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Protein

Xaa-Pro dipeptidase

Gene

pepQ

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Splits dipeptides with a prolyl residue in the C-terminal position and a polar or nonpolar amino acid at the N-terminal position. With much lower efficiency, also catalyzes the stereoselective hydrolysis of a wide variety of organophosphate triesters and organophosphonate diesters. Is able to hydrolyze the organophosphorus insecticide paraoxon and the p-nitrophenyl analogs of the nerve agents GB (sarin), GD (soman), GF, Vx and rVX.1 Publication

Catalytic activityi

Hydrolysis of Xaa-|-Pro dipeptides; also acts on aminoacyl-hydroxyproline analogs. No action on Pro-|-Pro.

Cofactori

Mn2+By similarityNote: Binds 2 manganese ions per subunit.By similarity

Kineticsi

Among the dipeptides described above, the highest catalytic efficiency is observed with dipeptides containing charge residues.

  1. KM=1.9 mM for Ala-Pro1 Publication
  2. KM=0.10 mM for Arg-Pro1 Publication
  3. KM=1.4 mM for Gly-Pro1 Publication
  4. KM=0.15 mM for His-Pro1 Publication
  5. KM=0.10 mM for Ile-Pro1 Publication
  6. KM=1.0 mM for Leu-Pro1 Publication
  7. KM=0.27 mM for Lys-Pro1 Publication
  8. KM=0.13 mM for Met-Pro1 Publication
  9. KM=0.43 mM for Phe-Pro1 Publication
  10. KM=0.31 mM for Pro-Pro1 Publication
  11. KM=0.46 mM for Ser-Pro1 Publication
  12. KM=0.16 mM for Tyr-Pro1 Publication
  13. KM=0.40 mM for Val-Pro1 Publication
  14. KM=38 mM for diisopropylfluorophosphate1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi246 – 2461Manganese 2By similarity
    Metal bindingi257 – 2571Manganese 1By similarity
    Metal bindingi257 – 2571Manganese 2By similarity
    Metal bindingi339 – 3391Manganese 1By similarity
    Metal bindingi384 – 3841Manganese 1By similarity
    Metal bindingi423 – 4231Manganese 1By similarity
    Metal bindingi423 – 4231Manganese 2By similarity

    GO - Molecular functioni

    • dipeptidase activity Source: EcoCyc
    • manganese ion binding Source: EcoCyc
    • metallodipeptidase activity Source: EcoCyc
    • phosphoric triester hydrolase activity Source: InterPro
    • proline dipeptidase activity Source: UniProtKB-EC

    GO - Biological processi

    • peptide catabolic process Source: EcoliWiki
    Complete GO annotation...

    Keywords - Molecular functioni

    Dipeptidase, Hydrolase, Metalloprotease, Protease

    Keywords - Ligandi

    Manganese, Metal-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:EG10698-MONOMER.
    ECOL316407:JW3823-MONOMER.
    MetaCyc:EG10698-MONOMER.

    Protein family/group databases

    MEROPSiM24.003.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Xaa-Pro dipeptidase (EC:3.4.13.9)
    Short name:
    X-Pro dipeptidase
    Alternative name(s):
    Imidodipeptidase
    Proline dipeptidase
    Short name:
    Prolidase
    Gene namesi
    Name:pepQ
    Ordered Locus Names:b3847, JW3823
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG10698. pepQ.

    Subcellular locationi

    GO - Cellular componenti

    • cytosol Source: EcoCyc
    Complete GO annotation...

    Pathology & Biotechi

    Biotechnological usei

    Can be utilized for the kinetic resolution of racemic phosphate esters.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 443443Xaa-Pro dipeptidasePRO_0000185089Add
    BLAST

    Proteomic databases

    EPDiP21165.
    PaxDbiP21165.
    PRIDEiP21165.

    2D gel databases

    SWISS-2DPAGEP21165.

    Interactioni

    Protein-protein interaction databases

    BioGridi4261838. 11 interactions.
    DIPiDIP-10460N.
    IntActiP21165. 4 interactions.
    MINTiMINT-1302254.
    STRINGi511145.b3847.

