PADC_BACSU
ID PADC_BACSU Reviewed; 161 AA.
AC O07006;
DT 10-OCT-2002, integrated into UniProtKB/Swiss-Prot.
DT 01-JUL-1997, sequence version 1.
DT 03-AUG-2022, entry version 120.
DE RecName: Full=Phenolic acid decarboxylase PadC {ECO:0000303|PubMed:9546183};
DE Short=PAD {ECO:0000303|PubMed:9546183};
DE EC=4.1.1.102 {ECO:0000269|PubMed:9546183};
GN Name=padC; Synonyms=pad, yveH; OrderedLocusNames=BSU34400;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168;
RA Denizot F.;
RL Submitted (APR-1997) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, CATALYTIC ACTIVITY, SUBUNIT,
RP SUBSTRATE SPECIFICITY, BIOPHYSICOCHEMICAL PROPERTIES, AND INDUCTION.
RC STRAIN=168;
RX PubMed=9546183; DOI=10.1128/aem.64.4.1466-1471.1998;
RA Cavin J.-F., Dartois V., Divies C.;
RT "Gene cloning, transcriptional analysis, purification, and characterization
RT of phenolic acid decarboxylase from Bacillus subtilis.";
RL Appl. Environ. Microbiol. 64:1466-1471(1998).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9384377; DOI=10.1038/36786;
RA Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA Yoshikawa H., Danchin A.;
RT "The complete genome sequence of the Gram-positive bacterium Bacillus
RT subtilis.";
RL Nature 390:249-256(1997).
RN [4]
RP INDUCTION.
RC STRAIN=168;
RX PubMed=17295427; DOI=10.1002/pmic.200600706;
RA Duy N.V., Maeder U., Tran N.P., Cavin J.-F., Tam le T., Albrecht D.,
RA Hecker M., Antelmann H.;
RT "The proteome and transcriptome analysis of Bacillus subtilis in response
RT to salicylic acid.";
RL Proteomics 7:698-710(2007).
RN [5]
RP DISRUPTION PHENOTYPE.
RC STRAIN=168 / 3NA;
RX PubMed=26658822; DOI=10.1007/s00253-015-7197-6;
RA Graf N., Wenzel M., Altenbuchner J.;
RT "Identification and characterization of the vanillin dehydrogenase YfmT in
RT Bacillus subtilis 3NA.";
RL Appl. Microbiol. Biotechnol. 100:3511-3521(2016).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (1.36 ANGSTROMS).
RG Joint center for structural genomics (JCSG);
RT "Crystal structure of phenolic acid decarboxylase (2635953) from Bacillus
RT subtilis at 1.36 a resolution.";
RL Submitted (FEB-2009) to the PDB data bank.
RN [7] {ECO:0007744|PDB:4ALB}
RP X-RAY CRYSTALLOGRAPHY (3.03 ANGSTROMS) IN COMPLEX WITH SUBSTRATE, REACTION
RP MECHANISM, ACTIVE SITE, SUBUNIT, AND MUTAGENESIS OF 11-TYR--TYR-13; TYR-11;
RP TYR-13; TYR-19; ARG-41; GLU-64; THR-68 AND THR-98.
RX DOI=10.1039/C2CY20015E;
RA Frank A., Eborall W., Hyde R., Hart S., Turkenburg J.P., Grogan G.;
RT "Mutational analysis of phenolic acid cecarboxylase from Bacillus subtilis
RT (BsPAD), which converts bio-derived phenolic acids to styrene
RT derivatives.";
RL Catal. Sci. Technol. 2:1568-1574(2012).
