PALY_RHOTO
ID PALY_RHOTO Reviewed; 716 AA.
AC P11544;
DT 01-OCT-1989, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1990, sequence version 2.
DT 03-AUG-2022, entry version 124.
DE RecName: Full=Phenylalanine/tyrosine ammonia-lyase;
DE EC=4.3.1.25 {ECO:0000269|PubMed:5102931};
DE AltName: Full=Bifunctional phenylalanine ammonia-lyase;
DE Short=Bifunctional PAL;
GN Name=PAL;
OS Rhodosporidium toruloides (Yeast) (Rhodotorula gracilis).
OC Eukaryota; Fungi; Dikarya; Basidiomycota; Pucciniomycotina;
OC Microbotryomycetes; Sporidiobolales; Sporidiobolaceae; Rhodotorula.
OX NCBI_TaxID=5286;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 10788 / CBS 14 / BCRC 20306 / IAM 13469 / JCM 10020 / NBRC 0559
RC / NRRL Y-1091;
RX PubMed=1773059; DOI=10.3109/10425179109020772;
RA Rasmussen O.F., Orum H.;
RT "Analysis of the gene for phenylalanine ammonia-lyase from Rhodosporidium
RT toruloides.";
RL DNA Seq. 1:207-211(1991).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 10788 / CBS 14 / BCRC 20306 / IAM 13469 / JCM 10020 / NBRC 0559
RC / NRRL Y-1091;
RX PubMed=2828184; DOI=10.1016/0378-1119(87)90375-1;
RA Anson J.G., Gilbert H.J., Oram J.D., Minton N.P.;
RT "Complete nucleotide sequence of the Rhodosporidium toruloides gene coding
RT for phenylalanine ammonia-lyase.";
RL Gene 58:189-199(1987).
RN [3]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC STRAIN=ATCC 10788 / CBS 14 / BCRC 20306 / IAM 13469 / JCM 10020 / NBRC 0559
RC / NRRL Y-1091;
RA Fukuhara N., Yoshino S., Yamamoto K., Se T., Sone S., Nakajima Y.,
RA Suzuki M., Makiguchi N.;
RT "L-phenylalanine ammonia lyase.";
RL Patent number EP0260919, 23-MAR-1988.
RN [4]
RP FUNCTION, CATALYTIC ACTIVITY, AND BIOPHYSICOCHEMICAL PROPERTIES.
RC STRAIN=ATCC 10788 / CBS 14 / BCRC 20306 / IAM 13469 / JCM 10020 / NBRC 0559
RC / NRRL Y-1091;
RX PubMed=5102931; DOI=10.1016/s0021-9258(18)62279-3;
RA Hodgins D.S.;
RT "Yeast phenylalanine ammonia-lyase. Purification, properties, and the
RT identification of catalytically essential dehydroalanine.";
RL J. Biol. Chem. 246:2977-2985(1971).
RN [5]
RP BIOPHYSICOCHEMICAL PROPERTIES, AND SUBUNIT.
RX DOI=10.1271/bbb1961.54.2839;
RA Adachi O., Matsushita K., Shinagawa E., Ameyama M.;
RT "Crystallization and properties of L-phenylalanine ammonia-lyase from
RT Rhodosporidium toruloides.";
RL Agric. Biol. Chem. 54:2839-2843(1990).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) IN COMPLEX WITH SUBSTRATE, PTM,
RP DEHYDRATION AT SER-212, AND SUBUNIT.
RX PubMed=15350127; DOI=10.1021/bi049053+;
RA Calabrese J.C., Jordan D.B., Boodhoo A., Sariaslani S., Vannelli T.;
RT "Crystal structure of phenylalanine ammonia lyase: multiple helix dipoles
RT implicated in catalysis.";
RL Biochemistry 43:11403-11416(2004).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS).
RX PubMed=16006165; DOI=10.1016/j.ymgme.2005.05.012;
RA Wang L., Gamez A., Sarkissian C.N., Straub M., Patch M.G., Han G.W.,
RA Striepeke S., Fitzpatrick P., Scriver C.R., Stevens R.C.;
RT "Structure-based chemical modification strategy for enzyme replacement
RT treatment of phenylketonuria.";
RL Mol. Genet. Metab. 86:134-140(2005).
