PAD_PORGI
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 25-MAY-2022, entry version 95.
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; Bacteroidetes; 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 OMA; GNYMSDG; -.
DR OrthoDB; 275461at2; -.
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; PTHR31377; 1.
DR Pfam; PF04371; PAD_porph; 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