    Structurei

    Secondary structure

    1
    443
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi4 – 2623Combined sources
    Beta strandi29 – 346Combined sources
    Helixi54 – 574Combined sources
    Beta strandi69 – 724Combined sources
    Beta strandi74 – 763Combined sources
    Beta strandi79 – 835Combined sources
    Beta strandi88 – 903Combined sources
    Helixi99 – 1024Combined sources
    Beta strandi104 – 1118Combined sources
    Helixi112 – 1143Combined sources
    Turni116 – 1183Combined sources
    Beta strandi126 – 1316Combined sources
    Helixi133 – 1386Combined sources
    Helixi143 – 1453Combined sources
    Helixi149 – 15911Combined sources
    Helixi164 – 18926Combined sources
    Helixi194 – 20512Combined sources
    Turni209 – 2113Combined sources
    Beta strandi212 – 2143Combined sources
    Beta strandi217 – 2204Combined sources
    Helixi221 – 2255Combined sources
    Beta strandi242 – 25110Combined sources
    Beta strandi254 – 26411Combined sources
    Beta strandi266 – 2683Combined sources
    Helixi269 – 28719Combined sources
    Helixi294 – 31118Combined sources
    Helixi320 – 3256Combined sources
    Turni326 – 3294Combined sources
    Helixi330 – 3323Combined sources
    Beta strandi342 – 3465Combined sources
    Beta strandi350 – 3523Combined sources
    Beta strandi380 – 3834Combined sources
    Beta strandi386 – 3883Combined sources
    Helixi391 – 3999Combined sources
    Helixi403 – 4053Combined sources
    Helixi408 – 4147Combined sources
    Helixi415 – 4173Combined sources
    Beta strandi419 – 4213Combined sources
    Beta strandi423 – 4286Combined sources
    Beta strandi433 – 4353Combined sources
    Helixi436 – 4394Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4QR8X-ray2.00A/B1-443[»]
    ProteinModelPortaliP21165.
    SMRiP21165. Positions 3-443.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4105D9Y. Bacteria.
    COG0006. LUCA.
    HOGENOMiHOG000290531.
    InParanoidiP21165.
    KOiK01271.
    OMAiMQDDTGT.
    PhylomeDBiP21165.

    Family and domain databases

    Gene3Di3.90.230.10. 1 hit.
    HAMAPiMF_01279. X_Pro_dipeptid. 1 hit.
    InterProiIPR000994. Pept_M24_structural-domain.
    IPR001131. Peptidase_M24B_aminopep-P_CS.
    IPR022846. X_Pro_dipept.
    [Graphical view]
    PfamiPF00557. Peptidase_M24. 1 hit.
    [Graphical view]
    SUPFAMiSSF55920. SSF55920. 1 hit.
    PROSITEiPS00491. PROLINE_PEPTIDASE. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P21165-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MESLASLYKN HIATLQERTR DALARFKLDA LLIHSGELFN VFLDDHPYPF
    60 70 80 90 100
    KVNPQFKAWV PVTQVPNCWL LVDGVNKPKL WFYLPVDYWH NVEPLPTSFW
    110 120 130 140 150
    TEDVEVIALP KADGIGSLLP AARGNIGYIG PVPERALQLG IEASNINPKG
    160 170 180 190 200
    VIDYLHYYRS FKTEYELACM REAQKMAVNG HRAAEEAFRS GMSEFDINIA
    210 220 230 240 250
    YLTATGHRDT DVPYSNIVAL NEHAAVLHYT KLDHQAPEEM RSFLLDAGAE
    260 270 280 290 300
    YNGYAADLTR TWSAKSDNDY AQLVKDVNDE QLALIATMKA GVSYVDYHIQ
    310 320 330 340 350
    FHQRIAKLLR KHQIITDMSE EAMVENDLTG PFMPHGIGHP LGLQVHDVAG
    360 370 380 390 400
    FMQDDSGTHL AAPAKYPYLR CTRILQPGMV LTIEPGIYFI ESLLAPWREG
    410 420 430 440
    QFSKHFNWQK IEALKPFGGI RIEDNVVIHE NNVENMTRDL KLA
    Length:443
    Mass (Da):50,176
    Last modified:October 1, 1993 - v2
    Checksum:iC5CB313DB774F670
    GO

