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Dipeptidyl aminopeptidase BII (DAP BII) (EC 3.4.14.-)

 DAPB2_PSEMX             Reviewed;         722 AA.
V5YM14;
24-JUN-2015, integrated into UniProtKB/Swiss-Prot.
19-FEB-2014, sequence version 1.
15-MAR-2017, entry version 18.
RecName: Full=Dipeptidyl aminopeptidase BII {ECO:0000312|EMBL:BAO18427.1};
Short=DAP BII {ECO:0000303|PubMed:24598890, ECO:0000303|PubMed:8892831};
EC=3.4.14.- {ECO:0000269|PubMed:24598890, ECO:0000269|PubMed:24637761, ECO:0000269|PubMed:24827749, ECO:0000269|PubMed:8892831};
Flags: Precursor;
Name=dapb2 {ECO:0000312|EMBL:BAO18427.1};
Pseudoxanthomonas mexicana.
Bacteria; Proteobacteria; Gammaproteobacteria; Xanthomonadales;
Xanthomonadaceae; Pseudoxanthomonas.
NCBI_TaxID=128785;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 25-44; 321-333;
467-489 AND 610-620, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL
PROPERTIES, CIRCULAR DICHROISM ANALYSIS, PHYLOGENETIC STUDY, SIGNAL,
ACTIVE SITES, AND MUTAGENESIS OF HIS-86; ASP-195; ASP-214; ASP-224;
ASP-522; ASP-574 AND SER-657.
STRAIN=WO24 {ECO:0000312|EMBL:BAO18427.1};
PubMed=24598890; DOI=10.1038/srep04292;
Suzuki Y., Sakamoto Y., Tanaka N., Okada H., Morikawa Y.,
Ogasawara W.;
"Identification of the catalytic triad of family S46 exopeptidases,
closely related to clan PA endopeptidases.";
Sci. Rep. 4:4292-4292(2014).
[2]
FUNCTION, CATALYTIC ACTIVITY, ENZYME REGULATION, BIOPHYSICOCHEMICAL
PROPERTIES, SUBSTRATE SPECIFICITY, SUBUNIT, AND BIOTECHNOLOGY.
STRAIN=WO24;
PubMed=8892831; DOI=10.1128/jb.178.21.6288-6295.1996;
Ogasawara W., Kobayashi G., Okada H., Morikawa Y.;
"Two types of novel dipeptidyl aminopeptidases from Pseudomonas sp.
strain WO24.";
J. Bacteriol. 178:6288-6295(1996).
[3]
CRYSTALLIZATION, CATALYTIC ACTIVITY, AND BIOPHYSICOCHEMICAL
PROPERTIES.
STRAIN=WO24;
PubMed=24637761; DOI=10.1107/S2053230X13034584;
Sakamoto Y., Suzuki Y., Iizuka I., Tateoka C., Roppongi S., Okada H.,
Nonaka T., Morikawa Y., Nakamura K.T., Ogasawara W., Tanaka N.;
"Crystallization and preliminary X-ray crystallographic studies of
dipeptidyl aminopeptidase BII from Pseudoxanthomonas mexicana WO24.";
Acta Crystallogr. F 70:221-224(2014).
[4] {ECO:0000244|PDB:3WOI, ECO:0000244|PDB:3WOJ, ECO:0000244|PDB:3WOK, ECO:0000244|PDB:3WOL, ECO:0000244|PDB:3WOM, ECO:0000244|PDB:3WON, ECO:0000244|PDB:3WOO, ECO:0000244|PDB:3WOP, ECO:0000244|PDB:3WOQ, ECO:0000244|PDB:3WOR}
X-RAY CRYSTALLOGRAPHY (1.74 ANGSTROMS) OF WILD-TYPE AND MUTANTS ALA-86
AND ALA-86/ALA-224/ALA-657 OF 25-722 OF PEPTIDE-FREE FORMS AND IN
COMPLEXES WITH PEPTIDE SUBSTRATES AND ZINC, FUNCTION, CATALYTIC
ACTIVITY, SUBSTRATE SPECIFICITY, REACTION MECHANISM, SUBUNIT, DOMAIN,
BIOTECHNOLOGY, PHYLOGENETIC STUDY, ACTIVE SITES, AND MUTAGENESIS OF
HIS-86; ASN-215; TRP-216; ASP-224; ASN-330; SER-657 AND ASP-674.
