DPP11_PORG3
ID DPP11_PORG3 Reviewed; 720 AA.
AC B2RID1;
DT 17-FEB-2016, integrated into UniProtKB/Swiss-Prot.
DT 01-JUL-2008, sequence version 1.
DT 03-AUG-2022, entry version 71.
DE RecName: Full=Asp/Glu-specific dipeptidyl-peptidase {ECO:0000303|PubMed:21896480};
DE EC=3.4.14.- {ECO:0000269|PubMed:21896480, ECO:0000269|PubMed:23246913};
DE AltName: Full=Dipeptidyl-peptidase 11 {ECO:0000303|PubMed:21896480};
DE Short=DPP11 {ECO:0000303|PubMed:21896480};
DE Flags: Precursor;
GN Name=dpp11 {ECO:0000312|EMBL:BAG33126.1};
GN OrderedLocusNames=PGN_0607 {ECO:0000312|EMBL:BAG33126.1};
OS Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM
OS 12257 / NCTC 11834 / 2561).
OC Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; Porphyromonadaceae;
OC Porphyromonas.
OX NCBI_TaxID=431947;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE
RP SPECIFICITY, BIOPHYSICOCHEMICAL PROPERTIES, ACTIVITY REGULATION,
RP SUBCELLULAR LOCATION, DISRUPTION PHENOTYPE, AND MUTAGENESIS OF SER-655.
RC STRAIN=ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561;
RX PubMed=21896480; DOI=10.1074/jbc.m111.278572;
RA Ohara-Nemoto Y., Shimoyama Y., Kimura S., Kon A., Haraga H., Ono T.,
RA Nemoto T.K.;
RT "Asp- and Glu-specific novel dipeptidyl peptidase 11 of Porphyromonas
RT gingivalis ensures utilization of proteinaceous energy sources.";
RL J. Biol. Chem. 286:38115-38127(2011).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561;
RX PubMed=18524787; DOI=10.1093/dnares/dsn013;
RA Naito M., Hirakawa H., Yamashita A., Ohara N., Shoji M., Yukitake H.,
RA Nakayama K., Toh H., Yoshimura F., Kuhara S., Hattori M., Hayashi T.,
RA Nakayama K.;
RT "Determination of the genome sequence of Porphyromonas gingivalis strain
RT ATCC 33277 and genomic comparison with strain W83 revealed extensive genome
RT rearrangements in P. gingivalis.";
RL DNA Res. 15:215-225(2008).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, AND MUTAGENESIS OF
RP ARG-673.
RC STRAIN=ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561;
RX PubMed=23246913; DOI=10.1016/j.biochi.2012.11.019;
RA Rouf S.M., Ohara-Nemoto Y., Hoshino T., Fujiwara T., Ono T., Nemoto T.K.;
RT "Discrimination based on Gly and Arg/Ser at position 673 between
RT dipeptidyl-peptidase (DPP) 7 and DPP11, widely distributed DPPs in
RT pathogenic and environmental gram-negative bacteria.";
RL Biochimie 95:824-832(2013).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (1.66 ANGSTROMS), DISULFIDE BOND, SUBUNIT, AND
RP MUTAGENESIS OF ARG-337 AND ARG-673.
RX PubMed=26057589; DOI=10.1038/srep11151;
RA Sakamoto Y., Suzuki Y., Iizuka I., Tateoka C., Roppongi S., Fujimoto M.,
RA Inaka K., Tanaka H., Yamada M., Ohta K., Gouda H., Nonaka T., Ogasawara W.,
RA Tanaka N.;
RT "Structural and mutational analyses of dipeptidyl peptidase 11 from
RT Porphyromonas gingivalis reveal the molecular basis for strict substrate
RT specificity.";
RL Sci. Rep. 5:11151-11151(2015).
CC -!- FUNCTION: Catalyzes the removal of dipeptides from the N-terminus of
CC oligopeptides. Shows a strict specificity for acidic residues (Asp or
CC Glu) in the P1 position, and has a hydrophobic residue preference at
CC the P2 position. Preferentially cleaves the synthetic substrate Leu-
CC Asp-methylcoumaryl-7-amide (Leu-Asp-MCA) as compared to Leu-Glu-MCA. Is
CC involved in amino acid metabolism and bacterial growth of
CC asaccharolytic P.gingivalis, that utilizes amino acids from
CC extracellular proteinaceous nutrients as energy and carbon sources.
