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Protein

D-aminopeptidase

Gene

dap

Organism
Ochrobactrum anthropi
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Hydrolyzes N-terminal residues in D-amino acid-containing peptides.

Catalytic activityi

Release of an N-terminal D-amino acid from a peptide, Xaa-|-Yaa-, in which Xaa is preferably D-Ala, D-Ser or D-Thr. D-amino acid amides and methyl esters also are hydrolyzed, as is glycine amide.2 Publications

Enzyme regulationi

Inhibited by beta-lactam compounds such as 6-aminopenicillic acid, 7-aminocephalosporanic acid, benzylpenicillin and ampicillin. Inhibited by p-chloromercuribenzoate.1 Publication

Absorptioni

Abs(max)=281 nm1 Publication

Kineticsi

  1. KM=0.65 mM for D-alanine amide (at 30 degrees Celsius)1 Publication

    pH dependencei

    Optimum pH is 8.5.1 Publication

    Temperature dependencei

    Optimum temperature is 45 degrees Celsius.1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei62 – 621NucleophileCurated
    Active sitei65 – 651Proton donor/acceptorCurated
    Binding sitei481 – 4811Substrate

    GO - Molecular functioni

    Complete GO annotation...

    Keywords - Molecular functioni

    Aminopeptidase, Hydrolase, Protease

    Enzyme and pathway databases

    SABIO-RKQ9ZBA9.

    Protein family/group databases

    MEROPSiS12.002.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    D-aminopeptidase (EC:3.4.11.19)
    Gene namesi
    Name:dap
    OrganismiOchrobactrum anthropi
    Taxonomic identifieri529 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesBrucellaceaeOchrobactrum

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi58 – 581M → F: No effect on enzymatic activity. 1 Publication
    Mutagenesisi61 – 611C → S: Alters sensitivity to p-chloromercuribenzoate. 1 Publication
    Mutagenesisi62 – 621S → G: Abolishes enzymatic activity. 1 Publication
    Mutagenesisi65 – 651K → N: Abolishes enzymatic activity. 1 Publication
    Mutagenesisi69 – 691C → S: No effect on enzymatic activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed1 Publication
    Chaini2 – 520519D-aminopeptidasePRO_0000250696Add
    BLAST

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    Structurei

    Secondary structure

    1
    520
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi7 – 148Combined sources
    Helixi16 – 194Combined sources
    Beta strandi22 – 3110Combined sources
    Beta strandi34 – 4512Combined sources
    Turni46 – 494Combined sources
    Helixi61 – 633Combined sources
    Helixi64 – 7512Combined sources
    Helixi79 – 824Combined sources
    Helixi83 – 897Combined sources
    Turni90 – 923Combined sources
    Helixi100 – 1045Combined sources
    Helixi113 – 1197Combined sources
    Helixi130 – 1389Combined sources
    Helixi155 – 16915Combined sources
    Helixi173 – 1808Combined sources
    Helixi182 – 1854Combined sources
    Helixi196 – 1983Combined sources
    Beta strandi205 – 2084Combined sources
    Turni209 – 2113Combined sources
    Beta strandi212 – 2154Combined sources
    Beta strandi224 – 2263Combined sources
    Beta strandi228 – 2303Combined sources
    Helixi232 – 24413Combined sources
    Turni245 – 2473Combined sources
    Helixi252 – 2565Combined sources
    Beta strandi269 – 2713Combined sources
    Beta strandi274 – 2796Combined sources
    Beta strandi282 – 29110Combined sources
    Beta strandi294 – 3018Combined sources
    Helixi302 – 3043Combined sources
    Beta strandi306 – 31611Combined sources
    Helixi318 – 33013Combined sources
    Helixi344 – 3463Combined sources
    Beta strandi348 – 3514Combined sources
    Turni353 – 3553Combined sources
    Beta strandi358 – 3636Combined sources
    Beta strandi368 – 3725Combined sources
    Beta strandi374 – 3763Combined sources
    Beta strandi378 – 3847Combined sources
    Beta strandi387 – 3893Combined sources
    Beta strandi394 – 3985Combined sources
    Beta strandi401 – 4066Combined sources
    Helixi407 – 4093Combined sources
    Beta strandi411 – 4177Combined sources
    Beta strandi428 – 4325Combined sources
    Turni433 – 4364Combined sources
    Beta strandi437 – 4448Combined sources
    Beta strandi447 – 4548Combined sources
    Beta strandi465 – 4684Combined sources
    Beta strandi471 – 4766Combined sources
    Beta strandi480 – 4834Combined sources
    Beta strandi486 – 4949Combined sources
    Beta strandi500 – 5078Combined sources
    Beta strandi510 – 5178Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1EI5X-ray1.90A1-520[»]
    ProteinModelPortaliQ9ZBA9.
    SMRiQ9ZBA9. Positions 3-520.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ9ZBA9.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni477 – 48711Important for specificityAdd
    BLAST