STRAIN=WO24 {ECO:0000303|PubMed:24827749};
PubMed=24827749; DOI=10.1038/srep04977;
Sakamoto Y., Suzuki Y., Iizuka I., Tateoka C., Roppongi S.,
Fujimoto M., Inaka K., Tanaka H., Masaki M., Ohta K., Okada H.,
Nonaka T., Morikawa Y., Nakamura K.T., Ogasawara W., Tanaka N.;
"S46 peptidases are the first exopeptidases to be members of clan
PA.";
Sci. Rep. 4:4977-4977(2014).
[5]
X-RAY CRYSTALLOGRAPHY (2.18 ANGSTROMS) OF MUTANT ARG-675 IN COMPLEX
WITH LEU-GLU DIPEPTIDE, AND MUTAGENESIS OF GLY-675.
PubMed=26057589; DOI=10.1038/srep11151;
Sakamoto Y., Suzuki Y., Iizuka I., Tateoka C., Roppongi S.,
Fujimoto M., Inaka K., Tanaka H., Yamada M., Ohta K., Gouda H.,
Nonaka T., Ogasawara W., Tanaka N.;
"Structural and mutational analyses of dipeptidyl peptidase 11 from
Porphyromonas gingivalis reveal the molecular basis for strict
substrate specificity.";
Sci. Rep. 5:11151-11151(2015).
-!- FUNCTION: Exopeptidase that catalyzes the removal of dipeptide
units (NH2-P2-P1-) from the free amino termini of oligopeptides
and small proteins (PubMed:24598890, PubMed:8892831,
PubMed:24827749). Peptide digestion is sequential and substrate
recognition is non-specific, with the exception that Pro is not
suitable as a P1 residue (PubMed:24827749). Removes many residues
of bioactive oligopeptides such as angiotensin I and neuromedin N
and cleaves also oxidized insulin B chain. Able to hydrolyze an X-
Pro bond, an imido bond. No endopeptidase activity
(PubMed:8892831). May play a physiological role in feeding
(PubMed:24598890). {ECO:0000269|PubMed:24598890,
ECO:0000269|PubMed:24827749, ECO:0000269|PubMed:8892831}.
-!- ENZYME REGULATION: Completely inhibited by the serine protease
inhibitor diisopropyl fluorophosphate (DFP) and potently inhibited
by 0.5 mM ZnCl(2), 10 mM o-phenanthlorine, phenylmethanesulfonyl
fluoride (PMSF) and N-tosyl-L-phenyl-alanyl chloromethyl ketone
(TPCK), but not by N-tosyl-L-lysyl chloromethyl ketone (TLCK).
Activity is not affected significantly by protease inhibitors,
such as chymostatin, leupeptin, N-ethylmaleimide (NEM),
iodoacetate (IAA), L-trans-epoxysuccinyl-leucylamido(4-
guanido)butane (E64) and pepstatin A or by CoCl(2), CaCl(2) and
EDTA. {ECO:0000269|PubMed:8892831}.
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=1.7 mM for Gly-Phe-pNA (at pH 8 and 37 degrees Celsius)
{ECO:0000269|PubMed:8892831};
KM=0.87 mM for Ala-Ala-pNA (at pH 8 and 37 degrees Celsius)
{ECO:0000269|PubMed:8892831};
KM=7.2 mM for Gly-Phe-beta-naphthylamine (at pH 8 and 37 degrees
Celsius) {ECO:0000269|PubMed:8892831};
Vmax=3.4 umol/min/mg enzyme with Gly-Phe-pNA as substrate
{ECO:0000269|PubMed:24598890, ECO:0000269|PubMed:24637761};
Vmax=10 umol/min/mg enzyme with Ala-Ala-pNA as substrate
{ECO:0000269|PubMed:24598890, ECO:0000269|PubMed:24637761};
Vmax=9.4 umol/min/mg enzyme with Gly-Phe-pNA as substrate (at pH
8 and 37 degrees Celsius) {ECO:0000269|PubMed:8892831};
Vmax=20 umol/min/mg enzyme with Ala-Ala-pNA as substrate (at pH
8 and 37 degrees Celsius) {ECO:0000269|PubMed:8892831};
Vmax=10 umol/min/mg enzyme with Gly-Phe-beta-naphthylamine as
substrate (at pH 8 and 37 degrees Celsius)
{ECO:0000269|PubMed:8892831};
pH dependence:
Optimum pH is 8 for the hydrolysis of Gly-Phe-pNA.
