PAL_TRIV2
ID PAL_TRIV2 Reviewed; 567 AA.
AC Q3M5Z3;
DT 03-SEP-2014, integrated into UniProtKB/Swiss-Prot.
DT 25-OCT-2005, sequence version 1.
DT 03-AUG-2022, entry version 101.
DE RecName: Full=Phenylalanine ammonia-lyase {ECO:0000303|PubMed:17240984};
DE EC=4.3.1.24 {ECO:0000269|PubMed:17240984, ECO:0000269|PubMed:18556022};
GN OrderedLocusNames=Ava_3988;
OS Trichormus variabilis (strain ATCC 29413 / PCC 7937) (Anabaena variabilis).
OC Bacteria; Cyanobacteria; Nostocales; Nostocaceae; Trichormus.
OX NCBI_TaxID=240292;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 29413 / PCC 7937;
RX PubMed=25197444; DOI=10.4056/sigs.3899418;
RA Thiel T., Pratte B.S., Zhong J., Goodwin L., Copeland A., Lucas S., Han C.,
RA Pitluck S., Land M.L., Kyrpides N.C., Woyke T.;
RT "Complete genome sequence of Anabaena variabilis ATCC 29413.";
RL Stand. Genomic Sci. 9:562-573(2014).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS), FUNCTION, CATALYTIC ACTIVITY,
RP SUBUNIT, BIOPHYSICOCHEMICAL PROPERTIES, PTM, DEHYDRATION AT SER-168, AND
RP MUTAGENESIS OF LEU-108.
RC STRAIN=ATCC 29413 / PCC 7937;
RX PubMed=17240984; DOI=10.1021/bi061774g;
RA Moffitt M.C., Louie G.V., Bowman M.E., Pence J., Noel J.P., Moore B.S.;
RT "Discovery of two cyanobacterial phenylalanine ammonia lyases: kinetic and
RT structural characterization.";
RL Biochemistry 46:1004-1012(2007).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS) OF 25-567 OF MUTANT SER-503/SER-565,
RP MUTAGENESIS OF 1-MET--ASN-21; CYS-503 AND CYS-565, CATALYTIC ACTIVITY,
RP FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, AND PTM.
RC STRAIN=ATCC 29413 / PCC 7937;
RX PubMed=18556022; DOI=10.1016/j.jmb.2008.05.025;
RA Wang L., Gamez A., Archer H., Abola E.E., Sarkissian C.N., Fitzpatrick P.,
RA Wendt D., Zhang Y., Vellard M., Bliesath J., Bell S.M., Lemontt J.F.,
RA Scriver C.R., Stevens R.C.;
RT "Structural and biochemical characterization of the therapeutic Anabaena
RT variabilis phenylalanine ammonia lyase.";
RL J. Mol. Biol. 380:623-635(2008).
CC -!- FUNCTION: Catalyzes the non-oxidative deamination of L-phenylalanine to
CC form trans-cinnamic acid, the first step in the phenylpropanoid
CC pathway. {ECO:0000269|PubMed:17240984, ECO:0000269|PubMed:18556022}.
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=4.3.1.24;
CC Evidence={ECO:0000269|PubMed:17240984, ECO:0000269|PubMed:18556022};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.06 mM for phenylalanine {ECO:0000269|PubMed:17240984,
CC ECO:0000269|PubMed:18556022};
CC Note=kcat is 4.3 sec(-1) for phenylalanine (PubMed:17240984). kcat is
CC 4.6 sec(-1) for phenylalanine (PubMed:18556022). Retains activity
CC after 10 minutes exposure to pH values between 4 and 12
CC (PubMed:18556022). {ECO:0000269|PubMed:17240984,
CC ECO:0000269|PubMed:18556022};
CC pH dependence:
CC Optimum pH is 7.7-8.5. {ECO:0000269|PubMed:17240984,
CC ECO:0000269|PubMed:18556022};
CC -!- PATHWAY: Phenylpropanoid metabolism; trans-cinnamate biosynthesis;
CC trans-cinnamate from L-phenylalanine: step 1/1.
CC -!- SUBUNIT: Homotetramer. {ECO:0000269|PubMed:17240984,
CC ECO:0000269|PubMed:18556022}.
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:0000250|UniProtKB:Q68G84}.
CC -!- SIMILARITY: Belongs to the PAL/histidase family. {ECO:0000305}.
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DR EMBL; CP000117; ABA23593.1; -; Genomic_DNA.