CC -!- FUNCTION: Catalyzes the non-oxidative deamination of L-phenylalanine
CC and L-tyrosine to form trans-cinnamic acid and p-coumaric acid
CC respectively with similar efficiencies. Facilitates the commitment step
CC in phenylpropanoid pathways that produce secondary metabolites such as
CC lignins, coumarins and flavonoids. {ECO:0000269|PubMed:5102931}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-phenylalanine = (E)-cinnamate + NH4(+);
CC Xref=Rhea:RHEA:21384, ChEBI:CHEBI:15669, ChEBI:CHEBI:28938,
CC ChEBI:CHEBI:58095; EC=4.3.1.25;
CC Evidence={ECO:0000269|PubMed:5102931};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-tyrosine = (E)-4-coumarate + NH4(+); Xref=Rhea:RHEA:24906,
CC ChEBI:CHEBI:12876, ChEBI:CHEBI:28938, ChEBI:CHEBI:58315; EC=4.3.1.25;
CC Evidence={ECO:0000269|PubMed:5102931};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.29 mM for L-phenylalanine {ECO:0000269|PubMed:5102931,
CC ECO:0000269|Ref.5};
CC KM=0.18 mM for L-tyrosine {ECO:0000269|PubMed:5102931,
CC ECO:0000269|Ref.5};
CC pH dependence:
CC Optimum pH is 8.5. {ECO:0000269|PubMed:5102931, ECO:0000269|Ref.5};
CC -!- PATHWAY: Phenylpropanoid metabolism; trans-cinnamate biosynthesis;
CC trans-cinnamate from L-phenylalanine: step 1/1. {ECO:0000305}.
CC -!- SUBUNIT: Homotetramer. Dimer of dimers. {ECO:0000269|PubMed:15350127,
CC ECO:0000269|Ref.5}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC -!- PTM: Contains an active site 4-methylidene-imidazol-5-one (MIO), which
CC is formed autocatalytically by cyclization and dehydration of residues
CC Ala-Ser-Gly. {ECO:0000269|PubMed:15350127}.
CC -!- SIMILARITY: Belongs to the PAL/histidase family. {ECO:0000305}.
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DR EMBL; X51513; CAA35886.1; -; Genomic_DNA.
DR EMBL; M18261; AAA33883.1; -; Genomic_DNA.
DR EMBL; X12702; CAA31209.1; -; mRNA.
DR PIR; A29607; A29607.
DR PIR; A56628; A56628.
DR PDB; 1T6J; X-ray; 2.10 A; A/B=1-716.
DR PDB; 1T6P; X-ray; 2.70 A; A/B/C/D/E/F/G/H=1-716.
DR PDB; 1Y2M; X-ray; 1.60 A; A/B/C/D=1-716.
DR PDBsum; 1T6J; -.
DR PDBsum; 1T6P; -.
DR PDBsum; 1Y2M; -.
DR AlphaFoldDB; P11544; -.
DR SMR; P11544; -.
DR BRENDA; 4.3.1.24; 5424.
DR BRENDA; 4.3.1.25; 5424.
DR UniPathway; UPA00713; UER00725.
DR EvolutionaryTrace; P11544; -.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0045548; F:phenylalanine ammonia-lyase activity; IEA:UniProtKB-EC.
DR GO; GO:0052883; F:tyrosine ammonia-lyase activity; IEA:UniProtKB-EC.
DR GO; GO:0009800; P:cinnamic acid biosynthetic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0006559; P:L-phenylalanine catabolic process; IEA:UniProtKB-KW.
DR CDD; cd00332; PAL-HAL; 1.
DR Gene3D; 1.10.274.20; -; 1.
DR Gene3D; 1.10.275.10; -; 1.
DR InterPro; IPR001106; Aromatic_Lyase.
DR InterPro; IPR024083; Fumarase/histidase_N.
DR InterPro; IPR008948; L-Aspartase-like.
DR InterPro; IPR022313; Phe/His_NH3-lyase_AS.
DR InterPro; IPR005922; Phe_NH3-lyase.
DR InterPro; IPR023144; Phe_NH3-lyase_shielding_dom_sf.
