PEPQ_ECOLI
ID PEPQ_ECOLI Reviewed; 443 AA.
AC P21165; P21176; Q2M8F0;
DT 01-MAY-1991, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1993, sequence version 2.
DT 03-AUG-2022, entry version 175.
DE RecName: Full=Xaa-Pro dipeptidase;
DE Short=X-Pro dipeptidase;
DE EC=3.4.13.9;
DE AltName: Full=Imidodipeptidase;
DE AltName: Full=Proline dipeptidase;
DE Short=Prolidase;
GN Name=pepQ; OrderedLocusNames=b3847, JW3823;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=2243799; DOI=10.1093/nar/18.21.6439;
RA Nakahigashi K., Inokuchi H.;
RT "Nucleotide sequence between the fadB gene and the rrnA operon from
RT Escherichia coli.";
RL Nucleic Acids Res. 18:6439-6439(1990).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=1379743; DOI=10.1126/science.1379743;
RA Daniels D.L., Plunkett G. III, Burland V.D., Blattner F.R.;
RT "Analysis of the Escherichia coli genome: DNA sequence of the region from
RT 84.5 to 86.5 minutes.";
RL Science 257:771-778(1992).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-438.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RA Nakahigashi K.;
RL Submitted (MAY-1990) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP PROTEIN SEQUENCE OF 1-5, FUNCTION, CHARACTERIZATION, SUBSTRATE SPECIFICITY,
RP AND KINETIC PARAMETERS.
RX PubMed=15313226; DOI=10.1016/j.abb.2004.06.022;
RA Park M.-S., Hill C.M., Li Y., Hardy R.K., Khanna H., Khang Y.-H.,
RA Raushel F.M.;
RT "Catalytic properties of the PepQ prolidase from Escherichia coli.";
RL Arch. Biochem. Biophys. 429:224-230(2004).
CC -!- FUNCTION: Splits dipeptides with a prolyl residue in the C-terminal
CC position and a polar or nonpolar amino acid at the N-terminal position.
CC With much lower efficiency, also catalyzes the stereoselective
CC hydrolysis of a wide variety of organophosphate triesters and
CC organophosphonate diesters. Is able to hydrolyze the organophosphorus
CC insecticide paraoxon and the p-nitrophenyl analogs of the nerve agents
CC GB (sarin), GD (soman), GF, Vx and rVX. {ECO:0000269|PubMed:15313226}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Hydrolysis of Xaa-|-Pro dipeptides. Also acts on aminoacyl-
CC hydroxyproline analogs. No action on Pro-|-Pro.; EC=3.4.13.9;
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000250};
CC Note=Binds 2 manganese ions per subunit. {ECO:0000250};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=1.9 mM for Ala-Pro {ECO:0000269|PubMed:15313226};
CC KM=0.10 mM for Arg-Pro {ECO:0000269|PubMed:15313226};
CC KM=1.4 mM for Gly-Pro {ECO:0000269|PubMed:15313226};
CC KM=0.15 mM for His-Pro {ECO:0000269|PubMed:15313226};
CC KM=0.10 mM for Ile-Pro {ECO:0000269|PubMed:15313226};
CC KM=1.0 mM for Leu-Pro {ECO:0000269|PubMed:15313226};
CC KM=0.27 mM for Lys-Pro {ECO:0000269|PubMed:15313226};
CC KM=0.13 mM for Met-Pro {ECO:0000269|PubMed:15313226};
CC KM=0.43 mM for Phe-Pro {ECO:0000269|PubMed:15313226};
CC KM=0.31 mM for Pro-Pro {ECO:0000269|PubMed:15313226};
CC KM=0.46 mM for Ser-Pro {ECO:0000269|PubMed:15313226};
CC KM=0.16 mM for Tyr-Pro {ECO:0000269|PubMed:15313226};
CC KM=0.40 mM for Val-Pro {ECO:0000269|PubMed:15313226};
CC KM=38 mM for diisopropylfluorophosphate
CC {ECO:0000269|PubMed:15313226};
CC Note=Among the dipeptides described above, the highest catalytic
CC efficiency is observed with dipeptides containing charge residues.;
CC -!- INTERACTION:
CC P21165; P33643: rluD; NbExp=2; IntAct=EBI-552580, EBI-558026;
CC -!- BIOTECHNOLOGY: Can be utilized for the kinetic resolution of racemic
CC phosphate esters.
CC -!- MISCELLANEOUS: Has a stereoselective preference for isomers with R-
CC configuration at the phosphorous center of organophosphonate diesters
CC and with S-configuration in organophosphate triesters.
