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Phenylalanine ammonia-lyase (EC 4.3.1.24)

 PAL_ANAVT               Reviewed;         567 AA.
Q3M5Z3;
03-SEP-2014, integrated into UniProtKB/Swiss-Prot.
25-OCT-2005, sequence version 1.
07-JUN-2017, entry version 83.
RecName: Full=Phenylalanine ammonia-lyase;
EC=4.3.1.24;
OrderedLocusNames=Ava_3988;
Anabaena variabilis (strain ATCC 29413 / PCC 7937).
Bacteria; Cyanobacteria; Nostocales; Nostocaceae; Anabaena.
NCBI_TaxID=240292;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 29413 / PCC 7937;
Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina T.,
Hammon N., Israni S., Pitluck S., Saunders E.H., Schmutz J.,
Larimer F., Land M., Kyrpides N., Mavrommatis K., Richardson P.;
"Complete sequence of Anabaena variabilis ATCC 29413.";
Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases.
[2]
X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS), FUNCTION, CATALYTIC ACTIVITY,
SUBUNIT, BIOPHYSICOCHEMICAL PROPERTIES, PTM, AND MUTAGENESIS OF
LEU-108.
STRAIN=ATCC 29413 / PCC 7937;
PubMed=17240984; DOI=10.1021/bi061774g;
Moffitt M.C., Louie G.V., Bowman M.E., Pence J., Noel J.P.,
Moore B.S.;
"Discovery of two cyanobacterial phenylalanine ammonia lyases: kinetic
and structural characterization.";
Biochemistry 46:1004-1012(2007).
[3]
X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS) OF 25-567 OF MUTANT
SER-503/SER-565, MUTAGENESIS OF 1-MET--ASN-21; CYS-503 AND CYS-565,
CATALYTIC ACTIVITY, FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT,
AND PTM.
STRAIN=ATCC 29413 / PCC 7937;
PubMed=18556022; DOI=10.1016/j.jmb.2008.05.025;
Wang L., Gamez A., Archer H., Abola E.E., Sarkissian C.N.,
Fitzpatrick P., Wendt D., Zhang Y., Vellard M., Bliesath J.,
Bell S.M., Lemontt J.F., Scriver C.R., Stevens R.C.;
"Structural and biochemical characterization of the therapeutic
Anabaena variabilis phenylalanine ammonia lyase.";
J. Mol. Biol. 380:623-635(2008).
-!- FUNCTION: Catalyzes the non-oxidative deamination of L-
phenylalanine to form trans-cinnamic acid, the first step in the
phenylpropanoid pathway. {ECO:0000269|PubMed:17240984,
ECO:0000269|PubMed:18556022}.
-!- CATALYTIC ACTIVITY: L-phenylalanine = trans-cinnamate + ammonia.
{ECO:0000269|PubMed:17240984, ECO:0000269|PubMed:18556022}.
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=0.06 mM for phenylalanine {ECO:0000269|PubMed:17240984,
ECO:0000269|PubMed:18556022};
Note=kcat is 4.3 sec(-1) for phenylalanine (PubMed:17240984).
kcat is 4.6 sec(-1) for phenylalanine (PubMed:18556022). Retains
activity after 10 minutes exposure to pH values between 4 and 12
(PubMed:18556022). {ECO:0000269|PubMed:17240984,
ECO:0000269|PubMed:18556022};
pH dependence:
Optimum pH is 7.7-8.5 (PubMed:17240984 and PubMed:18556022).
{ECO:0000269|PubMed:17240984, ECO:0000269|PubMed:18556022};
-!- PATHWAY: Phenylpropanoid metabolism; trans-cinnamate biosynthesis;
trans-cinnamate from L-phenylalanine: step 1/1.
-!- SUBUNIT: Homotetramer. {ECO:0000269|PubMed:17240984,
ECO:0000269|PubMed:18556022}.
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
-!- PTM: Contains an active site 4-methylidene-imidazol-5-one (MIO),
which is formed autocatalytically by cyclization and dehydration
of residues Ala-Ser-Gly.
-!- SIMILARITY: Belongs to the PAL/histidase family. {ECO:0000305}.
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EMBL; CP000117; ABA23593.1; -; Genomic_DNA.
PDB; 2NYN; X-ray; 1.90 A; A/B/C/D=1-567.
PDB; 3CZO; X-ray; 2.20 A; A/B/C/D=25-567.
PDBsum; 2NYN; -.
PDBsum; 3CZO; -.
ProteinModelPortal; Q3M5Z3; -.
SMR; Q3M5Z3; -.
STRING; 240292.Ava_3988; -.
EnsemblBacteria; ABA23593; ABA23593; Ava_3988.
KEGG; ava:Ava_3988; -.
eggNOG; ENOG4105C84; Bacteria.
eggNOG; COG2986; LUCA.
HOGENOM; HOG000237621; -.
KO; K10775; -.
OMA; CAPQVAG; -.
OrthoDB; POG091H04Z2; -.
BioCyc; AVAR240292:G7WH-9134-MONOMER; -.
UniPathway; UPA00713; UER00725.
EvolutionaryTrace; Q3M5Z3; -.
Proteomes; UP000002533; Chromosome.
GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
GO; GO:0045548; F:phenylalanine ammonia-lyase activity; IDA:UniProtKB.
GO; GO:0009072; P:aromatic amino acid family metabolic process; IDA:UniProtKB.
