ID   PAD_PORGI               Reviewed;         556 AA.
AC   Q9RQJ2; Q7BW72;
DT   16-AUG-2005, integrated into UniProtKB/Swiss-Prot.
DT   01-MAY-2000, sequence version 1.
DT   27-MAR-2024, entry version 99.
DE   RecName: Full=Peptidylarginine deiminase;
DE            EC=3.5.3.-;
DE   Flags: Precursor;
GN   OrderedLocusNames=PG_1424;
OS   Porphyromonas gingivalis (strain ATCC BAA-308 / W83).
OC   Bacteria; Bacteroidota; Bacteroidia; Bacteroidales; Porphyromonadaceae;
OC   Porphyromonas.
OX   NCBI_TaxID=242619;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 44-73, FUNCTION,
RP   ENZYME ACTIVITY, ACTIVITY REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, AND
RP   POSSIBLE COFACTOR.
RC   STRAIN=ATCC BAA-308 / W83;
RX   PubMed=10377098; DOI=10.1128/iai.67.7.3248-3256.1999;
RA   McGraw W.T., Potempa J., Farley D., Travis J.;
RT   "Purification, characterization, and sequence analysis of a potential
RT   virulence factor from Porphyromonas gingivalis, peptidylarginine
RT   deiminase.";
RL   Infect. Immun. 67:3248-3256(1999).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC BAA-308 / W83;
RX   PubMed=12949112; DOI=10.1128/jb.185.18.5591-5601.2003;
RA   Nelson K.E., Fleischmann R.D., DeBoy R.T., Paulsen I.T., Fouts D.E.,
RA   Eisen J.A., Daugherty S.C., Dodson R.J., Durkin A.S., Gwinn M.L.,
RA   Haft D.H., Kolonay J.F., Nelson W.C., Mason T.M., Tallon L., Gray J.,
RA   Granger D., Tettelin H., Dong H., Galvin J.L., Duncan M.J., Dewhirst F.E.,
RA   Fraser C.M.;
RT   "Complete genome sequence of the oral pathogenic bacterium Porphyromonas
RT   gingivalis strain W83.";
RL   J. Bacteriol. 185:5591-5601(2003).
CC   -!- FUNCTION: Deiminates the guanidino group of C-terminal arginine
CC       residues on a variety of peptides, including the vasoregulatory
CC       peptide-hormone bradykinin, to yield ammonia and a citrulline residue.
CC       May promote the growth of the pathogen in the periodontal pocket by
CC       producing ammonia, ammonia having a protective effect during acidic
CC       cleaning cycles in the mouth. {ECO:0000269|PubMed:10377098}.
CC   -!- COFACTOR:
CC       Name=FAD; Xref=ChEBI:CHEBI:57692; Evidence={ECO:0000305};
CC       Name=FMN; Xref=ChEBI:CHEBI:58210; Evidence={ECO:0000305};
CC   -!- ACTIVITY REGULATION: Inhibited by cysteine and TLCK. Inhibited by high
CC       concentration of thiourea and thio-L-citrulline.
CC       {ECO:0000269|PubMed:10377098}.
CC   -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC       Kinetic parameters:
CC         KM=2.9 uM for Benzoyl-L-arginine {ECO:0000269|PubMed:10377098};
CC         KM=28 uM for Benzoylglycyl-L-arginine {ECO:0000269|PubMed:10377098};
CC         KM=152 uM for BAA {ECO:0000269|PubMed:10377098};
CC         KM=874 uM for BAEE {ECO:0000269|PubMed:10377098};
CC         KM=141 uM for L-arginine {ECO:0000269|PubMed:10377098};
CC         KM=47 uM for BK {ECO:0000269|PubMed:10377098};
CC         Vmax=104 nmol/min/mg enzyme with Benzoyl-L-arginine as substrate
CC         {ECO:0000269|PubMed:10377098};
CC         Vmax=186 nmol/min/mg enzyme with Benzoylglycyl-L-arginine as
CC         substrate {ECO:0000269|PubMed:10377098};
CC         Vmax=77 nmol/min/mg enzyme with BAA as substrate
CC         {ECO:0000269|PubMed:10377098};
CC         Vmax=90 nmol/min/mg enzyme with BAEE as substrate
CC         {ECO:0000269|PubMed:10377098};
CC         Vmax=26 nmol/min/mg enzyme with L-arginine as substrate
CC         {ECO:0000269|PubMed:10377098};
CC         Vmax=117 nmol/min/mg enzyme with BK as substrate
CC         {ECO:0000269|PubMed:10377098};
CC       pH dependence:
CC         Optimum pH is 9.3. {ECO:0000269|PubMed:10377098};
CC   -!- SUBCELLULAR LOCATION: Secreted {ECO:0000305}.
