DPPA_BACSU
ID DPPA_BACSU Reviewed; 274 AA.
AC P26902; O34802;
DT 01-AUG-1992, integrated into UniProtKB/Swiss-Prot.
DT 16-JUN-2009, sequence version 3.
DT 03-AUG-2022, entry version 125.
DE RecName: Full=D-aminopeptidase;
DE EC=3.4.11.-;
GN Name=dppA; Synonyms=dciAA; OrderedLocusNames=BSU12920;
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;
RX PubMed=1766370; DOI=10.1111/j.1365-2958.1991.tb00814.x;
RA Mathiopoulos C., Mueller J.P., Slack F.J., Murphy C.G., Patankar S.,
RA Bukusoglu G., Sonenshein A.L.;
RT "A Bacillus subtilis dipeptide transport system expressed early during
RT sporulation.";
RL Mol. Microbiol. 5:1903-1913(1991).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168;
RA Devine K.M.;
RT "Sequence of the Bacillus subtilis genome between xlyA and ykoR.";
RL Submitted (NOV-1997) to the EMBL/GenBank/DDBJ databases.
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 SEQUENCE REVISION TO 190.
RX PubMed=19383706; DOI=10.1099/mic.0.027839-0;
RA Barbe V., Cruveiller S., Kunst F., Lenoble P., Meurice G., Sekowska A.,
RA Vallenet D., Wang T., Moszer I., Medigue C., Danchin A.;
RT "From a consortium sequence to a unified sequence: the Bacillus subtilis
RT 168 reference genome a decade later.";
RL Microbiology 155:1758-1775(2009).
RN [5]
RP PROTEIN SEQUENCE OF 1-14, AND CHARACTERIZATION.
RX PubMed=11069674; DOI=10.1046/j.1365-2958.2000.02117.x;
RA Cheggour A., Fanuel L., Duez C., Joris B., Bouillenne F., Devreese B.,
RA Van Driessche G., Van Beeumen J., Frere J.-M., Goffin C.;
RT "The dppA gene of Bacillus subtilis encodes a new D-aminopeptidase.";
RL Mol. Microbiol. 38:504-513(2000).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS), AND SUBUNIT.
RX PubMed=11473256; DOI=10.1038/90380;
RA Remaut H., Bompard-Gilles C., Goffin C., Frere J.-M., Van Beeumen J.;
RT "Structure of the Bacillus subtilis D-aminopeptidase DppA reveals a novel
RT self-compartmentalizing protease.";
RL Nat. Struct. Biol. 8:674-678(2001).
CC -!- FUNCTION: Hydrolyzes N-terminal residues in D-amino acid containing
CC peptides. Among the tested substrates, the highest activities are with
CC D-Ala-D-Ala and D-Ala-Gly-Gly. The physiological role is not clear.
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Note=Binds 2 Zn(2+) ions per subunit.;
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC pH dependence:
CC Optimum pH is 9-11.;
CC -!- SUBUNIT: Homodecamer. A 20 Angstroms wide channel runs through the
CC complex, giving access to a central chamber holding the active sites.
CC {ECO:0000269|PubMed:11473256}.
CC -!- DEVELOPMENTAL STAGE: Expressed early during sporulation.
CC -!- INDUCTION: Nutrient deficiency conditions, which also induce
CC sporulation.
CC -!- SIMILARITY: Belongs to the peptidase M55 family. {ECO:0000305}.
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DR EMBL; X56678; CAA40002.1; -; Genomic_DNA.
DR EMBL; AJ002571; CAA05572.1; -; Genomic_DNA.
DR EMBL; AL009126; CAB13149.2; -; Genomic_DNA.
DR PIR; S16647; S16647.
DR RefSeq; NP_389175.2; NC_000964.3.
DR RefSeq; WP_003245814.1; NZ_JNCM01000035.1.
DR PDB; 1HI9; X-ray; 2.40 A; A/B/C/D/E=1-274.
DR PDBsum; 1HI9; -.
DR AlphaFoldDB; P26902; -.
DR SMR; P26902; -.
DR STRING; 224308.BSU12920; -.
DR MEROPS; M55.001; -.
DR TCDB; 3.A.1.5.2; the atp-binding cassette (abc) superfamily.
DR PaxDb; P26902; -.
DR PRIDE; P26902; -.
DR EnsemblBacteria; CAB13149; CAB13149; BSU_12920.
DR GeneID; 936727; -.
DR KEGG; bsu:BSU12920; -.
DR PATRIC; fig|224308.179.peg.1404; -.
DR eggNOG; COG2362; Bacteria.
DR InParanoid; P26902; -.
DR OMA; ATGVTWP; -.
DR PhylomeDB; P26902; -.