CC {ECO:0000269|PubMed:21896480, ECO:0000269|PubMed:23246913}.
CC -!- ACTIVITY REGULATION: Enzyme activity is completely blocked by
CC diisopropyl-fluorophosphates, moderately by phenylmethylsulfonyl
CC fluoride (PMSF) and 4-(2-methyl)benzenesulfonyl fluoride, and slightly
CC by pepstatin in vitro. {ECO:0000269|PubMed:21896480}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC pH dependence:
CC Optimum pH is 7.0. {ECO:0000269|PubMed:21896480};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:26057589}.
CC -!- SUBCELLULAR LOCATION: Cell surface {ECO:0000269|PubMed:21896480}.
CC Note=Is exclusively cell-associated. {ECO:0000269|PubMed:21896480}.
CC -!- DISRUPTION PHENOTYPE: Cell growth is retarded. Complete loss of
CC hydrolysis for ac-DNLD- and LE-MCA. The efficiency of peptide
CC utilization of proteinaceous nutrients is reduced in mutant cells.
CC {ECO:0000269|PubMed:21896480}.
CC -!- SIMILARITY: Belongs to the peptidase S46 family. {ECO:0000305}.
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DR EMBL; BR000944; FAA00730.1; -; Genomic_DNA.
DR EMBL; AP009380; BAG33126.1; -; Genomic_DNA.
DR RefSeq; WP_012457641.1; NZ_CP025930.1.
DR PDB; 4XZY; X-ray; 2.70 A; A/B=1-720.
DR PDB; 4Y01; X-ray; 2.46 A; A/B=1-720.
DR PDB; 4Y02; X-ray; 1.96 A; A=1-720.
DR PDB; 4Y04; X-ray; 1.66 A; A=1-720.
DR PDB; 5JWF; X-ray; 2.40 A; A/B=22-720.
DR PDB; 5SDC; X-ray; 1.93 A; A/B=22-720.
DR PDB; 5SDD; X-ray; 1.84 A; A/B=22-720.
DR PDB; 5SDE; X-ray; 1.85 A; A/B=22-720.
DR PDB; 5SDF; X-ray; 1.88 A; A/B=22-720.
DR PDB; 5SDG; X-ray; 1.95 A; A/B=22-720.
DR PDB; 5SDH; X-ray; 2.31 A; A/B=22-720.
DR PDB; 5SDI; X-ray; 1.90 A; A/B=22-720.
DR PDB; 5SDJ; X-ray; 2.04 A; A/B=22-720.
DR PDB; 5SDK; X-ray; 1.98 A; A/B=22-720.
DR PDB; 5SDL; X-ray; 2.44 A; A/B=22-720.
DR PDB; 5SDM; X-ray; 2.04 A; A/B=22-720.
DR PDB; 5SDN; X-ray; 2.02 A; A/B=22-720.
DR PDB; 5SDO; X-ray; 2.05 A; A/B=22-720.
DR PDB; 5SDP; X-ray; 2.19 A; A/B=22-720.
DR PDB; 5SDQ; X-ray; 1.92 A; A/B=22-720.
DR PDB; 5SDR; X-ray; 2.08 A; A/B=22-720.
DR PDB; 5SDS; X-ray; 1.91 A; A/B=22-720.
DR PDB; 6JTB; X-ray; 1.50 A; A=1-720.
DR PDB; 6JTC; X-ray; 2.39 A; A/B=1-720.
DR PDBsum; 4XZY; -.
DR PDBsum; 4Y01; -.
DR PDBsum; 4Y02; -.
DR PDBsum; 4Y04; -.
DR PDBsum; 5JWF; -.
DR PDBsum; 5SDC; -.
DR PDBsum; 5SDD; -.
DR PDBsum; 5SDE; -.
DR PDBsum; 5SDF; -.
DR PDBsum; 5SDG; -.
DR PDBsum; 5SDH; -.
DR PDBsum; 5SDI; -.
DR PDBsum; 5SDJ; -.
