PEPQ_PYRFU
ID PEPQ_PYRFU Reviewed; 348 AA.
AC P81535;
DT 26-SEP-2001, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1998, sequence version 1.
DT 03-AUG-2022, entry version 145.
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=PF1343;
OS Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1).
OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC Pyrococcus.
OX NCBI_TaxID=186497;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-15, FUNCTION,
RP COFACTOR, SUBUNIT, AND BIOPHYSICOCHEMICAL PROPERTIES.
RC STRAIN=ATCC 43587 / DSM 3638 / JCM 8422 / Vc1;
RX PubMed=9733678; DOI=10.1128/jb.180.18.4781-4789.1998;
RA Ghosh M., Grunden A.M., Dunn D.M., Weiss R., Adams M.W.W.;
RT "Characterization of native and recombinant forms of an unusual cobalt-
RT dependent proline dipeptidase (Prolidase) from the hyperthermophilic
RT archaeon Pyrococcus furiosus.";
RL J. Bacteriol. 180:4781-4789(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43587 / DSM 3638 / JCM 8422 / Vc1;
RX PubMed=10430560; DOI=10.1093/genetics/152.4.1299;
RA Maeder D.L., Weiss R.B., Dunn D.M., Cherry J.L., Gonzalez J.M.,
RA DiRuggiero J., Robb F.T.;
RT "Divergence of the hyperthermophilic archaea Pyrococcus furiosus and P.
RT horikoshii inferred from complete genomic sequences.";
RL Genetics 152:1299-1305(1999).
RN [3]
RP CRYSTALLIZATION.
RC STRAIN=ATCC 43587 / DSM 3638 / JCM 8422 / Vc1;
RX PubMed=11223522; DOI=10.1107/s0907444900020187;
RA Willingham K., Maher M.J., Grunden A.M., Ghosh M., Adams M.W.W.,
RA Freeman H.C., Guss J.M.;
RT "Crystallization and characterization of the prolidase from Pyrococcus
RT furiosus.";
RL Acta Crystallogr. D 57:428-430(2001).
RN [4]
RP REVIEW.
RX PubMed=11210522; DOI=10.1016/s0076-6879(01)30395-6;
RA Grunden A.M., Ghosh M., Adams M.W.W.;
RT "Proline dipeptidase from Pyrococcus furiosus.";
RL Methods Enzymol. 330:433-445(2001).
RN [5]
RP MUTAGENESIS OF ASP-209; HIS-284 AND GLU-327.
RX PubMed=16243319; DOI=10.1016/j.febslet.2005.09.086;
RA Du X., Tove S., Kast-Hutcheson K., Grunden A.M.;
RT "Characterization of the dinuclear metal center of Pyrococcus furiosus
RT prolidase by analysis of targeted mutants.";
RL FEBS Lett. 579:6140-6146(2005).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEX WITH ZINC IONS.
RX PubMed=15005612; DOI=10.1021/bi0356451;
RA Maher M.J., Ghosh M., Grunden A.M., Menon A.L., Adams M.W.W., Freeman H.C.,
RA Guss J.M.;
RT "Structure of the prolidase from Pyrococcus furiosus.";
RL Biochemistry 43:2771-2783(2004).
CC -!- FUNCTION: Splits dipeptides with a prolyl in the C-terminal position
CC and a nonpolar amino acid at the N-terminal position.
CC {ECO:0000269|PubMed:9733678}.
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=Co(2+); Xref=ChEBI:CHEBI:48828;
CC Evidence={ECO:0000269|PubMed:9733678};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:9733678};
CC Note=Binds 2 cobalt ions per subunit. Co(2+) can be replaced by Mn(2+),
CC resulting in a 25% decrease in activity, but not by Mg(2+), Ca(2+),
CC Fe(2+), Zn(2+), Cu(2+), or Ni(2+). {ECO:0000269|PubMed:9733678};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=2.8 mM for Met-Pro {ECO:0000269|PubMed:9733678};
CC KM=3 mM for Leu-Pro {ECO:0000269|PubMed:9733678};
CC KM=4.2 mM for Val-Pro {ECO:0000269|PubMed:9733678};
CC KM=8.3 mM for Ala-Pro {ECO:0000269|PubMed:9733678};
CC KM=20 mM for Phe-Pro {ECO:0000269|PubMed:9733678};
CC Vmax=645 umol/min/mg enzyme with Met-Pro as substrate
CC {ECO:0000269|PubMed:9733678};
CC Vmax=645 umol/min/mg enzyme with Leu-Pro as substrate
CC {ECO:0000269|PubMed:9733678};
CC Vmax=175 umol/min/mg enzyme with Val-Pro as substrate
CC {ECO:0000269|PubMed:9733678};
CC Vmax=250 umol/min/mg enzyme with Ala-Pro as substrate
CC {ECO:0000269|PubMed:9733678};
CC Vmax=1000 umol/min/mg enzyme with Phe-Pro as substrate
CC {ECO:0000269|PubMed:9733678};
CC pH dependence:
CC Optimum pH is 7.0. {ECO:0000269|PubMed:9733678};
CC Temperature dependence:
CC Optimum temperature is 100 degrees Celsius. Highly thermostable.