DR PANTHER; PTHR10362; PTHR10362; 1.
DR Pfam; PF00221; Lyase_aromatic; 1.
DR SUPFAM; SSF48557; SSF48557; 1.
DR TIGRFAMs; TIGR01226; phe_am_lyase; 1.
DR PROSITE; PS00488; PAL_HISTIDASE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Lyase; Phenylalanine catabolism;
KW Phenylpropanoid metabolism.
FT CHAIN 1..716
FT /note="Phenylalanine/tyrosine ammonia-lyase"
FT /id="PRO_0000215432"
FT ACT_SITE 110
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000250|UniProtKB:Q68G84"
FT BINDING 270
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q68G84"
FT BINDING 360
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q68G84"
FT BINDING 366
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q68G84"
FT BINDING 397
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q68G84"
FT BINDING 468
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:15350127"
FT BINDING 496
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:15350127"
FT BINDING 499
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q68G84"
FT MOD_RES 212
FT /note="2,3-didehydroalanine (Ser)"
FT /evidence="ECO:0000269|PubMed:15350127"
FT CROSSLNK 211..213
FT /note="5-imidazolinone (Ala-Gly)"
FT /evidence="ECO:0000269|PubMed:15350127"
FT CONFLICT 4..37
FT /note="SLDSISHSFANGVASAKQAVNGASTNLAVAGSHL -> RPTSQSQARTC
FT (in Ref. 2; AAA33883)"
FT /evidence="ECO:0000305"
FT HELIX 30..33
FT /evidence="ECO:0007829|PDB:1Y2M"
FT HELIX 44..52
FT /evidence="ECO:0007829|PDB:1Y2M"
FT STRAND 56..58
FT /evidence="ECO:0007829|PDB:1Y2M"
FT STRAND 60..62
FT /evidence="ECO:0007829|PDB:1Y2M"
FT HELIX 69..77
FT /evidence="ECO:0007829|PDB:1Y2M"
FT STRAND 82..84
FT /evidence="ECO:0007829|PDB:1Y2M"
FT HELIX 88..101
FT /evidence="ECO:0007829|PDB:1Y2M"
FT HELIX 103..107
FT /evidence="ECO:0007829|PDB:1Y2M"
FT HELIX 125..138
FT /evidence="ECO:0007829|PDB:1Y2M"
FT HELIX 147..149
FT /evidence="ECO:0007829|PDB:1Y2M"
FT HELIX 162..176
FT /evidence="ECO:0007829|PDB:1Y2M"
FT STRAND 179..181
FT /evidence="ECO:0007829|PDB:1Y2M"
FT HELIX 185..196
FT /evidence="ECO:0007829|PDB:1Y2M"
FT STRAND 204..206
FT /evidence="ECO:0007829|PDB:1Y2M"
FT HELIX 215..225
FT /evidence="ECO:0007829|PDB:1Y2M"
FT STRAND 232..237
FT /evidence="ECO:0007829|PDB:1Y2M"
FT STRAND 240..245
FT /evidence="ECO:0007829|PDB:1Y2M"
FT HELIX 246..252
FT /evidence="ECO:0007829|PDB:1Y2M"
FT HELIX 264..269
FT /evidence="ECO:0007829|PDB:1Y2M"
FT STRAND 270..272
FT /evidence="ECO:0007829|PDB:1Y2M"
FT HELIX 273..303
FT /evidence="ECO:0007829|PDB:1Y2M"
FT HELIX 308..311
FT /evidence="ECO:0007829|PDB:1Y2M"
FT HELIX 313..315