CC -!- FUNCTION: Involved in the decarboxylation and detoxification of
CC phenolic derivatives. It is able to catalyze the decarboxylation of
CC ferulic, p-coumaric and caffeic acids. {ECO:0000269|PubMed:9546183}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(E)-4-coumarate + H(+) = 4-hydroxystyrene + CO2;
CC Xref=Rhea:RHEA:33227, ChEBI:CHEBI:1883, ChEBI:CHEBI:12876,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:16526; EC=4.1.1.102;
CC Evidence={ECO:0000269|PubMed:9546183};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(E)-cinnamate + H(+) = CO2 + styrene; Xref=Rhea:RHEA:46920,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:15669, ChEBI:CHEBI:16526,
CC ChEBI:CHEBI:27452; EC=4.1.1.102;
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(E)-ferulate + H(+) = 2-methoxy-4-vinylphenol + CO2;
CC Xref=Rhea:RHEA:33807, ChEBI:CHEBI:15378, ChEBI:CHEBI:16526,
CC ChEBI:CHEBI:29749, ChEBI:CHEBI:42438; EC=4.1.1.102;
CC Evidence={ECO:0000269|PubMed:9546183};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=1.1 mM for ferulic acid {ECO:0000269|PubMed:9546183};
CC KM=1.3 mM for p-coumaric acid {ECO:0000269|PubMed:9546183};
CC KM=2.6 mM for caffeic acid {ECO:0000269|PubMed:9546183};
CC Vmax=280 umol/min/mg enzyme for ferulic acid
CC {ECO:0000269|PubMed:9546183};
CC Vmax=265 umol/min/mg enzyme for p-coumaric acid
CC {ECO:0000269|PubMed:9546183};
CC Vmax=180 umol/min/mg enzyme for caffeic acid
CC {ECO:0000269|PubMed:9546183};
CC pH dependence:
CC Optimum pH is 5.0. {ECO:0000269|PubMed:9546183};
CC Temperature dependence:
CC Optimum temperature is 40-45 degrees Celsius.
CC {ECO:0000269|PubMed:9546183};
CC -!- SUBUNIT: Homodimer. {ECO:0000305|PubMed:9546183, ECO:0000305|Ref.7}.
CC -!- INDUCTION: By ferulic, p-coumaric and caffeic acids (at protein level)
CC (PubMed:9546183). Cells extracts from caffeic acid-induced cells
CC exhibited lower activity on the three acids, which indicates that
CC caffeic acid could be a less efficient inducer (PubMed:9546183). Up-
CC regulated by salicylate (PubMed:17295427).
CC {ECO:0000269|PubMed:17295427, ECO:0000269|PubMed:9546183}.
CC -!- DISRUPTION PHENOTYPE: No longer metabolizes ferulic acid
CC (PubMed:26658822). {ECO:0000269|PubMed:26658822}.
CC -!- SIMILARITY: Belongs to the PadC family. {ECO:0000305}.
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DR EMBL; AF017117; AAC46254.1; -; Genomic_DNA.
DR EMBL; Z94043; CAB08020.1; -; Genomic_DNA.
DR EMBL; AL009126; CAB15445.1; -; Genomic_DNA.
DR PIR; D69671; D69671.
DR RefSeq; NP_391320.1; NC_000964.3.
DR RefSeq; WP_003243190.1; NZ_JNCM01000033.1.
DR PDB; 2P8G; X-ray; 1.36 A; A=1-161.
DR PDB; 4ALB; X-ray; 3.03 A; A/B/C=1-161.
DR PDBsum; 2P8G; -.
DR PDBsum; 4ALB; -.
DR AlphaFoldDB; O07006; -.
DR SMR; O07006; -.
DR STRING; 224308.BSU34400; -.
DR PaxDb; O07006; -.
DR PRIDE; O07006; -.
DR DNASU; 938579; -.
DR EnsemblBacteria; CAB15445; CAB15445; BSU_34400.
DR GeneID; 938579; -.
DR KEGG; bsu:BSU34400; -.
DR PATRIC; fig|224308.179.peg.3727; -.
DR eggNOG; COG3479; Bacteria.
DR InParanoid; O07006; -.
DR OMA; VCFQNDH; -.
DR PhylomeDB; O07006; -.
DR BioCyc; BSUB:BSU34400-MON; -.
DR EvolutionaryTrace; O07006; -.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0016831; F:carboxy-lyase activity; IEA:UniProtKB-KW.
DR GO; GO:0019439; P:aromatic compound catabolic process; IEA:UniProtKB-KW.
DR GO; GO:0009636; P:response to toxic substance; IEA:UniProtKB-KW.
DR CDD; cd14241; PAD; 1.
DR Gene3D; 2.40.128.20; -; 1.
DR InterPro; IPR012674; Calycin.
DR InterPro; IPR008729; PA_de_COase.
DR PANTHER; PTHR40087; PTHR40087; 1.
