ID PEPD_DICDI Reviewed; 501 AA.
AC Q55E60;
DT 08-APR-2008, integrated into UniProtKB/Swiss-Prot.
DT 24-MAY-2005, sequence version 1.
DT 27-MAR-2024, entry version 115.
DE RecName: Full=Xaa-Pro dipeptidase;
DE Short=X-Pro dipeptidase;
DE EC=3.4.13.9;
DE AltName: Full=Imidodipeptidase;
DE AltName: Full=Peptidase D;
DE AltName: Full=Proline dipeptidase;
DE Short=Prolidase;
GN Name=pepd; Synonyms=prd; ORFNames=DDB_G0269382;
OS Dictyostelium discoideum (Social amoeba).
OC Eukaryota; Amoebozoa; Evosea; Eumycetozoa; Dictyostelia; Dictyosteliales;
OC Dictyosteliaceae; Dictyostelium.
OX NCBI_TaxID=44689;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=AX4;
RX PubMed=15875012; DOI=10.1038/nature03481;
RA Eichinger L., Pachebat J.A., Gloeckner G., Rajandream M.A., Sucgang R.,
RA Berriman M., Song J., Olsen R., Szafranski K., Xu Q., Tunggal B.,
RA Kummerfeld S., Madera M., Konfortov B.A., Rivero F., Bankier A.T.,
RA Lehmann R., Hamlin N., Davies R., Gaudet P., Fey P., Pilcher K., Chen G.,
RA Saunders D., Sodergren E.J., Davis P., Kerhornou A., Nie X., Hall N.,
RA Anjard C., Hemphill L., Bason N., Farbrother P., Desany B., Just E.,
RA Morio T., Rost R., Churcher C.M., Cooper J., Haydock S., van Driessche N.,
RA Cronin A., Goodhead I., Muzny D.M., Mourier T., Pain A., Lu M., Harper D.,
RA Lindsay R., Hauser H., James K.D., Quiles M., Madan Babu M., Saito T.,
RA Buchrieser C., Wardroper A., Felder M., Thangavelu M., Johnson D.,
RA Knights A., Loulseged H., Mungall K.L., Oliver K., Price C., Quail M.A.,
RA Urushihara H., Hernandez J., Rabbinowitsch E., Steffen D., Sanders M.,
RA Ma J., Kohara Y., Sharp S., Simmonds M.N., Spiegler S., Tivey A.,
RA Sugano S., White B., Walker D., Woodward J.R., Winckler T., Tanaka Y.,
RA Shaulsky G., Schleicher M., Weinstock G.M., Rosenthal A., Cox E.C.,
RA Chisholm R.L., Gibbs R.A., Loomis W.F., Platzer M., Kay R.R.,
RA Williams J.G., Dear P.H., Noegel A.A., Barrell B.G., Kuspa A.;
RT "The genome of the social amoeba Dictyostelium discoideum.";
RL Nature 435:43-57(2005).
RN [2]
RP PROTEIN SEQUENCE OF 49-56 AND 491-501, AND IDENTIFICATION BY MASS
RP SPECTROMETRY.
RA Bienvenut W.V., Veltman D.M., Insall R.H.;
RL Submitted (JAN-2010) to UniProtKB.
CC -!- FUNCTION: Dipeptidase that catalyzes the hydrolysis of dipeptides with
CC a prolyl (Xaa-Pro) or hydroxyprolyl residue in the C-terminal position.
CC {ECO:0000250|UniProtKB:P12955}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + Xaa-L-Pro dipeptide = an L-alpha-amino acid + L-proline;
CC Xref=Rhea:RHEA:76407, ChEBI:CHEBI:15377, ChEBI:CHEBI:59869,
CC ChEBI:CHEBI:60039, ChEBI:CHEBI:195196; EC=3.4.13.9;
CC Evidence={ECO:0000250|UniProtKB:P12955};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000250|UniProtKB:P12955};
CC Note=Binds 2 manganese ions per subunit.
CC {ECO:0000250|UniProtKB:P12955};
CC -!- SUBUNIT: Homodimer. {ECO:0000250|UniProtKB:P12955}.
CC -!- SIMILARITY: Belongs to the peptidase M24B family. Eukaryotic-type
CC prolidase subfamily. {ECO:0000305}.
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DR EMBL; AAFI02000005; EAL72041.1; -; Genomic_DNA.
DR RefSeq; XP_645921.1; XM_640829.1.
DR AlphaFoldDB; Q55E60; -.
DR SMR; Q55E60; -.
DR STRING; 44689.Q55E60; -.
DR MEROPS; M24.007; -.
DR PaxDb; 44689-DDB0266378; -.