{ECO:0000269|PubMed:8892831};
Temperature dependence:
Optimum temperature is approximately 30 degrees Celsius for the
hydrolysis of Gly-Phe-pNA. Stable at a temperature below 20
degrees Celsius for 30 minutes. {ECO:0000269|PubMed:8892831};
-!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:24827749,
ECO:0000269|PubMed:8892831}.
-!- DOMAIN: The chymotrypsin fold (25-276 and 574-722) is the
catalytic domain and the alpha-helical domain (277-573) is the
regulatory domain necessary for exopeptidase activity.
{ECO:0000269|PubMed:24827749}.
-!- BIOTECHNOLOGY: Designing engineered forms of this protein with the
ability to produce custom dipeptides potentially may have a number
of commercial and industrial uses including food industry
(PubMed:8892831, PubMed:24827749). Maybe useful for drug design
(PubMed:24827749). {ECO:0000303|PubMed:24827749,
ECO:0000303|PubMed:8892831}.
-!- SIMILARITY: Belongs to the peptidase S46 family.
{ECO:0000305|PubMed:24598890, ECO:0000305|PubMed:24827749}.
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EMBL; AB889525; BAO18427.1; -; Genomic_DNA.
PDB; 3WOI; X-ray; 2.10 A; A/B=25-722.
PDB; 3WOJ; X-ray; 2.20 A; A/B=25-722.
PDB; 3WOK; X-ray; 1.95 A; A/B=25-722.
PDB; 3WOL; X-ray; 1.74 A; A/B=25-722.
PDB; 3WOM; X-ray; 1.86 A; A/B=25-722.
PDB; 3WON; X-ray; 1.75 A; A/B=25-722.
PDB; 3WOO; X-ray; 1.80 A; A/B=25-722.
PDB; 3WOP; X-ray; 1.95 A; A/B=25-722.
PDB; 3WOQ; X-ray; 1.82 A; A/B=25-722.
PDB; 3WOR; X-ray; 2.10 A; A/B=25-722.
PDB; 4Y06; X-ray; 2.18 A; A/B=1-722.
PDBsum; 3WOI; -.
PDBsum; 3WOJ; -.
PDBsum; 3WOK; -.
PDBsum; 3WOL; -.
PDBsum; 3WOM; -.
PDBsum; 3WON; -.
PDBsum; 3WOO; -.
PDBsum; 3WOP; -.
PDBsum; 3WOQ; -.
PDBsum; 3WOR; -.
PDBsum; 4Y06; -.
SMR; V5YM14; -.
MEROPS; S46.003; -.
GO; GO:0008239; F:dipeptidyl-peptidase activity; IDA:UniProtKB.
GO; GO:0042802; F:identical protein binding; IDA:UniProtKB.
GO; GO:0042803; F:protein homodimerization activity; IDA:UniProtKB.
GO; GO:0070009; F:serine-type aminopeptidase activity; IDA:UniProtKB.
GO; GO:0051603; P:proteolysis involved in cellular protein catabolic process; IDA:UniProtKB.
InterPro; IPR019500; Pep_S46.
InterPro; IPR009003; Peptidase_S1_PA.
Pfam; PF10459; Peptidase_S46; 1.
SUPFAM; SSF50494; SSF50494; 3.
1: Evidence at protein level;
3D-structure; Aminopeptidase; Direct protein sequencing;
Disulfide bond; Hydrolase; Protease; Signal.
SIGNAL 1 24 {ECO:0000269|PubMed:24598890}.
CHAIN 25 722 Dipeptidyl aminopeptidase BII.
{ECO:0000255}.
/FTId=PRO_0000433463.
REGION 215 216 Substrate-binding.
{ECO:0000269|PubMed:24827749}.
REGION 655 657 Substrate-binding.
{ECO:0000269|PubMed:24827749}.
REGION 673 674 Substrate-binding.
{ECO:0000269|PubMed:24827749}.
ACT_SITE 86 86 Charge relay system.
{ECO:0000305|PubMed:24598890,
ECO:0000305|PubMed:24827749}.
ACT_SITE 224 224 Charge relay system.
{ECO:0000305|PubMed:24598890,
ECO:0000305|PubMed:24827749}.
ACT_SITE 657 657 Charge relay system.
{ECO:0000305|PubMed:24598890,
ECO:0000305|PubMed:24827749}.
BINDING 330 330 Substrate. {ECO:0000269|PubMed:24827749}.
DISULFID 70 87 {ECO:0000244|PDB:3WOL,
ECO:0000269|PubMed:24827749}.