    Sequence similaritiesi

    Belongs to the peptidase S12 family.Curated

    Family and domain databases

    Gene3Di2.40.128.50. 2 hits.
    3.40.710.10. 1 hit.
    HAMAPiMF_01960. D_aminopeptidase.
    InterProiIPR001466. Beta-lactam-related.
    IPR012338. Beta-lactam/transpept-like.
    IPR027279. D_amino_pept/lipop.
    IPR009090. D_amino_pept_B/C.
    IPR023645. DAP.
    IPR012856. DAP_B_dom.
    IPR012857. DAP_C_dom.
    [Graphical view]
    PfamiPF00144. Beta-lactamase. 1 hit.
    PF07930. DAP_B. 1 hit.
    PF07932. DAP_C. 1 hit.
    [Graphical view]
    SUPFAMiSSF50886. SSF50886. 2 hits.
    SSF56601. SSF56601. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    Q9ZBA9-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSKFDTSALE AFVRHIPQNY KGPGGVVAVV KDGEVVLQHA WGFADLRTRT
    60 70 80 90 100
    PMTLDTRMPI CSVSKQFTCA VLLDAVGEPE LLDDALEAYL DKFEDERPAV
    110 120 130 140 150
    RDLCNNQSGL RDYWALSVLC GADPEGVFLP AQAQSLLRRL KTTHFEPGSH
    160 170 180 190 200
    YSYCNGNFRI LADLIEAHTG RTLVDILSER IFAPAGMKRA ELISDTALFD
    210 220 230 240 250
    ECTGYEGDTV RGFLPATNRI QWMGDAGICA SLNDMIAWEQ FIDATRDDES
    260 270 280 290 300
    GLYRRLSGPQ TFKDGVAAPY GFGLNLHETG GKRLTGHGGA LRGWRCQRWH
    310 320 330 340 350
    CADERLSTIA MFNFEGGASE VAFKLMNIAL GVSSSEVSRV EADSAWFGSW
    360 370 380 390 400
    LDDETGLVLS LEDAGHGRMK ARFGTSPEMM DVVSANEARS AVTTIRRDGE
    410 420 430 440 450
    TIELVRASEN LRLSMKRVKG EAKHDIIGRY HSDELDADLL LVSEGGAIYG
    460 470 480 490 500
    AFEGFLGKSD MYPLYSVGSD VWLLPVQRSM DAPSPGEWKL VFRRDDKGEI
    510 520
    TGLSVGCWLA RGVEYRRVQP
    Length:520
    Mass (Da):57,392
    Last modified:January 23, 2007 - v3
    Checksum:iCB364A8061DFBF4A
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M84523 Genomic DNA. Translation: AAA25519.1.
    PIRiA42209.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M84523 Genomic DNA. Translation: AAA25519.1.
    PIRiA42209.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1EI5X-ray1.90A1-520[»]
    ProteinModelPortaliQ9ZBA9.
    SMRiQ9ZBA9. Positions 3-520.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein family/group databases

    MEROPSiS12.002.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Enzyme and pathway databases

    SABIO-RKQ9ZBA9.

    Miscellaneous databases

    EvolutionaryTraceiQ9ZBA9.

    Family and domain databases

    Gene3Di2.40.128.50. 2 hits.
    3.40.710.10. 1 hit.
    HAMAPiMF_01960. D_aminopeptidase.
    InterProiIPR001466. Beta-lactam-related.
    IPR012338. Beta-lactam/transpept-like.
    IPR027279. D_amino_pept/lipop.
    IPR009090. D_amino_pept_B/C.
    IPR023645. DAP.
    IPR012856. DAP_B_dom.
    IPR012857. DAP_C_dom.
    [Graphical view]
    PfamiPF00144. Beta-lactamase. 1 hit.
    PF07930. DAP_B. 1 hit.
    PF07932. DAP_C. 1 hit.
    [Graphical view]
    SUPFAMiSSF50886. SSF50886. 2 hits.
    SSF56601. SSF56601. 1 hit.
    ProtoNetiSearch...

    Publicationsi

    1. "Structural similarity of D-aminopeptidase carboxypeptidase DD and beta-lactamases."
      Asano Y., Kato Y., Yamada A., Kondo K.
      Biochemistry 31:2316-2328(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], MUTAGENESIS OF MET-58; CYS-61; SER-62; LYS-65 AND CYS-69, ENZYME REGULATION.
      Strain: ATCC 49237 / SCRC C1-38.
    2. "Properties of a novel D-stereospecific aminopeptidase from Ochrobactrum anthropi."
      Asano Y., Nakazawa A., Kato Y., Kondo K.
      J. Biol. Chem. 264:14233-14239(1989) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 2-26, SUBUNIT, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES.
      Strain: ATCC 49237 / SCRC C1-38.
    3. "Specificity inversion of Ochrobactrum anthropi D-aminopeptidase to a D,D-carboxypeptidase with new penicillin binding activity by directed mutagenesis."
      Delmarcelle M., Boursoit M.-C., Filee P., Baurin S.L., Frere J.-M., Joris B.
      Protein Sci. 14:2296-2303(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: CATALYTIC ACTIVITY.
    4. "Crystal structure of a D-aminopeptidase from Ochrobactrum anthropi, a new member of the 'penicillin-recognizing enzyme' family."
      Bompard-Gilles C., Remaut H., Villeret V., Prange T., Fanuel L., Delmarcelle M., Joris B., Frere J.-M., Van Beeumen J.
      Structure 8:971-980(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 1-520, PROBABLE ACTIVE SITE.

    Entry informationi

    Entry nameiDAP_OCHAN
    AccessioniPrimary (citable) accession number: Q9ZBA9
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 3, 2006
    Last sequence update: January 23, 2007
    Last modified: May 27, 2015
    This is version 58 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Direct protein sequencing

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. Peptidase families
      Classification of peptidase families and list of entries
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3

    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 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.