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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

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>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

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>This subsection of the ‘Function’ section describes biophysical and chemical properties, such as maximal absorption, kinetic parameters, pH dependence, redox potentials and temperature dependence.<p><a href='/help/biophysicochemical_properties' target='_top'>More...</a></p>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

    <p>This subsection of the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section describes the metabolic pathway(s) associated with a protein.<p><a href='/help/pathway' target='_top'>More...</a></p>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/tyrosine ammonia-lyase (PAL), Phenylalanine ammonia-lyase (AAT19DRAFT_16462), Phenylalanine ammonia-lyase (FGENESH: predicted gene_9.166), 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
    <p>This subsection of the ‘Function’ section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>Active sitei110Proton donor/acceptorBy similarity1
    <p>This subsection of the ‘Function’ section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei366SubstrateBy similarity1
    Binding sitei468Substrate1 Publication1
    Binding sitei496Substrate1 Publication1

    <p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

    GO - Biological processi

    <p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

    Molecular functionLyase
    Biological processPhenylpropanoid metabolism

    Enzyme and pathway databases

    BRENDA Comprehensive Enzyme Information System

    More...
    BRENDAi
    4.3.1.24 5424

    UniPathway: a resource for the exploration and annotation of metabolic pathways

    More...
    UniPathwayi
    UPA00713;UER00725

    <p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
    Recommended name:
    Phenylalanine/tyrosine ammonia-lyase (EC:4.3.1.25)
    Alternative name(s):
    Bifunctional phenylalanine ammonia-lyase
    Short name:
    Bifunctional PAL
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
    Name:PAL
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiRhodosporidium toruloides (Yeast) (Rhodotorula gracilis)
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri5286 [NCBI]
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiEukaryotaFungiDikaryaBasidiomycotaPucciniomycotinaMicrobotryomycetesSporidiobolalesSporidiobolaceaeRhodotorula

    <p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

    Keywords - Cellular componenti

    Cytoplasm

    <p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00002154321 – 716Phenylalanine/tyrosine ammonia-lyaseAdd BLAST716

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the <a href="http://www.uniprot.org/help/ptm_processing_section">PTM / Processing</a> section describes <strong>covalent linkages</strong> of various types formed <strong>between two proteins (interchain cross-links)</strong> or <strong>between two parts of the same protein (intrachain cross-links)</strong>, except the disulfide bonds that are annotated in the <a href="http://www.uniprot.org/manual/disulfid">'Disulfide bond'</a> subsection.<p><a href='/help/crosslnk' target='_top'>More...</a></p>Cross-linki211 ↔ 2135-imidazolinone (Ala-Gly)1 Publication
    <p>This subsection of the ‘PTM / Processing’ section specifies the position and type of each modified residue excluding <a href="http://www.uniprot.org/manual/lipid">lipids</a>, <a href="http://www.uniprot.org/manual/carbohyd">glycans</a> and <a href="http://www.uniprot.org/manual/crosslnk">protein cross-links</a>.<p><a href='/help/mod_res' target='_top'>More...</a></p>Modified residuei2122,3-didehydroalanine (Ser)1 Publication1

    <p>This subsection of the <a href="http://www.uniprot.org/help/ptm_processing_section">PTM/processing</a> section describes post-translational modifications (PTMs). This subsection <strong>complements</strong> the information provided at the sequence level or describes modifications for which <strong>position-specific data is not yet available</strong>.<p><a href='/help/post-translational_modification' target='_top'>More...</a></p>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

    PRoteomics IDEntifications database

    More...
    PRIDEi
    P11544

    <p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

    <p>This subsection of the <a href="http://www.uniprot.org/help/interaction_section">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

    Homotetramer. Dimer of dimers.2 Publications

    <p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

    Secondary structure

    1716
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details

    3D structure databases

    Select the link destinations:

    Protein Data Bank Europe

    More...
    PDBei

    Protein Data Bank RCSB

    More...
    RCSB PDBi

    Protein Data Bank Japan

    More...
    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[»]

    Protein Model Portal of the PSI-Nature Structural Biology Knowledgebase

    More...
    ProteinModelPortali
    P11544

    SWISS-MODEL Repository - a database of annotated 3D protein structure models

    More...
    SMRi
    P11544

    Database of comparative protein structure models

    More...
    ModBasei
    Search...