DR PDBsum; 5SDK; -.
DR PDBsum; 5SDL; -.
DR PDBsum; 5SDM; -.
DR PDBsum; 5SDN; -.
DR PDBsum; 5SDO; -.
DR PDBsum; 5SDP; -.
DR PDBsum; 5SDQ; -.
DR PDBsum; 5SDR; -.
DR PDBsum; 5SDS; -.
DR PDBsum; 6JTB; -.
DR PDBsum; 6JTC; -.
DR AlphaFoldDB; B2RID1; -.
DR SMR; B2RID1; -.
DR STRING; 431947.PGN_0607; -.
DR MEROPS; S46.002; -.
DR PRIDE; B2RID1; -.
DR EnsemblBacteria; BAG33126; BAG33126; PGN_0607.
DR GeneID; 29255834; -.
DR KEGG; pgn:PGN_0607; -.
DR eggNOG; COG3591; Bacteria.
DR HOGENOM; CLU_013776_0_0_10; -.
DR OMA; ADTDNWM; -.
DR BioCyc; PGIN431947:G1G2V-668-MON; -.
DR Proteomes; UP000008842; Chromosome.
DR GO; GO:0009986; C:cell surface; IDA:UniProtKB.
DR GO; GO:0008239; F:dipeptidyl-peptidase activity; IDA:UniProtKB.
DR GO; GO:0042277; F:peptide binding; IDA:UniProtKB.
DR GO; GO:0070009; F:serine-type aminopeptidase activity; IEA:InterPro.
DR GO; GO:0048588; P:developmental cell growth; IMP:UniProtKB.
DR GO; GO:0043171; P:peptide catabolic process; IDA:UniProtKB.
DR GO; GO:0006508; P:proteolysis; IEA:UniProtKB-KW.
DR Gene3D; 2.40.10.10; -; 1.
DR InterPro; IPR019500; Pep_S46.
DR InterPro; IPR009003; Peptidase_S1_PA.
DR InterPro; IPR043504; Peptidase_S1_PA_chymotrypsin.
DR PANTHER; PTHR38469; PTHR38469; 1.
DR Pfam; PF10459; Peptidase_S46; 1.
DR SUPFAM; SSF50494; SSF50494; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Aminopeptidase; Disulfide bond; Hydrolase; Protease;
KW Serine protease; Signal.
FT SIGNAL 1..21
FT /evidence="ECO:0000255"
FT CHAIN 22..720
FT /note="Asp/Glu-specific dipeptidyl-peptidase"
FT /id="PRO_5005662231"
FT ACT_SITE 85
FT /note="Charge relay system"
FT /evidence="ECO:0000250|UniProtKB:V5YM14,
FT ECO:0000305|PubMed:26057589"
FT ACT_SITE 227
FT /note="Charge relay system"
FT /evidence="ECO:0000250|UniProtKB:V5YM14,
FT ECO:0000305|PubMed:26057589"
FT ACT_SITE 655
FT /note="Charge relay system"
FT /evidence="ECO:0000250|UniProtKB:V5YM14,
FT ECO:0000305|PubMed:21896480, ECO:0000305|PubMed:26057589"
FT SITE 673
FT /note="Is essential for the Asp/Glu P1 specificity of
FT DPP11; involved in the recognition of the Asp/Glu residue
FT at the P1 position of substrate peptides"
FT /evidence="ECO:0000269|PubMed:26057589"
FT DISULFID 69..86
FT /evidence="ECO:0000269|PubMed:26057589,
FT ECO:0007744|PDB:4XZY, ECO:0007744|PDB:4Y02,
FT ECO:0007744|PDB:4Y04"
FT MUTAGEN 337
FT /note="R->A,N: Significant increase (or preservation) of
FT the catalytic activity."
FT /evidence="ECO:0000269|PubMed:26057589"
FT MUTAGEN 655
FT /note="S->A: Loss of catalytic activity."
FT /evidence="ECO:0000269|PubMed:21896480"
FT MUTAGEN 673
FT /note="R->A: Loss of catalytic activity."