DISULFID 166 174 {ECO:0000244|PDB:3WOL,
ECO:0000269|PubMed:24827749}.
MUTAGEN 86 86 H->A: Loss of enzymatic activity. Loss of
enzymatic activity; when associated with
A-224 and A-657.
{ECO:0000269|PubMed:24598890,
ECO:0000269|PubMed:24827749}.
MUTAGEN 195 195 D->A: Decreased enzymatic activity to 23
percent relative to wild-type.
{ECO:0000269|PubMed:24598890}.
MUTAGEN 214 214 D->A: Decreased enzymatic activity to 1.5
percent relative to wild-type.
{ECO:0000269|PubMed:24598890}.
MUTAGEN 214 214 D->N: Decreased enzymatic activity to 3.0
percent relative to wild-type.
{ECO:0000269|PubMed:24598890}.
MUTAGEN 215 215 N->A: Loss of enzymatic activity.
{ECO:0000269|PubMed:24827749}.
MUTAGEN 216 216 W->A: Loss of enzymatic activity.
{ECO:0000269|PubMed:24827749}.
MUTAGEN 224 224 D->A: Decreased enzymatic activity to
0.026 percent relative to wild-type. Loss
of enzymatic activity; when associated
with A-86 and A-657.
{ECO:0000269|PubMed:24598890,
ECO:0000269|PubMed:24827749}.
MUTAGEN 224 224 D->N: Decreased enzymatic activity to
0.15 percent relative to wild-type.
{ECO:0000269|PubMed:24598890}.
MUTAGEN 330 330 N->A: Loss of enzymatic activity.
{ECO:0000269|PubMed:24827749}.
MUTAGEN 522 522 D->A: Decreased enzymatic activity to 32
percent relative to wild-type.
{ECO:0000269|PubMed:24598890}.
MUTAGEN 522 522 D->N: Decreased enzymatic activity to 16
percent relative to wild-type.
{ECO:0000269|PubMed:24598890}.
MUTAGEN 574 574 D->A: Decreased enzymatic activity to 83
percent relative to wild-type.
{ECO:0000269|PubMed:24598890}.
MUTAGEN 574 574 D->N: Decreased enzymatic activity to 21
percent relative to wild-type.
{ECO:0000269|PubMed:24598890}.
MUTAGEN 657 657 S->A: Loss of enzymatic activity. Loss of
enzymatic activity; when associated with
A-86 and A-224.
{ECO:0000269|PubMed:24598890,
ECO:0000269|PubMed:24827749}.
MUTAGEN 674 674 D->A: Loss of enzymatic activity.
{ECO:0000269|PubMed:24827749}.
MUTAGEN 675 675 G->R: Acquires the enzymatic activity for
synthetic substrates with Asp/Glu at P1
position. {ECO:0000269|PubMed:26057589}.
HELIX 31 33 {ECO:0000244|PDB:3WOL}.
HELIX 34 44 {ECO:0000244|PDB:3WOL}.
HELIX 50 54 {ECO:0000244|PDB:3WOL}.
HELIX 61 63 {ECO:0000244|PDB:3WOL}.
STRAND 64 66 {ECO:0000244|PDB:3WOL}.
STRAND 68 74 {ECO:0000244|PDB:3WOL}.
STRAND 80 83 {ECO:0000244|PDB:3WOL}.
HELIX 85 94 {ECO:0000244|PDB:3WOL}.
STRAND 98 100 {ECO:0000244|PDB:3WOL}.
HELIX 102 105 {ECO:0000244|PDB:3WOL}.
HELIX 112 114 {ECO:0000244|PDB:3WOL}.
STRAND 124 132 {ECO:0000244|PDB:3WOL}.
HELIX 134 142 {ECO:0000244|PDB:3WOL}.
TURN 143 146 {ECO:0000244|PDB:3WOL}.
HELIX 148 166 {ECO:0000244|PDB:3WOL}.
STRAND 172 179 {ECO:0000244|PDB:3WOL}.
TURN 180 183 {ECO:0000244|PDB:3WOL}.
STRAND 184 193 {ECO:0000244|PDB:3WOL}.
STRAND 195 201 {ECO:0000244|PDB:3WOL}.
HELIX 204 207 {ECO:0000244|PDB:3WOL}.
TURN 208 210 {ECO:0000244|PDB:3WOL}.
HELIX 211 214 {ECO:0000244|PDB:3WOL}.
STRAND 226 232 {ECO:0000244|PDB:3WOL}.
STRAND 266 271 {ECO:0000244|PDB:3WOL}.