    Sequence cautioni

    The sequence CAA38501 differs from that shown. Reason: Frameshift at position 430. The resulting sequence is much longer and includes the sequence of yigZ.Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X54687 Genomic DNA. Translation: CAA38501.1. Frameshift.
    M87049 Genomic DNA. Translation: AAA67644.1.
    U00096 Genomic DNA. Translation: AAC76850.1.
    AP009048 Genomic DNA. Translation: BAE77456.1.
    X52837 Genomic DNA. No translation available.
    PIRiH65189.
    RefSeqiNP_418289.1. NC_000913.3.
    WP_000444561.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC76850; AAC76850; b3847.
    BAE77456; BAE77456; BAE77456.
    GeneIDi948335.
    KEGGiecj:JW3823.
    eco:b3847.
    PATRICi32123191. VBIEscCol129921_3961.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X54687 Genomic DNA. Translation: CAA38501.1. Frameshift.
    M87049 Genomic DNA. Translation: AAA67644.1.
    U00096 Genomic DNA. Translation: AAC76850.1.
    AP009048 Genomic DNA. Translation: BAE77456.1.
    X52837 Genomic DNA. No translation available.
    PIRiH65189.
    RefSeqiNP_418289.1. NC_000913.3.
    WP_000444561.1. NZ_LN832404.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4QR8X-ray2.00A/B1-443[»]
    ProteinModelPortaliP21165.
    SMRiP21165. Positions 3-443.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4261838. 11 interactions.
    DIPiDIP-10460N.
    IntActiP21165. 4 interactions.
    MINTiMINT-1302254.
    STRINGi511145.b3847.

    Protein family/group databases

    MEROPSiM24.003.

    2D gel databases

    SWISS-2DPAGEP21165.

    Proteomic databases

    EPDiP21165.
    PaxDbiP21165.
    PRIDEiP21165.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC76850; AAC76850; b3847.
    BAE77456; BAE77456; BAE77456.
    GeneIDi948335.
    KEGGiecj:JW3823.
    eco:b3847.
    PATRICi32123191. VBIEscCol129921_3961.

    Organism-specific databases

    EchoBASEiEB0692.
    EcoGeneiEG10698. pepQ.

    Phylogenomic databases

    eggNOGiENOG4105D9Y. Bacteria.
    COG0006. LUCA.
    HOGENOMiHOG000290531.
    InParanoidiP21165.
    KOiK01271.
    OMAiMQDDTGT.
    PhylomeDBiP21165.

    Enzyme and pathway databases

    BioCyciEcoCyc:EG10698-MONOMER.
    ECOL316407:JW3823-MONOMER.
    MetaCyc:EG10698-MONOMER.

    Miscellaneous databases

    PROiP21165.

    Family and domain databases

    Gene3Di3.90.230.10. 1 hit.
    HAMAPiMF_01279. X_Pro_dipeptid. 1 hit.
    InterProiIPR000994. Pept_M24_structural-domain.
    IPR001131. Peptidase_M24B_aminopep-P_CS.
    IPR022846. X_Pro_dipept.
    [Graphical view]
    PfamiPF00557. Peptidase_M24. 1 hit.
    [Graphical view]
    SUPFAMiSSF55920. SSF55920. 1 hit.
    PROSITEiPS00491. PROLINE_PEPTIDASE. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiPEPQ_ECOLI
    AccessioniPrimary (citable) accession number: P21165
    Secondary accession number(s): P21176, Q2M8F0
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 1, 1991
    Last sequence update: October 1, 1993
    Last modified: September 7, 2016
    This is version 141 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Has a stereoselective preference for isomers with R-configuration at the phosphorous center of organophosphonate diesters and with S-configuration in organophosphate triesters.

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. Peptidase families
      Classification of peptidase families and list of entries
    4. SIMILARITY comments
      Index of protein domains and families

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.