DR PDB; 2NYN; X-ray; 1.90 A; A/B/C/D=1-567.
DR PDB; 3CZO; X-ray; 2.20 A; A/B/C/D=25-567.
DR PDB; 5LTM; X-ray; 2.41 A; A/B=25-563.
DR PDBsum; 2NYN; -.
DR PDBsum; 3CZO; -.
DR PDBsum; 5LTM; -.
DR AlphaFoldDB; Q3M5Z3; -.
DR SMR; Q3M5Z3; -.
DR STRING; 240292.Ava_3988; -.
DR EnsemblBacteria; ABA23593; ABA23593; Ava_3988.
DR KEGG; ava:Ava_3988; -.
DR eggNOG; COG2986; Bacteria.
DR HOGENOM; CLU_014801_3_2_3; -.
DR OMA; CAPQVAG; -.
DR BRENDA; 4.3.1.24; 322.
DR UniPathway; UPA00713; UER00725.
DR EvolutionaryTrace; Q3M5Z3; -.
DR Proteomes; UP000002533; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0045548; F:phenylalanine ammonia-lyase activity; IDA:UniProtKB.
DR GO; GO:0009072; P:aromatic amino acid family metabolic process; IDA:UniProtKB.
DR GO; GO:0009800; P:cinnamic acid biosynthetic process; IDA:UniProtKB.
DR GO; GO:0006559; P:L-phenylalanine catabolic process; IEA:UniProtKB-KW.
DR GO; GO:0009699; P:phenylpropanoid biosynthetic process; IDA:UniProtKB.
DR GO; GO:0051289; P:protein homotetramerization; IDA:UniProtKB.
DR CDD; cd00332; PAL-HAL; 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 PANTHER; PTHR10362; PTHR10362; 1.
DR Pfam; PF00221; Lyase_aromatic; 1.
DR SUPFAM; SSF48557; SSF48557; 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..567
FT /note="Phenylalanine ammonia-lyase"
FT /id="PRO_0000429966"
FT ACT_SITE 78
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000250|UniProtKB:Q68G84"
FT BINDING 223
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q68G84"
FT BINDING 311
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q68G84"
FT BINDING 314
FT /ligand="substrate"
FT /evidence="ECO:0000255"
FT BINDING 317
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q68G84"
FT BINDING 347
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q68G84"
FT BINDING 451
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q68G84"
FT MOD_RES 168
FT /note="2,3-didehydroalanine (Ser)"
FT /evidence="ECO:0000269|PubMed:17240984"
FT CROSSLNK 167..169
FT /note="5-imidazolinone (Ala-Gly)"
FT /evidence="ECO:0000269|PubMed:17240984"
FT MUTAGEN 1..21
FT /note="Missing: No effect on enzyme activity."
FT /evidence="ECO:0000269|PubMed:18556022"
FT MUTAGEN 108
FT /note="L->A: Slightly decreases catalytic rate."
FT /evidence="ECO:0000269|PubMed:17240984"
FT MUTAGEN 108
FT /note="L->G: Decreases catalytic rate."
FT /evidence="ECO:0000269|PubMed:17240984"
FT MUTAGEN 503
FT /note="C->S: Prevents formation of artifactual disulfide
FT bonds and increases solubility; when associated with S-
FT 565."
FT /evidence="ECO:0000269|PubMed:18556022"
FT MUTAGEN 565
FT /note="C->S: Prevents formation of artifactual disulfide
FT bonds and increases solubility; when associated with S-
FT 503."