FT /evidence="ECO:0000269|PubMed:26057589"
FT MUTAGEN 673
FT /note="R->G: Drastically decreased but still significant
FT activities against Asp/Glu substrates, as well as
FT detectable activity against substrates harboring
FT hydrophobic residues at the P1 position."
FT /evidence="ECO:0000269|PubMed:26057589"
FT MUTAGEN 673
FT /note="R->S: The Asp/Glu preference is inverted, i.e.,
FT peptidase activity toward Leu-Asp-MCA nearly disappears,
FT whereas that to Leu-Glu-MCA partially remains."
FT /evidence="ECO:0000269|PubMed:23246913"
FT HELIX 28..30
FT /evidence="ECO:0007829|PDB:6JTB"
FT HELIX 31..40
FT /evidence="ECO:0007829|PDB:6JTB"
FT HELIX 47..50
FT /evidence="ECO:0007829|PDB:6JTB"
FT STRAND 53..55
FT /evidence="ECO:0007829|PDB:6JTB"
FT HELIX 58..61
FT /evidence="ECO:0007829|PDB:6JTB"
FT STRAND 62..65
FT /evidence="ECO:0007829|PDB:6JTB"
FT TURN 66..68
FT /evidence="ECO:0007829|PDB:6JTB"
FT STRAND 69..73
FT /evidence="ECO:0007829|PDB:6JTB"
FT STRAND 79..82
FT /evidence="ECO:0007829|PDB:6JTB"
FT HELIX 84..93
FT /evidence="ECO:0007829|PDB:6JTB"
FT STRAND 97..99
FT /evidence="ECO:0007829|PDB:6JTB"
FT HELIX 101..104
FT /evidence="ECO:0007829|PDB:6JTB"
FT HELIX 111..113
FT /evidence="ECO:0007829|PDB:6JTB"
FT STRAND 122..130
FT /evidence="ECO:0007829|PDB:6JTB"
FT HELIX 132..139
FT /evidence="ECO:0007829|PDB:6JTB"
FT HELIX 149..151
FT /evidence="ECO:0007829|PDB:6JTB"
FT HELIX 153..164
FT /evidence="ECO:0007829|PDB:6JTB"
FT HELIX 168..171
FT /evidence="ECO:0007829|PDB:6JTB"
FT STRAND 175..182
FT /evidence="ECO:0007829|PDB:6JTB"
FT HELIX 183..185
FT /evidence="ECO:0007829|PDB:6JTB"
FT STRAND 187..196
FT /evidence="ECO:0007829|PDB:6JTB"
FT STRAND 199..204
FT /evidence="ECO:0007829|PDB:6JTB"
FT HELIX 207..210
FT /evidence="ECO:0007829|PDB:6JTB"
FT TURN 211..219
FT /evidence="ECO:0007829|PDB:6JTB"
FT STRAND 229..235
FT /evidence="ECO:0007829|PDB:6JTB"
FT STRAND 259..262
FT /evidence="ECO:0007829|PDB:6JTB"
FT STRAND 269..274
FT /evidence="ECO:0007829|PDB:6JTB"
FT HELIX 285..293
FT /evidence="ECO:0007829|PDB:6JTB"
FT HELIX 295..316
FT /evidence="ECO:0007829|PDB:6JTB"
FT HELIX 318..347
FT /evidence="ECO:0007829|PDB:6JTB"
FT HELIX 350..367
FT /evidence="ECO:0007829|PDB:6JTB"
FT HELIX 372..400
FT /evidence="ECO:0007829|PDB:6JTB"
FT TURN 401..404
FT /evidence="ECO:0007829|PDB:6JTB"
FT HELIX 406..409
FT /evidence="ECO:0007829|PDB:6JTB"
FT HELIX 415..420
FT /evidence="ECO:0007829|PDB:6JTB"
FT STRAND 422..424
FT /evidence="ECO:0007829|PDB:4Y01"