CC -!- SIMILARITY: Belongs to the peptidase M24B family. Bacterial-type
CC prolidase subfamily. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAA38501.1; Type=Frameshift; Note=The resulting sequence is much longer and includes the sequence of yigZ.; Evidence={ECO:0000305};
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DR EMBL; X54687; CAA38501.1; ALT_FRAME; Genomic_DNA.
DR EMBL; M87049; AAA67644.1; -; Genomic_DNA.
DR EMBL; U00096; AAC76850.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE77456.1; -; Genomic_DNA.
DR EMBL; X52837; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR PIR; H65189; H65189.
DR RefSeq; NP_418289.1; NC_000913.3.
DR RefSeq; WP_000444561.1; NZ_STEB01000021.1.
DR PDB; 4QR8; X-ray; 2.00 A; A/B=1-443.
DR PDBsum; 4QR8; -.
DR AlphaFoldDB; P21165; -.
DR SMR; P21165; -.
DR BioGRID; 4261838; 32.
DR DIP; DIP-10460N; -.
DR IntAct; P21165; 4.
DR STRING; 511145.b3847; -.
DR MEROPS; M24.003; -.
DR SWISS-2DPAGE; P21165; -.
DR jPOST; P21165; -.
DR PaxDb; P21165; -.
DR PRIDE; P21165; -.
DR EnsemblBacteria; AAC76850; AAC76850; b3847.
DR EnsemblBacteria; BAE77456; BAE77456; BAE77456.
DR GeneID; 67414369; -.
DR GeneID; 948335; -.
DR KEGG; ecj:JW3823; -.
DR KEGG; eco:b3847; -.
DR PATRIC; fig|1411691.4.peg.2863; -.
DR EchoBASE; EB0692; -.
DR eggNOG; COG0006; Bacteria.
DR HOGENOM; CLU_050675_0_0_6; -.
DR InParanoid; P21165; -.
DR OMA; DFWHKVA; -.
DR PhylomeDB; P21165; -.
DR BioCyc; EcoCyc:EG10698-MON; -.
DR BioCyc; MetaCyc:EG10698-MON; -.
DR PRO; PR:P21165; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0004177; F:aminopeptidase activity; IBA:GO_Central.
DR GO; GO:0016805; F:dipeptidase activity; IDA:EcoCyc.
DR GO; GO:0030145; F:manganese ion binding; IDA:EcoCyc.
DR GO; GO:0070573; F:metallodipeptidase activity; IDA:EcoCyc.
DR GO; GO:0008233; F:peptidase activity; IBA:GO_Central.
DR GO; GO:0016795; F:phosphoric triester hydrolase activity; IEA:InterPro.
DR GO; GO:0102009; F:proline dipeptidase activity; IEA:UniProtKB-EC.
DR GO; GO:0043171; P:peptide catabolic process; IGI:EcoliWiki.
DR GO; GO:0006508; P:proteolysis; IEA:UniProtKB-KW.
DR Gene3D; 3.40.350.10; -; 1.
DR Gene3D; 3.90.230.10; -; 1.
DR HAMAP; MF_01279; X_Pro_dipeptid; 1.
DR InterPro; IPR029149; Creatin/AminoP/Spt16_NTD.
DR InterPro; IPR036005; Creatinase/aminopeptidase-like.
DR InterPro; IPR000994; Pept_M24.
DR InterPro; IPR001131; Peptidase_M24B_aminopep-P_CS.
DR InterPro; IPR022846; X_Pro_dipept.
DR Pfam; PF00557; Peptidase_M24; 1.
DR SUPFAM; SSF55920; SSF55920; 1.
DR PROSITE; PS00491; PROLINE_PEPTIDASE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Dipeptidase; Direct protein sequencing; Hydrolase; Manganese;
KW Metal-binding; Metalloprotease; Protease; Reference proteome.