GO; GO:0009800; P:cinnamic acid biosynthetic process; IDA:UniProtKB.
GO; GO:0009699; P:phenylpropanoid biosynthetic process; IDA:UniProtKB.
GO; GO:0051289; P:protein homotetramerization; IDA:UniProtKB.
CDD; cd00332; PAL-HAL; 1.
Gene3D; 1.10.275.10; -; 1.
InterPro; IPR001106; Aromatic_Lyase.
InterPro; IPR024083; Fumarase/histidase_N.
InterPro; IPR008948; L-Aspartase-like.
InterPro; IPR022313; Phe/His_NH3-lyase_AS.
Pfam; PF00221; Lyase_aromatic; 1.
SUPFAM; SSF48557; SSF48557; 1.
PROSITE; PS00488; PAL_HISTIDASE; 1.
1: Evidence at protein level;
3D-structure; Complete proteome; Cytoplasm; Lyase;
Phenylpropanoid metabolism.
CHAIN 1 567 Phenylalanine ammonia-lyase.
/FTId=PRO_0000429966.
ACT_SITE 78 78 Proton donor/acceptor. {ECO:0000250}.
BINDING 314 314 Substrate. {ECO:0000255}.
BINDING 317 317 Substrate. {ECO:0000250}.
MOD_RES 168 168 2,3-didehydroalanine (Ser).
CROSSLNK 167 169 5-imidazolinone (Ala-Gly).
MUTAGEN 1 21 Missing: No effect on enzyme activity.
{ECO:0000269|PubMed:18556022}.
MUTAGEN 108 108 L->A: Slightly decreases catalytic rate.
{ECO:0000269|PubMed:17240984}.
MUTAGEN 108 108 L->G: Decreases catalytic rate.
{ECO:0000269|PubMed:17240984}.
MUTAGEN 503 503 C->S: Prevents formation of artifactual
disulfide bonds and increases solubility;
when associated with S-565.
{ECO:0000269|PubMed:18556022}.
MUTAGEN 565 565 C->S: Prevents formation of artifactual
disulfide bonds and increases solubility;
when associated with S-503.
{ECO:0000269|PubMed:18556022}.
STRAND 26 31 {ECO:0000244|PDB:2NYN}.
HELIX 35 44 {ECO:0000244|PDB:2NYN}.
STRAND 48 50 {ECO:0000244|PDB:2NYN}.
HELIX 54 71 {ECO:0000244|PDB:2NYN}.
TURN 78 80 {ECO:0000244|PDB:3CZO}.
HELIX 85 87 {ECO:0000244|PDB:3CZO}.
HELIX 95 107 {ECO:0000244|PDB:2NYN}.
STRAND 112 115 {ECO:0000244|PDB:2NYN}.
HELIX 118 132 {ECO:0000244|PDB:2NYN}.
HELIX 141 153 {ECO:0000244|PDB:2NYN}.
STRAND 155 157 {ECO:0000244|PDB:2NYN}.
STRAND 160 163 {ECO:0000244|PDB:2NYN}.
STRAND 166 169 {ECO:0000244|PDB:2NYN}.
HELIX 171 181 {ECO:0000244|PDB:2NYN}.
STRAND 188 192 {ECO:0000244|PDB:2NYN}.
STRAND 195 198 {ECO:0000244|PDB:2NYN}.
HELIX 199 205 {ECO:0000244|PDB:2NYN}.
HELIX 217 222 {ECO:0000244|PDB:2NYN}.
STRAND 223 225 {ECO:0000244|PDB:2NYN}.
HELIX 226 256 {ECO:0000244|PDB:2NYN}.
HELIX 262 264 {ECO:0000244|PDB:2NYN}.
HELIX 266 270 {ECO:0000244|PDB:2NYN}.
HELIX 275 288 {ECO:0000244|PDB:2NYN}.
STRAND 292 295 {ECO:0000244|PDB:2NYN}.
STRAND 306 308 {ECO:0000244|PDB:3CZO}.
HELIX 314 317 {ECO:0000244|PDB:2NYN}.
HELIX 319 341 {ECO:0000244|PDB:2NYN}.
STRAND 346 351 {ECO:0000244|PDB:2NYN}.
HELIX 352 354 {ECO:0000244|PDB:2NYN}.
STRAND 356 358 {ECO:0000244|PDB:2NYN}.
HELIX 366 394 {ECO:0000244|PDB:2NYN}.
TURN 396 400 {ECO:0000244|PDB:2NYN}.
HELIX 404 406 {ECO:0000244|PDB:2NYN}.
HELIX 419 435 {ECO:0000244|PDB:2NYN}.
HELIX 440 442 {ECO:0000244|PDB:2NYN}.
TURN 445 451 {ECO:0000244|PDB:2NYN}.
HELIX 458 495 {ECO:0000244|PDB:2NYN}.
STRAND 496 498 {ECO:0000244|PDB:3CZO}.
HELIX 500 502 {ECO:0000244|PDB:2NYN}.
HELIX 506 519 {ECO:0000244|PDB:2NYN}.
HELIX 533 535 {ECO:0000244|PDB:2NYN}.
HELIX 538 550 {ECO:0000244|PDB:2NYN}.
HELIX 554 557 {ECO:0000244|PDB:2NYN}.
HELIX 558 562 {ECO:0000244|PDB:2NYN}.
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


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