CC {ECO:0000269|PubMed:9733678};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:15005612,
CC ECO:0000269|PubMed:9733678}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm.
CC -!- MISCELLANEOUS: Cobalt 1 is the tight-binding and cobalt 2 is the loose-
CC binding metal center.
CC -!- SIMILARITY: Belongs to the peptidase M24B family. Archaeal-type
CC prolidase subfamily. {ECO:0000305}.
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DR EMBL; AF060010; AAC61259.1; -; Genomic_DNA.
DR EMBL; AE009950; AAL81467.1; -; Genomic_DNA.
DR PIR; T46973; T46973.
DR RefSeq; WP_011012489.1; NC_018092.1.
DR PDB; 1PV9; X-ray; 2.00 A; A/B=1-348.
DR PDBsum; 1PV9; -.
DR AlphaFoldDB; P81535; -.
DR SMR; P81535; -.
DR STRING; 186497.PF1343; -.
DR MEROPS; M24.008; -.
DR PRIDE; P81535; -.
DR EnsemblBacteria; AAL81467; AAL81467; PF1343.
DR GeneID; 41713146; -.
DR KEGG; pfu:PF1343; -.
DR PATRIC; fig|186497.12.peg.1406; -.
DR eggNOG; arCOG01000; Archaea.
DR HOGENOM; CLU_017266_4_2_2; -.
DR OMA; DIYNAMW; -.
DR OrthoDB; 14436at2157; -.
DR PhylomeDB; P81535; -.
DR BRENDA; 3.4.13.9; 5243.
DR EvolutionaryTrace; P81535; -.
DR Proteomes; UP000001013; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0008237; F:metallopeptidase activity; IEA:UniProtKB-KW.
DR GO; GO:0102009; F:proline dipeptidase activity; IEA:UniProtKB-EC.
DR GO; GO:0006508; P:proteolysis; IEA:UniProtKB-KW.
DR Gene3D; 3.40.350.10; -; 1.
DR Gene3D; 3.90.230.10; -; 1.
DR InterPro; IPR029149; Creatin/AminoP/Spt16_NTD.
DR InterPro; IPR036005; Creatinase/aminopeptidase-like.
DR InterPro; IPR000587; Creatinase_N.
DR InterPro; IPR000994; Pept_M24.
DR InterPro; IPR001714; Pept_M24_MAP.
DR InterPro; IPR001131; Peptidase_M24B_aminopep-P_CS.
DR Pfam; PF01321; Creatinase_N; 1.
DR Pfam; PF00557; Peptidase_M24; 1.
DR PRINTS; PR00599; MAPEPTIDASE.
DR SUPFAM; SSF53092; SSF53092; 1.
DR SUPFAM; SSF55920; SSF55920; 1.
DR PROSITE; PS00491; PROLINE_PEPTIDASE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cobalt; Cytoplasm; Dipeptidase; Direct protein sequencing;
KW Hydrolase; Metal-binding; Metalloprotease; Protease; Reference proteome.
FT CHAIN 1..348
FT /note="Xaa-Pro dipeptidase"
FT /id="PRO_0000185093"
FT BINDING 209
FT /ligand="Co(2+)"
FT /ligand_id="ChEBI:CHEBI:48828"
FT /ligand_label="2"
FT BINDING 220
FT /ligand="Co(2+)"
FT /ligand_id="ChEBI:CHEBI:48828"
FT /ligand_label="1"
FT BINDING 220
FT /ligand="Co(2+)"
FT /ligand_id="ChEBI:CHEBI:48828"
FT /ligand_label="2"
FT BINDING 284
FT /ligand="Co(2+)"
FT /ligand_id="ChEBI:CHEBI:48828"
FT /ligand_label="1"
FT BINDING 313
FT /ligand="Co(2+)"
FT /ligand_id="ChEBI:CHEBI:48828"
FT /ligand_label="1"
FT BINDING 327
FT /ligand="Co(2+)"
FT /ligand_id="ChEBI:CHEBI:48828"
FT /ligand_label="1"
FT BINDING 327
FT /ligand="Co(2+)"
FT /ligand_id="ChEBI:CHEBI:48828"
FT /ligand_label="2"
FT MUTAGEN 209
FT /note="D->A: 1300-fold reduction in activity."