FT /evidence="ECO:0007829|PDB:1Y2M"
FT TURN 316..319
FT /evidence="ECO:0007829|PDB:1Y2M"
FT HELIX 323..336
FT /evidence="ECO:0007829|PDB:1Y2M"
FT STRAND 340..343
FT /evidence="ECO:0007829|PDB:1Y2M"
FT HELIX 345..348
FT /evidence="ECO:0007829|PDB:1Y2M"
FT HELIX 363..366
FT /evidence="ECO:0007829|PDB:1Y2M"
FT HELIX 368..391
FT /evidence="ECO:0007829|PDB:1Y2M"
FT STRAND 396..401
FT /evidence="ECO:0007829|PDB:1Y2M"
FT TURN 402..405
FT /evidence="ECO:0007829|PDB:1Y2M"
FT STRAND 406..408
FT /evidence="ECO:0007829|PDB:1Y2M"
FT HELIX 416..443
FT /evidence="ECO:0007829|PDB:1Y2M"
FT TURN 446..448
FT /evidence="ECO:0007829|PDB:1Y2M"
FT HELIX 454..456
FT /evidence="ECO:0007829|PDB:1Y2M"
FT HELIX 461..463
FT /evidence="ECO:0007829|PDB:1Y2M"
FT HELIX 468..484
FT /evidence="ECO:0007829|PDB:1Y2M"
FT HELIX 489..491
FT /evidence="ECO:0007829|PDB:1Y2M"
FT TURN 496..499
FT /evidence="ECO:0007829|PDB:1Y2M"
FT STRAND 500..502
FT /evidence="ECO:0007829|PDB:1Y2M"
FT HELIX 506..560
FT /evidence="ECO:0007829|PDB:1Y2M"
FT TURN 561..566
FT /evidence="ECO:0007829|PDB:1Y2M"
FT HELIX 569..585
FT /evidence="ECO:0007829|PDB:1Y2M"
FT HELIX 593..611
FT /evidence="ECO:0007829|PDB:1Y2M"
FT TURN 612..614
FT /evidence="ECO:0007829|PDB:1Y2M"
FT HELIX 619..646
FT /evidence="ECO:0007829|PDB:1Y2M"
FT HELIX 649..651
FT /evidence="ECO:0007829|PDB:1Y2M"
FT HELIX 653..656
FT /evidence="ECO:0007829|PDB:1Y2M"
FT HELIX 662..670
FT /evidence="ECO:0007829|PDB:1Y2M"
FT TURN 671..673
FT /evidence="ECO:0007829|PDB:1T6P"
FT HELIX 681..684
FT /evidence="ECO:0007829|PDB:1Y2M"
FT HELIX 691..703
FT /evidence="ECO:0007829|PDB:1Y2M"
FT TURN 704..707
FT /evidence="ECO:0007829|PDB:1T6P"
FT HELIX 708..714
FT /evidence="ECO:0007829|PDB:1Y2M"
SQ SEQUENCE 716 AA; 76880 MW; 0C1DF61769A4E5E6 CRC64;
MAPSLDSISH SFANGVASAK QAVNGASTNL AVAGSHLPTT QVTQVDIVEK MLAAPTDSTL
ELDGYSLNLG DVVSAARKGR PVRVKDSDEI RSKIDKSVEF LRSQLSMSVY GVTTGFGGSA
DTRTEDAISL QKALLEHQLC GVLPSSFDSF RLGRGLENSL PLEVVRGAMT IRVNSLTRGH
SAVRLVVLEA LTNFLNHGIT PIVPLRGTIS ASGDLSPLSY IAAAISGHPD SKVHVVHEGK
EKILYAREAM ALFNLEPVVL GPKEGLGLVN GTAVSASMAT LALHDAHMLS LLSQSLTAMT
VEAMVGHAGS FHPFLHDVTR PHPTQIEVAG NIRKLLEGSR FAVHHEEEVK VKDDEGILRQ
DRYPLRTSPQ WLGPLVSDLI HAHAVLTIEA GQSTTDNPLI DVENKTSHHG GNFQAAAVAN
TMEKTRLGLA QIGKLNFTQL TEMLNAGMNR GLPSCLAAED PSLSYHCKGL DIAAAAYTSE
LGHLANPVTT HVQPAEMANQ AVNSLALISA RRTTESNDVL SLLLATHLYC VLQAIDLRAI
EFEFKKQFGP AIVSLIDQHF GSAMTGSNLR DELVEKVNKT LAKRLEQTNS YDLVPRWHDA
FSFAAGTVVE VLSSTSLSLA AVNAWKVAAA ESAISLTRQV RETFWSAAST SSPALSYLSP
RTQILYAFVR EELGVKARRG DVFLGKQEVT IGSNVSKIYE AIKSGRINNV LLKMLA