DR BioCyc; BSUB:BSU12920-MON; -.
DR BRENDA; 3.4.11.19; 658.
DR EvolutionaryTrace; P26902; -.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0004177; F:aminopeptidase activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0008237; F:metallopeptidase activity; IEA:UniProtKB-KW.
DR GO; GO:0006508; P:proteolysis; IEA:UniProtKB-KW.
DR GO; GO:0030435; P:sporulation resulting in formation of a cellular spore; IEA:UniProtKB-KW.
DR CDD; cd00281; DAP_dppA; 1.
DR Gene3D; 3.40.50.10780; -; 1.
DR InterPro; IPR033824; DppA.
DR InterPro; IPR027476; DppA_N.
DR InterPro; IPR007035; Peptidase_M55.
DR InterPro; IPR036177; Peptidase_M55_sf.
DR Pfam; PF04951; Peptidase_M55; 1.
DR PIRSF; PIRSF015853; Pep_DppA; 1.
DR SUPFAM; SSF63992; SSF63992; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Aminopeptidase; Direct protein sequencing; Hydrolase;
KW Metal-binding; Metalloprotease; Protease; Reference proteome; Sporulation;
KW Zinc.
FT CHAIN 1..274
FT /note="D-aminopeptidase"
FT /id="PRO_0000208269"
FT ACT_SITE 115
FT /note="Nucleophile"
FT BINDING 8
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT BINDING 8
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT BINDING 10
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT BINDING 60
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT BINDING 104
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT BINDING 133
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT CONFLICT 190
FT /note="A -> R (in Ref. 2; CAA05572)"
FT /evidence="ECO:0000305"
FT CONFLICT 199
FT /note="A -> P (in Ref. 1; CAA40002)"
FT /evidence="ECO:0000305"
FT STRAND 2..7
FT /evidence="ECO:0007829|PDB:1HI9"
FT HELIX 18..20
FT /evidence="ECO:0007829|PDB:1HI9"
FT HELIX 28..48
FT /evidence="ECO:0007829|PDB:1HI9"
FT STRAND 52..58
FT /evidence="ECO:0007829|PDB:1HI9"
FT TURN 68..70
FT /evidence="ECO:0007829|PDB:1HI9"
FT STRAND 75..81
FT /evidence="ECO:0007829|PDB:1HI9"
FT HELIX 86..88
FT /evidence="ECO:0007829|PDB:1HI9"
FT STRAND 96..103
FT /evidence="ECO:0007829|PDB:1HI9"
FT STRAND 109..111
FT /evidence="ECO:0007829|PDB:1HI9"
FT STRAND 116..118
FT /evidence="ECO:0007829|PDB:1HI9"
FT STRAND 121..126
FT /evidence="ECO:0007829|PDB:1HI9"
FT STRAND 129..131
FT /evidence="ECO:0007829|PDB:1HI9"
FT HELIX 133..143
FT /evidence="ECO:0007829|PDB:1HI9"
FT STRAND 148..154
FT /evidence="ECO:0007829|PDB:1HI9"
FT HELIX 155..162
FT /evidence="ECO:0007829|PDB:1HI9"
FT STRAND 169..178
FT /evidence="ECO:0007829|PDB:1HI9"
FT STRAND 181..184
FT /evidence="ECO:0007829|PDB:1HI9"
FT HELIX 187..203
FT /evidence="ECO:0007829|PDB:1HI9"
FT HELIX 205..207
FT /evidence="ECO:0007829|PDB:1HI9"
FT STRAND 218..225
FT /evidence="ECO:0007829|PDB:1HI9"
FT HELIX 226..232
FT /evidence="ECO:0007829|PDB:1HI9"
FT STRAND 238..240
FT /evidence="ECO:0007829|PDB:1HI9"
FT STRAND 244..250
FT /evidence="ECO:0007829|PDB:1HI9"
FT HELIX 254..268
FT /evidence="ECO:0007829|PDB:1HI9"
SQ SEQUENCE 274 AA; 30159 MW; 09A9F6410ADCFD38 CRC64;
MKLYMSVDME GISGLPDDTF VDSGKRNYER GRLIMTEEAN YCIAEAFNSG CTEVLVNDSH
SKMNNLMVEK LHPEADLISG DVKPFSMVEG LDDTFRGALF LGYHARASTP GVMSHSMIFG
VRHFYINDRP VGELGLNAYV AGYYDVPVLM VAGDDRAAKE AEELIPNVTT AAVKQTISRS
AVKCLSPAKA GRLLTEKTAF ALQNKDKVKP LTPPDRPVLS IEFANYGQAE WANLMPGTEI
KTGTTTVQFQ AKDMLEAYQA MLVMTELAMR TSFC