CC   -!- SIMILARITY: Belongs to the agmatine deiminase family. {ECO:0000305}.
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DR   EMBL; AF100668; AAF06719.1; -; Genomic_DNA.
DR   EMBL; AE015924; AAQ66478.1; -; Genomic_DNA.
DR   RefSeq; WP_005873463.1; NC_002950.2.
DR   PDB; 4YT9; X-ray; 1.50 A; A=44-475.
DR   PDB; 4YTB; X-ray; 1.40 A; A=44-475.
DR   PDB; 4YTG; X-ray; 1.80 A; A=44-475.
DR   PDB; 5AK7; X-ray; 1.46 A; A=49-484.
DR   PDB; 5AK8; X-ray; 1.48 A; A=49-484.
DR   PDB; 6I0X; X-ray; 1.60 A; A/B=44-475.
DR   PDBsum; 4YT9; -.
DR   PDBsum; 4YTB; -.
DR   PDBsum; 4YTG; -.
DR   PDBsum; 5AK7; -.
DR   PDBsum; 5AK8; -.
DR   PDBsum; 6I0X; -.
DR   AlphaFoldDB; Q9RQJ2; -.
DR   SMR; Q9RQJ2; -.
DR   STRING; 242619.PG_1424; -.
DR   EnsemblBacteria; AAQ66478; AAQ66478; PG_1424.
DR   GeneID; 29256112; -.
DR   KEGG; pgi:PG_1424; -.
DR   eggNOG; COG2957; Bacteria.
DR   HOGENOM; CLU_026427_0_0_10; -.
DR   BRENDA; 3.5.3.15; 756.
DR   SABIO-RK; Q9RQJ2; -.
DR   Proteomes; UP000000588; Chromosome.
DR   GO; GO:0005576; C:extracellular region; IEA:UniProtKB-SubCell.
DR   GO; GO:0004668; F:protein-arginine deiminase activity; IEA:InterPro.
DR   GO; GO:0009446; P:putrescine biosynthetic process; IEA:InterPro.
DR   DisProt; DP02931; -.
DR   InterPro; IPR007466; Peptidyl-Arg-deiminase_porph.
DR   PANTHER; PTHR31377; AGMATINE DEIMINASE-RELATED; 1.
DR   PANTHER; PTHR31377:SF0; AGMATINE DEIMINASE-RELATED; 1.
DR   Pfam; PF04371; PAD_porph; 1.
DR   SUPFAM; SSF55909; Pentein; 1.
PE   1: Evidence at protein level;
KW   3D-structure; Direct protein sequencing; FAD; Flavoprotein; FMN; Hydrolase;
KW   Reference proteome; Secreted; Signal.
FT   SIGNAL          1..23
FT                   /evidence="ECO:0000255"
FT   PROPEP          24..43
FT                   /evidence="ECO:0000305|PubMed:10377098"
FT                   /id="PRO_0000001044"
FT   CHAIN           44..556
FT                   /note="Peptidylarginine deiminase"
FT                   /id="PRO_0000001045"
FT   ACT_SITE        351
FT                   /note="Amidino-cysteine intermediate"
FT                   /evidence="ECO:0000250"
FT   STRAND          52..57
FT                   /evidence="ECO:0007829|PDB:4YTB"
FT   STRAND          64..72
FT                   /evidence="ECO:0007829|PDB:4YTB"
FT   HELIX           77..86
FT                   /evidence="ECO:0007829|PDB:4YTB"
FT   STRAND          89..95
FT                   /evidence="ECO:0007829|PDB:4YTB"
FT   HELIX           96..109
FT                   /evidence="ECO:0007829|PDB:4YTB"
FT   HELIX           113..115
FT                   /evidence="ECO:0007829|PDB:4YTB"
FT   STRAND          116..120
FT                   /evidence="ECO:0007829|PDB:4YTB"
FT   HELIX           128..131
FT                   /evidence="ECO:0007829|PDB:4YTB"
FT   STRAND          134..138
FT                   /evidence="ECO:0007829|PDB:4YTB"
FT   TURN            139..141
FT                   /evidence="ECO:0007829|PDB:4YTB"
FT   STRAND          142..153
FT                   /evidence="ECO:0007829|PDB:4YTB"
FT   HELIX           155..159
FT                   /evidence="ECO:0007829|PDB:4YTB"
FT   HELIX           161..168
FT                   /evidence="ECO:0007829|PDB:4YTB"
FT   STRAND          172..179
FT                   /evidence="ECO:0007829|PDB:4YTB"
FT   HELIX           181..183