    MobiDB: a database of protein disorder and mobility annotations

    More...
    MobiDBi
    Search...

    Miscellaneous databases

    Relative evolutionary importance of amino acids within a protein sequence

    More...
    EvolutionaryTracei
    P11544

    <p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

    <p>This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

    Belongs to the PAL/histidase family.Curated

    Family and domain databases

    Conserved Domains Database

    More...
    CDDi
    cd00332 PAL-HAL, 1 hit

    Gene3D Structural and Functional Annotation of Protein Families

    More...
    Gene3Di
    1.10.274.20, 1 hit
    1.10.275.10, 1 hit

    Integrated resource of protein families, domains and functional sites

    More...
    InterProi
    View protein in InterPro
    IPR001106 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_sf

    The PANTHER Classification System

    More...
    PANTHERi
    PTHR10362 PTHR10362, 1 hit

    Pfam protein domain database

    More...
    Pfami
    View protein in Pfam
    PF00221 Lyase_aromatic, 1 hit

    Superfamily database of structural and functional annotation

    More...
    SUPFAMi
    SSF48557 SSF48557, 1 hit

    TIGRFAMs; a protein family database

    More...
    TIGRFAMsi
    TIGR01226 phe_am_lyase, 1 hit

    PROSITE; a protein domain and family database

    More...
    PROSITEi
    View protein in PROSITE
    PS00488 PAL_HISTIDASE, 1 hit

    <p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>.<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

    <p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>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
    <p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i0C1DF61769A4E5E6
    GO

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the ‘Sequence’ section reports difference(s) between the canonical sequence (displayed by default in the entry) and the different sequence submissions merged in the entry. These various submissions may originate from different sequencing projects, different types of experiments, or different biological samples. Sequence conflicts are usually of unknown origin.<p><a href='/help/conflict' target='_top'>More...</a></p>Sequence conflicti4 – 37SLDSI…AGSHL → RPTSQSQARTC in AAA33883 (PubMed:2828184).CuratedAdd BLAST34

    Sequence databases

    Select the link destinations:

    EMBL nucleotide sequence database

    More...
    EMBLi

    GenBank nucleotide sequence database

    More...
    GenBanki

    DNA Data Bank of Japan; a nucleotide sequence database

    More...
    DDBJi
    Links Updated
    X51513 Genomic DNA Translation: CAA35886.1
    M18261 Genomic DNA Translation: AAA33883.1
    X12702 mRNA Translation: CAA31209.1

    Protein sequence database of the Protein Information Resource

    More...
    PIRi
    A29607
    A56628

    <p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

    <p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>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

    UniPathwayi
    UPA00713;UER00725

    BRENDAi4.3.1.24 5424

    Miscellaneous databases

    EvolutionaryTraceiP11544

    Family and domain databases

    CDDicd00332 PAL-HAL, 1 hit
    Gene3Di1.10.274.20, 1 hit
    1.10.275.10, 1 hit
    InterProiView protein in InterPro
    IPR001106 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_sf
    PANTHERiPTHR10362 PTHR10362, 1 hit
    PfamiView protein in Pfam
    PF00221 Lyase_aromatic, 1 hit
    SUPFAMiSSF48557 SSF48557, 1 hit
    TIGRFAMsiTIGR01226 phe_am_lyase, 1 hit
    PROSITEiView protein in PROSITE
    PS00488 PAL_HISTIDASE, 1 hit

    ProtoNet; Automatic hierarchical classification of proteins

    More...
    ProtoNeti
    Search...

    <p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

    <p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiPALY_RHOTO
    <p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P11544
    <p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 1, 1989
    Last sequence update: November 1, 1990
    Last modified: December 5, 2018
    This is version 115 of the entry and version 2 of the sequence. See complete history.
    <p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    <p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

    Keywords - Technical termi

    3D-structure

    Documents

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