DR Pfam; PF05870; PA_decarbox; 1.
DR PIRSF; PIRSF011561; PAD; 1.
DR SUPFAM; SSF50814; SSF50814; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Aromatic hydrocarbons catabolism; Decarboxylase;
KW Detoxification; Lyase; Reference proteome.
FT CHAIN 1..161
FT /note="Phenolic acid decarboxylase PadC"
FT /id="PRO_0000108125"
FT ACT_SITE 19
FT /note="Proton donor"
FT /evidence="ECO:0000305|Ref.7"
FT ACT_SITE 64
FT /note="Proton acceptor"
FT /evidence="ECO:0000269|Ref.7"
FT BINDING 11
FT /ligand="substrate"
FT /evidence="ECO:0000269|Ref.7"
FT BINDING 13
FT /ligand="substrate"
FT /evidence="ECO:0000269|Ref.7"
FT BINDING 41
FT /ligand="substrate"
FT /evidence="ECO:0000269|Ref.7"
FT MUTAGEN 11..13
FT /note="YTY->FTF: No ferulic acid decarboxylation."
FT /evidence="ECO:0000269|Ref.7"
FT MUTAGEN 11
FT /note="Y->F: 3% decarboxylation of ferulic acid."
FT /evidence="ECO:0000269|Ref.7"
FT MUTAGEN 13
FT /note="Y->F: 2% decarboxylation of ferulic acid."
FT /evidence="ECO:0000269|Ref.7"
FT MUTAGEN 19
FT /note="Y->A: 4% decarboxylation of ferulic acid."
FT /evidence="ECO:0000269|Ref.7"
FT MUTAGEN 41
FT /note="R->A: No ferulic acid decarboxylation."
FT /evidence="ECO:0000269|Ref.7"
FT MUTAGEN 64
FT /note="E->A: No ferulic acid decarboxylation."
FT /evidence="ECO:0000269|Ref.7"
FT MUTAGEN 68
FT /note="T->V: 52% decarboxylation of ferulic acid."
FT /evidence="ECO:0000269|Ref.7"
FT MUTAGEN 98
FT /note="T->A: 76% decarboxylation of ferulic acid."
FT /evidence="ECO:0000269|Ref.7"
FT HELIX 1..4
FT /evidence="ECO:0007829|PDB:2P8G"
FT STRAND 7..12
FT /evidence="ECO:0007829|PDB:2P8G"
FT STRAND 18..25
FT /evidence="ECO:0007829|PDB:2P8G"
FT STRAND 28..33
FT /evidence="ECO:0007829|PDB:2P8G"
FT TURN 37..40
FT /evidence="ECO:0007829|PDB:2P8G"
FT STRAND 42..47
FT /evidence="ECO:0007829|PDB:2P8G"
FT STRAND 49..54
FT /evidence="ECO:0007829|PDB:2P8G"
FT STRAND 57..63
FT /evidence="ECO:0007829|PDB:2P8G"
FT STRAND 69..75
FT /evidence="ECO:0007829|PDB:2P8G"
FT HELIX 76..78
FT /evidence="ECO:0007829|PDB:2P8G"
FT STRAND 80..87
FT /evidence="ECO:0007829|PDB:2P8G"
FT HELIX 89..93
FT /evidence="ECO:0007829|PDB:2P8G"
FT HELIX 95..98
FT /evidence="ECO:0007829|PDB:2P8G"
FT HELIX 102..104
FT /evidence="ECO:0007829|PDB:2P8G"
FT HELIX 106..115
FT /evidence="ECO:0007829|PDB:2P8G"
FT STRAND 122..135
FT /evidence="ECO:0007829|PDB:2P8G"
FT HELIX 152..158
FT /evidence="ECO:0007829|PDB:2P8G"
SQ SEQUENCE 161 AA; 19077 MW; BAF73F679D0FC313 CRC64;
MENFIGSHMI YTYENGWEYE IYIKNDHTID YRIHSGMVAG RWVRDQEVNI VKLTEGVYKV
SWTEPTGTDV SLNFMPNEKR MHGIIFFPKW VHEHPEITVC YQNDHIDLMK ESREKYETYP
KYVVPEFAEI TFLKNEGVDN EEVISKAPYE GMTDDIRAGR L