FT HELIX 426..443
FT /evidence="ECO:0007829|PDB:6JTB"
FT HELIX 450..467
FT /evidence="ECO:0007829|PDB:6JTB"
FT HELIX 470..472
FT /evidence="ECO:0007829|PDB:6JTB"
FT HELIX 475..478
FT /evidence="ECO:0007829|PDB:6JTB"
FT HELIX 479..484
FT /evidence="ECO:0007829|PDB:6JTB"
FT HELIX 488..498
FT /evidence="ECO:0007829|PDB:6JTB"
FT HELIX 504..512
FT /evidence="ECO:0007829|PDB:6JTB"
FT HELIX 516..520
FT /evidence="ECO:0007829|PDB:6JTB"
FT HELIX 523..542
FT /evidence="ECO:0007829|PDB:6JTB"
FT HELIX 543..545
FT /evidence="ECO:0007829|PDB:6JTB"
FT HELIX 546..564
FT /evidence="ECO:0007829|PDB:6JTB"
FT STRAND 566..568
FT /evidence="ECO:0007829|PDB:5JWF"
FT STRAND 574..576
FT /evidence="ECO:0007829|PDB:4XZY"
FT STRAND 578..584
FT /evidence="ECO:0007829|PDB:6JTB"
FT STRAND 587..590
FT /evidence="ECO:0007829|PDB:6JTB"
FT STRAND 593..595
FT /evidence="ECO:0007829|PDB:6JTB"
FT STRAND 597..600
FT /evidence="ECO:0007829|PDB:6JTB"
FT HELIX 601..607
FT /evidence="ECO:0007829|PDB:6JTB"
FT HELIX 613..615
FT /evidence="ECO:0007829|PDB:6JTB"
FT HELIX 619..627
FT /evidence="ECO:0007829|PDB:6JTB"
FT HELIX 631..633
FT /evidence="ECO:0007829|PDB:6JTC"
FT STRAND 636..638
FT /evidence="ECO:0007829|PDB:5JWF"
FT STRAND 641..646
FT /evidence="ECO:0007829|PDB:6JTB"
FT STRAND 658..660
FT /evidence="ECO:0007829|PDB:6JTB"
FT STRAND 666..673
FT /evidence="ECO:0007829|PDB:6JTB"
FT HELIX 675..681
FT /evidence="ECO:0007829|PDB:6JTB"
FT TURN 686..688
FT /evidence="ECO:0007829|PDB:6JTB"
FT STRAND 691..695
FT /evidence="ECO:0007829|PDB:6JTB"
FT HELIX 696..705
FT /evidence="ECO:0007829|PDB:6JTB"
FT HELIX 710..715
FT /evidence="ECO:0007829|PDB:6JTB"
SQ SEQUENCE 720 AA; 81938 MW; 95D117E5770CFF7D CRC64;
MKKRLLLPLF AALCLSQIAH ADEGMWLMQQ LGRKYAQMKE RGLKMKEYDL YNPNGTSLKD
AVVLFDGGCT GEVVSDRGLV LTNHHCGYDM IQAHSTLEHN YLENGFWAMR EADELPNKDI
SVVFIDKIED VTDYVKKELK AIKDPNSMDY LSPKYLQKLA DKKAGKNFSA KNPGLSVEIK
AFYGGNLYLM FTKKTYTDVR LVGAPPSSIG KFGADTDNWI WPRHTGDFSI FRIYADKNGN
PAPYSEDNVP LKPKRFFNIS LGGVQENDYA MIMGFPGTTH RYFTASEVDE WKSIDNDIRI
RMRDIRQGVM LREMLADPQI KIMYSAKYAA SQNAYKRAIG ANWAIKTRGL RQNKQAMQDR
LIAWGAKQGT PRYEEAVHEI DATVAKRADL RRRYWMIEEG IIRGIEFARS PIPTEDETKA
LQGNDASARK EAIDKIRTRY SKFANKDYSA EVDKKVAVAM LTEYLKEIPY ENLPLHLRLV
KDRFAGDVQA YVDDIFARSV FGSEAQFDAF AAVPSVEKLA EDPMVLFASS VFDEYRKLYN
ELRPYDDPIL RAQRTYIAGL LEMDGDQDQF PDANLTLRFT YGQVKGYSPR DNVYYGHQTT
LDGVMEKEDP DNWEFVVDPK LKAVYERKDF GRYADRSGRM PVAFCATTHT TGGNSGSPVM
NANGELIGLN FDRNWEGVGG DIQYLADYQR SIIVDIRYVL LVIDKVGGCQ RLLDEMNIVP