FT                   /evidence="ECO:0007829|PDB:4YTB"
FT   STRAND          188..195
FT                   /evidence="ECO:0007829|PDB:4YTB"
FT   HELIX           197..200
FT                   /evidence="ECO:0007829|PDB:4YTB"
FT   TURN            201..204
FT                   /evidence="ECO:0007829|PDB:4YTB"
FT   HELIX           207..218
FT                   /evidence="ECO:0007829|PDB:4YTB"
FT   STRAND          221..226
FT                   /evidence="ECO:0007829|PDB:4YTB"
FT   STRAND          232..234
FT                   /evidence="ECO:0007829|PDB:4YTB"
FT   HELIX           237..239
FT                   /evidence="ECO:0007829|PDB:4YTB"
FT   STRAND          241..245
FT                   /evidence="ECO:0007829|PDB:4YTB"
FT   STRAND          248..253
FT                   /evidence="ECO:0007829|PDB:4YTB"
FT   HELIX           261..272
FT                   /evidence="ECO:0007829|PDB:4YTB"
FT   STRAND          279..281
FT                   /evidence="ECO:0007829|PDB:4YTB"
FT   STRAND          283..288
FT                   /evidence="ECO:0007829|PDB:4YTB"
FT   STRAND          290..292
FT                   /evidence="ECO:0007829|PDB:6I0X"
FT   STRAND          299..301
FT                   /evidence="ECO:0007829|PDB:4YTB"
FT   STRAND          304..309
FT                   /evidence="ECO:0007829|PDB:4YTB"
FT   HELIX           313..326
FT                   /evidence="ECO:0007829|PDB:4YTB"
FT   STRAND          331..336
FT                   /evidence="ECO:0007829|PDB:4YTB"
FT   STRAND          339..341
FT                   /evidence="ECO:0007829|PDB:4YTB"
FT   HELIX           350..352
FT                   /evidence="ECO:0007829|PDB:4YTB"
FT   STRAND          354..357
FT                   /evidence="ECO:0007829|PDB:4YTB"
FT   STRAND          362..366
FT                   /evidence="ECO:0007829|PDB:4YTB"
FT   STRAND          371..373
FT                   /evidence="ECO:0007829|PDB:4YTB"
FT   STRAND          379..386
FT                   /evidence="ECO:0007829|PDB:4YTB"
FT   STRAND          392..401
FT                   /evidence="ECO:0007829|PDB:4YTB"
FT   STRAND          408..411
FT                   /evidence="ECO:0007829|PDB:4YTB"
FT   STRAND          413..416
FT                   /evidence="ECO:0007829|PDB:4YTB"
FT   STRAND          419..423
FT                   /evidence="ECO:0007829|PDB:4YTB"
FT   STRAND          432..441
FT                   /evidence="ECO:0007829|PDB:4YTB"
FT   STRAND          446..450
FT                   /evidence="ECO:0007829|PDB:4YTB"
FT   STRAND          458..462
FT                   /evidence="ECO:0007829|PDB:4YTB"
SQ   SEQUENCE   556 AA;  61730 MW;  6E189E508868DCF6 CRC64;
     MKKLLQAKAL ILALGLFQLP AIAQTQMQAD RTNGQFATEE MQRAFQETNP PAGPVRAIAE
     YERSAAVLVR YPFGIPMELI KELAKNDKVI TIVASESQKN TVITQYTQSG VNLSNCDFII
     AKTDSYWTRD YTGWFAMYDT NKVGLVDFIY NRPRPNDDEF PKYEAQYLGI EMFGMKLKQT
     GGNYMTDGYG SAVQSHIAYT ENSSLSQAQV NQKMKDYLGI THHDVVQDPN GEYINHVDCW
     GKYLAPNKIL IRKVPDNHPQ HQALEDMAAY FAAQTCAWGT KYEVYRALAT NEQPYTNSLI
     LNNRVFVPVN GPASVDNDAL NVYKTAMPGY EIIGVKGASG TPWLGTDALH CRTHEVADKG
     YLYIKHYPIL GEQAGPDYKI EADVVSCANA TISPVQCYYR INGSGSFKAA DMTMESTGHY
     TYSFTGLNKN DKVEYYISAA DNSGRKETYP FIGEPDPFKF TCMNETNTCT VTGAAKALRA
     WFNAGRSELA VSVSLNIAGT YRIKLYNTAG EEVAAMTKEL VAGTSVFSMD VYSQAPGTYV
     LVVEGNGIRE TMKILK
//