FT /evidence="ECO:0000269|PubMed:18556022"
FT STRAND 26..31
FT /evidence="ECO:0007829|PDB:2NYN"
FT HELIX 35..44
FT /evidence="ECO:0007829|PDB:2NYN"
FT STRAND 48..50
FT /evidence="ECO:0007829|PDB:2NYN"
FT HELIX 54..71
FT /evidence="ECO:0007829|PDB:2NYN"
FT TURN 78..80
FT /evidence="ECO:0007829|PDB:3CZO"
FT HELIX 85..87
FT /evidence="ECO:0007829|PDB:3CZO"
FT HELIX 95..107
FT /evidence="ECO:0007829|PDB:2NYN"
FT STRAND 112..115
FT /evidence="ECO:0007829|PDB:2NYN"
FT HELIX 118..132
FT /evidence="ECO:0007829|PDB:2NYN"
FT HELIX 141..153
FT /evidence="ECO:0007829|PDB:2NYN"
FT STRAND 155..157
FT /evidence="ECO:0007829|PDB:2NYN"
FT STRAND 160..163
FT /evidence="ECO:0007829|PDB:2NYN"
FT HELIX 171..181
FT /evidence="ECO:0007829|PDB:2NYN"
FT STRAND 188..192
FT /evidence="ECO:0007829|PDB:2NYN"
FT STRAND 195..198
FT /evidence="ECO:0007829|PDB:2NYN"
FT HELIX 199..205
FT /evidence="ECO:0007829|PDB:2NYN"
FT HELIX 217..222
FT /evidence="ECO:0007829|PDB:2NYN"
FT STRAND 223..225
FT /evidence="ECO:0007829|PDB:2NYN"
FT HELIX 226..256
FT /evidence="ECO:0007829|PDB:2NYN"
FT HELIX 262..264
FT /evidence="ECO:0007829|PDB:2NYN"
FT HELIX 266..270
FT /evidence="ECO:0007829|PDB:2NYN"
FT HELIX 275..288
FT /evidence="ECO:0007829|PDB:2NYN"
FT STRAND 292..295
FT /evidence="ECO:0007829|PDB:2NYN"
FT STRAND 306..308
FT /evidence="ECO:0007829|PDB:3CZO"
FT HELIX 314..317
FT /evidence="ECO:0007829|PDB:2NYN"
FT HELIX 319..341
FT /evidence="ECO:0007829|PDB:2NYN"
FT STRAND 346..351
FT /evidence="ECO:0007829|PDB:2NYN"
FT HELIX 352..354
FT /evidence="ECO:0007829|PDB:2NYN"
FT STRAND 356..358
FT /evidence="ECO:0007829|PDB:2NYN"
FT HELIX 366..394
FT /evidence="ECO:0007829|PDB:2NYN"
FT TURN 396..400
FT /evidence="ECO:0007829|PDB:2NYN"
FT HELIX 404..406
FT /evidence="ECO:0007829|PDB:2NYN"
FT HELIX 419..435
FT /evidence="ECO:0007829|PDB:2NYN"
FT HELIX 440..442
FT /evidence="ECO:0007829|PDB:2NYN"
FT TURN 445..451
FT /evidence="ECO:0007829|PDB:2NYN"
FT HELIX 458..495
FT /evidence="ECO:0007829|PDB:2NYN"
FT STRAND 496..498
FT /evidence="ECO:0007829|PDB:3CZO"
FT HELIX 500..502
FT /evidence="ECO:0007829|PDB:2NYN"
FT HELIX 506..519
FT /evidence="ECO:0007829|PDB:2NYN"
FT HELIX 533..535
FT /evidence="ECO:0007829|PDB:2NYN"
FT HELIX 538..550
FT /evidence="ECO:0007829|PDB:2NYN"
FT HELIX 554..557
FT /evidence="ECO:0007829|PDB:2NYN"
FT HELIX 558..562
FT /evidence="ECO:0007829|PDB:2NYN"
SQ SEQUENCE 567 AA; 61741 MW; 20DC10E873A061FA CRC64;
MKTLSQAQSK TSSQQFSFTG NSSANVIIGN QKLTINDVAR VARNGTLVSL TNNTDILQGI
QASCDYINNA VESGEPIYGV TSGFGGMANV AISREQASEL QTNLVWFLKT GAGNKLPLAD
VRAAMLLRAN SHMRGASGIR LELIKRMEIF LNAGVTPYVY EFGSIGASGD LVPLSYITGS
LIGLDPSFKV DFNGKEMDAP TALRQLNLSP LTLLPKEGLA MMNGTSVMTG IAANCVYDTQ
ILTAIAMGVH ALDIQALNGT NQSFHPFIHN SKPHPGQLWA ADQMISLLAN SQLVRDELDG
KHDYRDHELI QDRYSLRCLP QYLGPIVDGI SQIAKQIEIE INSVTDNPLI DVDNQASYHG
GNFLGQYVGM GMDHLRYYIG LLAKHLDVQI ALLASPEFSN GLPPSLLGNR ERKVNMGLKG
LQICGNSIMP LLTFYGNSIA DRFPTHAEQF NQNINSQGYT SATLARRSVD IFQNYVAIAL
MFGVQAVDLR TYKKTGHYDA RACLSPATER LYSAVRHVVG QKPTSDRPYI WNDNEQGLDE
HIARISADIA AGGVIVQAVQ DILPCLH
