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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)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei110 – 1101Proton donor/acceptorBy similarity
    Binding sitei366 – 3661SubstrateBy similarity
    Binding sitei468 – 4681Substrate1 Publication
    Binding sitei496 – 4961Substrate1 Publication

    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)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 716716Phenylalanine/tyrosine ammonia-lyasePRO_0000215432Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Cross-linki211 ↔ 2135-imidazolinone (Ala-Gly)
    Modified residuei212 – 21212,3-didehydroalanine (Ser)

    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.

    Interactioni

    Subunit structurei

    Homotetramer. Dimer of dimers.2 Publications

    Structurei

    Secondary structure

    1
    716
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi30 – 334Combined sources
    Helixi44 – 529Combined sources
    Beta strandi56 – 583Combined sources
    Beta strandi60 – 623Combined sources
    Helixi69 – 779Combined sources
    Beta strandi82 – 843Combined sources
    Helixi88 – 10114Combined sources
    Helixi103 – 1075Combined sources
    Helixi125 – 13814Combined sources
    Helixi147 – 1493Combined sources
    Helixi162 – 17615Combined sources
    Beta strandi179 – 1813Combined sources
    Helixi185 – 19612Combined sources
    Beta strandi204 – 2063Combined sources
    Beta strandi209 – 2135Combined sources
    Helixi215 – 22511Combined sources
    Beta strandi232 – 2376Combined sources
    Beta strandi240 – 2456Combined sources
    Helixi246 – 2527Combined sources
    Helixi264 – 2696Combined sources
    Beta strandi270 – 2723Combined sources
    Helixi273 – 30331Combined sources
    Helixi308 – 3114Combined sources
    Helixi313 – 3153Combined sources
    Turni316 – 3194Combined sources
    Helixi323 – 33614Combined sources
    Beta strandi340 – 3434Combined sources
    Helixi345 – 3484Combined sources
    Helixi363 – 3664Combined sources
    Helixi368 – 39124Combined sources
    Beta strandi396 – 4016Combined sources
    Turni402 – 4054Combined sources
    Beta strandi406 – 4083Combined sources
    Helixi416 – 44328Combined sources
    Turni446 – 4483Combined sources
    Helixi454 – 4563Combined sources
    Helixi461 – 4633Combined sources
    Helixi468 – 48417Combined sources
    Helixi489 – 4913Combined sources
    Turni496 – 4994Combined sources
    Beta strandi500 – 5023Combined sources
    Helixi506 – 56055Combined sources
    Turni561 – 5666Combined sources
    Helixi569 – 58517Combined sources
    Helixi593 – 61119Combined sources
    Turni612 – 6143Combined sources
    Helixi619 – 64628Combined sources
    Helixi649 – 6513Combined sources
    Helixi653 – 6564Combined sources
    Helixi662 – 6709Combined sources
    Turni671 – 6733Combined sources
    Helixi681 – 6844Combined sources
    Helixi691 – 70313Combined sources
    Turni704 – 7074Combined sources
    Helixi708 – 7147Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    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. Positions 26-716.
    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)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti4 – 3734SLDSI…AGSHL → RPTSQSQARTC in AAA33883 (PubMed:2828184).CuratedAdd
    BLAST

    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
    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. Positions 26-716.
    ModBaseiSearch...
    MobiDBiSearch...

    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: September 7, 2016
    This is version 108 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.