISA RRTTESNDVL SLLLATHLYC VLQAIDLRAI EFEFKKQFGP
    560 570 580 590 600
    AIVSLIDQHF GSAMTGSNLR DELVEKVNKT LAKRLEQTNS YDLVPRWHDA
    610 620 630 640 650
    FSFAAGTVVE VLSSTSLSLA AVNAWKVAAA ESAISLTRQV RETFWSAAST
    660 670 680 690 700
    SSPALSYLSP RTQILYAFVR EELGVKARRG DVFLGKQEVT IGSNVSKIYE
    710
    AIKSGRINNV LLKMLA
    Length:716
    Mass (Da):76,880
    Last modified:November 1, 1990 - v2
    Checksum:i0C1DF61769A4E5E6
    GO

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti4 – 37SLDSI…AGSHL → RPTSQSQARTC in AAA33883 (PubMed:2828184).CuratedAdd BLAST34

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X51513 Genomic DNA. Translation: CAA35886.1.
    M18261 Genomic DNA. Translation: AAA33883.1.
    X12702 mRNA. Translation: CAA31209.1.
    PIRiA29607.
    A56628.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X51513 Genomic DNA. Translation: CAA35886.1.
    M18261 Genomic DNA. Translation: AAA33883.1.
    X12702 mRNA. Translation: CAA31209.1.
    PIRiA29607.
    A56628.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1T6JX-ray2.10A/B1-716[»]
    1T6PX-ray2.70A/B/C/D/E/F/G/H1-716[»]
    1Y2MX-ray1.60A/B/C/D1-716[»]
    ProteinModelPortaliP11544.
    SMRiP11544.
    ModBaseiSearch...
    MobiDBiSearch...

    Proteomic databases

    PRIDEiP11544.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Enzyme and pathway databases

    UniPathwayiUPA00713; UER00725.
    BRENDAi4.3.1.24. 5424.

    Miscellaneous databases

    EvolutionaryTraceiP11544.

    Family and domain databases

    CDDicd00332. PAL-HAL. 1 hit.
    Gene3Di1.10.275.10. 1 hit.
    InterProiIPR001106. Aromatic_Lyase.
    IPR024083. Fumarase/histidase_N.
    IPR008948. L-Aspartase-like.
    IPR022313. Phe/His_NH3-lyase_AS.
    IPR005922. Phe_NH3-lyase.
    [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...

    Entry informationi

    Entry nameiPALY_RHOTO
    AccessioniPrimary (citable) accession number: P11544
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1989
    Last sequence update: November 1, 1990
    Last modified: November 2, 2016
    This is version 110 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    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.