FT CHAIN 1..443
FT /note="Xaa-Pro dipeptidase"
FT /id="PRO_0000185089"
FT BINDING 246
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 257
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 257
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 339
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 384
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 423
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 423
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT HELIX 4..26
FT /evidence="ECO:0007829|PDB:4QR8"
FT STRAND 29..34
FT /evidence="ECO:0007829|PDB:4QR8"
FT HELIX 54..57
FT /evidence="ECO:0007829|PDB:4QR8"
FT STRAND 69..72
FT /evidence="ECO:0007829|PDB:4QR8"
FT STRAND 74..76
FT /evidence="ECO:0007829|PDB:4QR8"
FT STRAND 79..83
FT /evidence="ECO:0007829|PDB:4QR8"
FT STRAND 88..90
FT /evidence="ECO:0007829|PDB:4QR8"
FT HELIX 99..102
FT /evidence="ECO:0007829|PDB:4QR8"
FT STRAND 104..111
FT /evidence="ECO:0007829|PDB:4QR8"
FT HELIX 112..114
FT /evidence="ECO:0007829|PDB:4QR8"
FT TURN 116..118
FT /evidence="ECO:0007829|PDB:4QR8"
FT STRAND 126..131
FT /evidence="ECO:0007829|PDB:4QR8"
FT HELIX 133..138
FT /evidence="ECO:0007829|PDB:4QR8"
FT HELIX 143..145
FT /evidence="ECO:0007829|PDB:4QR8"
FT HELIX 149..159
FT /evidence="ECO:0007829|PDB:4QR8"
FT HELIX 164..189
FT /evidence="ECO:0007829|PDB:4QR8"
FT HELIX 194..205
FT /evidence="ECO:0007829|PDB:4QR8"
FT TURN 209..211
FT /evidence="ECO:0007829|PDB:4QR8"
FT STRAND 212..214
FT /evidence="ECO:0007829|PDB:4QR8"
FT STRAND 217..220
FT /evidence="ECO:0007829|PDB:4QR8"
FT HELIX 221..225
FT /evidence="ECO:0007829|PDB:4QR8"
FT STRAND 242..251
FT /evidence="ECO:0007829|PDB:4QR8"
FT STRAND 254..264
FT /evidence="ECO:0007829|PDB:4QR8"
FT STRAND 266..268
FT /evidence="ECO:0007829|PDB:4QR8"
FT HELIX 269..287
FT /evidence="ECO:0007829|PDB:4QR8"
FT HELIX 294..311
FT /evidence="ECO:0007829|PDB:4QR8"
FT HELIX 320..325
FT /evidence="ECO:0007829|PDB:4QR8"
FT TURN 326..329
FT /evidence="ECO:0007829|PDB:4QR8"
FT HELIX 330..332
FT /evidence="ECO:0007829|PDB:4QR8"
FT STRAND 342..346
FT /evidence="ECO:0007829|PDB:4QR8"
FT STRAND 350..352
FT /evidence="ECO:0007829|PDB:4QR8"
FT STRAND 380..383
FT /evidence="ECO:0007829|PDB:4QR8"
FT STRAND 386..388
FT /evidence="ECO:0007829|PDB:4QR8"
FT HELIX 391..399
FT /evidence="ECO:0007829|PDB:4QR8"
FT HELIX 403..405
FT /evidence="ECO:0007829|PDB:4QR8"
FT HELIX 408..414
FT /evidence="ECO:0007829|PDB:4QR8"
FT HELIX 415..417
FT /evidence="ECO:0007829|PDB:4QR8"
FT STRAND 419..421
FT /evidence="ECO:0007829|PDB:4QR8"
FT STRAND 423..428
FT /evidence="ECO:0007829|PDB:4QR8"
FT STRAND 433..435
FT /evidence="ECO:0007829|PDB:4QR8"
FT HELIX 436..439
FT /evidence="ECO:0007829|PDB:4QR8"
SQ SEQUENCE 443 AA; 50176 MW; C5CB313DB774F670 CRC64;
MESLASLYKN HIATLQERTR DALARFKLDA LLIHSGELFN VFLDDHPYPF KVNPQFKAWV
PVTQVPNCWL LVDGVNKPKL WFYLPVDYWH NVEPLPTSFW TEDVEVIALP KADGIGSLLP
AARGNIGYIG PVPERALQLG IEASNINPKG VIDYLHYYRS FKTEYELACM REAQKMAVNG
HRAAEEAFRS GMSEFDINIA YLTATGHRDT DVPYSNIVAL NEHAAVLHYT KLDHQAPEEM
RSFLLDAGAE YNGYAADLTR TWSAKSDNDY AQLVKDVNDE QLALIATMKA GVSYVDYHIQ
FHQRIAKLLR KHQIITDMSE EAMVENDLTG PFMPHGIGHP LGLQVHDVAG FMQDDSGTHL
AAPAKYPYLR CTRILQPGMV LTIEPGIYFI ESLLAPWREG QFSKHFNWQK IEALKPFGGI
RIEDNVVIHE NNVENMTRDL KLA