FT /evidence="ECO:0000269|PubMed:16243319"
FT MUTAGEN 284
FT /note="H->A,L: 2000-fold reduction in activity."
FT /evidence="ECO:0000269|PubMed:16243319"
FT MUTAGEN 327
FT /note="E->L: Loss of activity."
FT /evidence="ECO:0000269|PubMed:16243319"
FT HELIX 9..14
FT /evidence="ECO:0007829|PDB:1PV9"
FT STRAND 19..22
FT /evidence="ECO:0007829|PDB:1PV9"
FT HELIX 25..32
FT /evidence="ECO:0007829|PDB:1PV9"
FT STRAND 41..45
FT /evidence="ECO:0007829|PDB:1PV9"
FT STRAND 48..54
FT /evidence="ECO:0007829|PDB:1PV9"
FT HELIX 55..57
FT /evidence="ECO:0007829|PDB:1PV9"
FT HELIX 58..64
FT /evidence="ECO:0007829|PDB:1PV9"
FT STRAND 69..74
FT /evidence="ECO:0007829|PDB:1PV9"
FT HELIX 77..81
FT /evidence="ECO:0007829|PDB:1PV9"
FT TURN 82..84
FT /evidence="ECO:0007829|PDB:1PV9"
FT STRAND 86..90
FT /evidence="ECO:0007829|PDB:1PV9"
FT HELIX 96..104
FT /evidence="ECO:0007829|PDB:1PV9"
FT STRAND 110..113
FT /evidence="ECO:0007829|PDB:1PV9"
FT HELIX 115..122
FT /evidence="ECO:0007829|PDB:1PV9"
FT HELIX 127..150
FT /evidence="ECO:0007829|PDB:1PV9"
FT HELIX 157..170
FT /evidence="ECO:0007829|PDB:1PV9"
FT STRAND 174..178
FT /evidence="ECO:0007829|PDB:1PV9"
FT STRAND 181..184
FT /evidence="ECO:0007829|PDB:1PV9"
FT HELIX 185..189
FT /evidence="ECO:0007829|PDB:1PV9"
FT STRAND 205..210
FT /evidence="ECO:0007829|PDB:1PV9"
FT STRAND 212..214
FT /evidence="ECO:0007829|PDB:1PV9"
FT STRAND 221..229
FT /evidence="ECO:0007829|PDB:1PV9"
FT HELIX 232..251
FT /evidence="ECO:0007829|PDB:1PV9"
FT HELIX 258..271
FT /evidence="ECO:0007829|PDB:1PV9"
FT HELIX 275..277
FT /evidence="ECO:0007829|PDB:1PV9"
FT STRAND 282..285
FT /evidence="ECO:0007829|PDB:1PV9"
FT STRAND 287..297
FT /evidence="ECO:0007829|PDB:1PV9"
FT STRAND 309..312
FT /evidence="ECO:0007829|PDB:1PV9"
FT STRAND 315..318
FT /evidence="ECO:0007829|PDB:1PV9"
FT TURN 319..321
FT /evidence="ECO:0007829|PDB:1PV9"
FT STRAND 322..325
FT /evidence="ECO:0007829|PDB:1PV9"
FT STRAND 327..332
FT /evidence="ECO:0007829|PDB:1PV9"
FT STRAND 334..340
FT /evidence="ECO:0007829|PDB:1PV9"
SQ SEQUENCE 348 AA; 39387 MW; 6BA956FAA9C18FB5 CRC64;
MKERLEKLVK FMDENSIDRV FIAKPVNVYY FSGTSPLGGG YIIVDGDEAT LYVPELEYEM
AKEESKLPVV KFKKFDEIYE ILKNTETLGI EGTLSYSMVE NFKEKSNVKE FKKIDDVIKD
LRIIKTKEEI EIIEKACEIA DKAVMAAIEE ITEGKREREV AAKVEYLMKM NGAEKPAFDT
IIASGHRSAL PHGVASDKRI ERGDLVVIDL GALYNHYNSD ITRTIVVGSP NEKQREIYEI
VLEAQKRAVE AAKPGMTAKE LDSIAREIIK EYGYGDYFIH SLGHGVGLEI HEWPRISQYD
ETVLKEGMVI TIEPGIYIPK LGGVRIEDTV LITENGAKRL TKTERELL