HELIX 282 290 {ECO:0000244|PDB:3WOL}.
HELIX 292 313 {ECO:0000244|PDB:3WOL}.
HELIX 315 320 {ECO:0000244|PDB:3WOL}.
HELIX 322 345 {ECO:0000244|PDB:3WOL}.
HELIX 347 363 {ECO:0000244|PDB:3WOL}.
HELIX 364 369 {ECO:0000244|PDB:3WOL}.
HELIX 370 387 {ECO:0000244|PDB:3WOL}.
HELIX 390 399 {ECO:0000244|PDB:3WOL}.
HELIX 403 417 {ECO:0000244|PDB:3WOL}.
HELIX 422 424 {ECO:0000244|PDB:3WOL}.
HELIX 431 433 {ECO:0000244|PDB:3WOL}.
HELIX 434 443 {ECO:0000244|PDB:3WOL}.
HELIX 444 446 {ECO:0000244|PDB:3WOL}.
HELIX 450 465 {ECO:0000244|PDB:3WOL}.
HELIX 469 471 {ECO:0000244|PDB:3WOL}.
HELIX 474 480 {ECO:0000244|PDB:3WOL}.
STRAND 482 484 {ECO:0000244|PDB:3WOM}.
HELIX 485 496 {ECO:0000244|PDB:3WOL}.
HELIX 503 511 {ECO:0000244|PDB:3WOL}.
HELIX 514 518 {ECO:0000244|PDB:3WOL}.
HELIX 523 566 {ECO:0000244|PDB:3WOL}.
STRAND 580 586 {ECO:0000244|PDB:3WOL}.
STRAND 595 597 {ECO:0000244|PDB:3WOL}.
STRAND 599 602 {ECO:0000244|PDB:3WOL}.
HELIX 603 608 {ECO:0000244|PDB:3WOL}.
HELIX 620 627 {ECO:0000244|PDB:3WOL}.
TURN 637 639 {ECO:0000244|PDB:3WOL}.
STRAND 643 648 {ECO:0000244|PDB:3WOL}.
STRAND 660 662 {ECO:0000244|PDB:3WOL}.
STRAND 668 675 {ECO:0000244|PDB:3WOL}.
HELIX 677 683 {ECO:0000244|PDB:3WOL}.
HELIX 688 690 {ECO:0000244|PDB:3WOL}.
STRAND 693 697 {ECO:0000244|PDB:3WOL}.
HELIX 698 707 {ECO:0000244|PDB:3WOL}.
HELIX 712 717 {ECO:0000244|PDB:3WOL}.
SEQUENCE 722 AA; 78698 MW; 5CD59AD3A975C760 CRC64;
MRPNLLAAAI AVPLSLLAAQ IAQAGEGMWV PQQLPEIAGP LKKAGLKLSP QQISDLTGDP
MGAVVALGGC TASFVSPNGL VVTNHHCAYG AIQLNSTAEN NLIKNGFNAP TTADEVSAGP
NARVFVLDEI TDVTKDAKAA IAAAGDDALA RTKALEAFEK KLIADCEAEA GFRCRLYSFS
GGNTYRLFKN LEIKDVRLAY APPGSVGKFG GDIDNWMWPR HTGDFAFYRA YVGKDGKPAA
FSKDNVPYQP KHWLKFADQP LGAGDFVMVA GYPGSTNRYA LAAEFDNTAQ WTYPTIARHY
KNQIAMVEAA GKQNADIQVK YAATMAGWNN TSKNYDGQLE GFKRIDAAGQ KLREEAAVLG
WLKGQGAKGQ PALDAHAKLL DLLEQSKATR DRDLTLALFN NTAMLGSATQ LYRLSIEREK
PNAERESGYQ ERDLPAIEGG LKQLERRYVA AMDRQLQEYW LNEYIKLPAD QRVAAVDAWL
GGNDAAAVKR ALDRLAGTKL GSTEERLKWF AADRKAFEAS NDPAIQYAVA VMPTLLKLEQ
ERKTRAGENL AARPVYLQAL ADYKKSQGEF VYPDANLSLR ITFGNVMGYA PKDGMEYTPF
TTLEGVVAKE TGQDPFDSPK ALLDAVAAKR YGGLEDKRIG SVPVNYLSDL DITGGNSGSP
VLDAHGKLVG LAFDGNWESV SSNWVFDPKM TRMIAVDGRY LRWIMQEVYP APQLLKEMNV
GK


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