DR EnsemblProtists; EAL72041; EAL72041; DDB_G0269382.
DR GeneID; 8616862; -.
DR KEGG; ddi:DDB_G0269382; -.
DR dictyBase; DDB_G0269382; pepD.
DR eggNOG; KOG2737; Eukaryota.
DR HOGENOM; CLU_017266_1_2_1; -.
DR InParanoid; Q55E60; -.
DR OMA; YVTDCDL; -.
DR PhylomeDB; Q55E60; -.
DR PRO; PR:Q55E60; -.
DR Proteomes; UP000002195; Chromosome 1.
DR GO; GO:0030145; F:manganese ion binding; IEA:InterPro.
DR GO; GO:0070006; F:metalloaminopeptidase activity; IEA:InterPro.
DR GO; GO:0008233; F:peptidase activity; IBA:GO_Central.
DR GO; GO:0102009; F:proline dipeptidase activity; IEA:UniProtKB-EC.
DR GO; GO:0006508; P:proteolysis; IBA:GO_Central.
DR CDD; cd01087; Prolidase; 1.
DR Gene3D; 3.90.230.10; Creatinase/methionine aminopeptidase superfamily; 1.
DR Gene3D; 3.40.350.10; Creatinase/prolidase N-terminal domain; 1.
DR InterPro; IPR007865; Aminopep_P_N.
DR InterPro; IPR029149; Creatin/AminoP/Spt16_NTD.
DR InterPro; IPR036005; Creatinase/aminopeptidase-like.
DR InterPro; IPR000994; Pept_M24.
DR PANTHER; PTHR48392; -; 1.
DR PANTHER; PTHR48392:SF2; PEPTIDASE D; 1.
DR Pfam; PF05195; AMP_N; 1.
DR Pfam; PF00557; Peptidase_M24; 1.
DR SMART; SM01011; AMP_N; 1.
DR SUPFAM; SSF55920; Creatinase/aminopeptidase; 1.
DR SUPFAM; SSF53092; Creatinase/prolidase N-terminal domain; 1.
PE 1: Evidence at protein level;
KW Dipeptidase; Direct protein sequencing; Hydrolase; Manganese;
KW Metal-binding; Metalloprotease; Protease; Reference proteome.
FT CHAIN 1..501
FT /note="Xaa-Pro dipeptidase"
FT /id="PRO_0000328066"
FT BINDING 278
FT /ligand="a dipeptide"
FT /ligand_id="ChEBI:CHEBI:90799"
FT /evidence="ECO:0000250|UniProtKB:P12955"
FT BINDING 299
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P12955"
FT BINDING 310
FT /ligand="a dipeptide"
FT /ligand_id="ChEBI:CHEBI:90799"
FT /evidence="ECO:0000250|UniProtKB:P12955"
FT BINDING 310
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P12955"
FT BINDING 310
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P12955"
FT BINDING 393
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P12955"
FT BINDING 400
FT /ligand="a dipeptide"
FT /ligand_id="ChEBI:CHEBI:90799"
FT /evidence="ECO:0000250|UniProtKB:P12955"
FT BINDING 417
FT /ligand="a dipeptide"
FT /ligand_id="ChEBI:CHEBI:90799"
FT /evidence="ECO:0000250|UniProtKB:P12955"
FT BINDING 431
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P12955"
FT BINDING 471
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P12955"
FT BINDING 471
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P12955"
SQ SEQUENCE 501 AA; 56426 MW; 359939E7B9E35E3A CRC64;
MSVHPRNQGK DDCCEKTHLD SQYSPGYYWL GNNTLKVPLV LHKENRQRLV SQILSKHKDQ
VKENSFILLE SGKSTMQYDT DHEPLFKQER YFFWTFGSDI PDCFGIVGLD EQATSILCIP
KLPAEYATWM GEIRSKEYYK SIFLVDQVLY VDEMMDYLKS KNASTIYTIL GTNTDSGSTF
VEPQYPGLRE TFNVNNTLLF PEIAECRVIK SPKEVEVIRY CVDASVSAHK HVMRKVKVGL
KEYQCESEFL HHVYNEWGCR NVGYTCICAA NKNSAVLHYG HAGEPNSATI SENGFCLFDM
GAEYHSYTAD ITCSFPATGK FSPEQRVVYQ AVLDASVAVM EAMRPGVSWV DMHKLAERCI
LAALLKAGIL VGDLQDLIAN KIGSVFFPHG LGHFLGLDTH DVGGYLGDCQ PKVHSLRTTR
TLKAGMVITS EPGCYFINHL LTQALSNPET AKFFNLTELD KYRNIGGVRI EDDILVTETG
CDNLSKNLPR TIDEIEAFML K
//
