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P39045

- DAC_ACTSP

UniProt

P39045 - DAC_ACTSP

Protein

D-alanyl-D-alanine carboxypeptidase

Gene

dac

Organism
Actinomadura sp. (strain R39)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 88 (01 Oct 2014)
      Sequence version 1 (01 Feb 1995)
      Previous versions | rss
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    • Comment

    Functioni

    Removes C-terminal D-alanyl residues from sugar-peptide cell wall precursors.

    Catalytic activityi

    Preferential cleavage: (Ac)(2)-L-Lys-D-Ala-|-D-Ala. Also transpeptidation of peptidyl-alanyl moieties that are N-acyl substituents of D-alanine.

    Enzyme regulationi

    Inhibited by benzylpenicillin, cephaloridine, ampicillin and cetiofur.1 Publication

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei98 – 981Acyl-ester intermediate
    Active sitei101 – 1011Proton acceptor
    Active sitei347 – 3471By similarity
    Binding sitei459 – 4591Substrate

    GO - Molecular functioni

    1. serine-type D-Ala-D-Ala carboxypeptidase activity Source: UniProtKB-EC

    GO - Biological processi

    1. peptidoglycan biosynthetic process Source: UniProtKB-UniPathway
    2. regulation of cell shape Source: UniProtKB-KW
    3. response to antibiotic Source: UniProtKB-KW

    Keywords - Molecular functioni

    Carboxypeptidase, Hydrolase, Protease

    Keywords - Biological processi

    Antibiotic resistance, Cell shape, Cell wall biogenesis/degradation, Peptidoglycan synthesis

    Enzyme and pathway databases

    SABIO-RKP39045.
    UniPathwayiUPA00219.

    Protein family/group databases

    MEROPSiS13.002.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    D-alanyl-D-alanine carboxypeptidase (EC:3.4.16.4)
    Short name:
    DD-carboxypeptidase
    Short name:
    DD-peptidase
    Alternative name(s):
    Penicillin-binding protein
    Short name:
    PBP
    Gene namesi
    Name:dac
    OrganismiActinomadura sp. (strain R39)
    Taxonomic identifieri72570 [NCBI]
    Taxonomic lineageiBacteriaActinobacteriaActinobacteridaeActinomycetalesStreptosporangineaeThermomonosporaceaeActinomadura

    Subcellular locationi

    GO - Cellular componenti

    1. extracellular region Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Secreted

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Signal peptidei1 – 49491 PublicationAdd
    BLAST
    Chaini50 – 515466D-alanyl-D-alanine carboxypeptidasePRO_0000027240Add
    BLAST
    Propeptidei516 – 53823Removed in mature formPRO_0000308945Add
    BLAST

    Interactioni

    Structurei

    Secondary structure

    1
    538
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi51 – 6111
    Helixi65 – 673
    Beta strandi71 – 788
    Turni79 – 813
    Beta strandi84 – 896
    Helixi97 – 993
    Helixi100 – 11112
    Beta strandi117 – 12610
    Beta strandi132 – 1354
    Beta strandi137 – 1415
    Beta strandi145 – 1473
    Helixi149 – 16113
    Beta strandi165 – 1673
    Beta strandi171 – 1744
    Helixi189 – 1913
    Helixi195 – 1973
    Beta strandi205 – 2073
    Turni208 – 2114
    Beta strandi212 – 22110
    Beta strandi230 – 2323
    Helixi234 – 2363
    Turni237 – 2393
    Beta strandi240 – 2445
    Beta strandi247 – 2493
    Beta strandi258 – 2603
    Beta strandi267 – 2759
    Beta strandi281 – 2866
    Helixi290 – 30415
    Beta strandi313 – 3153
    Beta strandi326 – 33510
    Helixi336 – 34611
    Helixi349 – 36416
    Helixi369 – 38214
    Beta strandi395 – 3973
    Beta strandi403 – 4053
    Helixi406 – 41712
    Beta strandi418 – 4214
    Helixi422 – 4287
    Helixi437 – 4404
    Helixi441 – 4433
    Turni451 – 4555
    Beta strandi457 – 4593
    Beta strandi466 – 4738
    Beta strandi480 – 4878
    Beta strandi490 – 4923
    Helixi495 – 50814

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1W79X-ray1.80A/B/C/D50-538[»]
    1W8QX-ray2.85A/B/C/D50-538[»]
    1W8YX-ray2.40A/B/C/D50-538[»]
    2VGJX-ray2.40A/B/C/D50-538[»]
    2VGKX-ray2.25A/B/C/D50-538[»]
    2WKEX-ray2.20A/B/C/D50-515[»]
    2XDMX-ray2.40A/B/C/D50-515[»]
    2XK1X-ray2.80A/B/C/D50-515[»]
    2XLNX-ray2.40A/B/C/D50-538[»]
    2Y4AX-ray2.70A/B/C/D50-515[»]
    2Y55X-ray2.60A/B/C/D50-515[»]
    2Y59X-ray2.50A/B/C/D50-515[»]
    3ZCZX-ray2.60A/B/C/D50-516[»]
    3ZVTX-ray3.10A/B/C/D50-515[»]
    3ZVWX-ray2.00A/B/C/D50-515[»]
    4B4XX-ray2.65A/B/C/D50-515[»]
    4B4ZX-ray2.20A/B/C/D50-515[»]
    4BENX-ray2.15A/B/C/D50-515[»]
    ProteinModelPortaliP39045.
    SMRiP39045. Positions 50-515.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP39045.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni146 – 319174Absent in class-A beta-lactamasesAdd
    BLAST

    Sequence similaritiesi

    Belongs to the peptidase S13 family.Curated

    Keywords - Domaini

    Signal

    Family and domain databases

    Gene3Di3.40.710.10. 2 hits.
    InterProiIPR012338. Beta-lactam/transpept-like.
    IPR000667. Peptidase_S13.
    [Graphical view]
    PfamiPF02113. Peptidase_S13. 1 hit.
    [Graphical view]
    PRINTSiPR00922. DADACBPTASE3.
    SUPFAMiSSF56601. SSF56601. 1 hit.
    TIGRFAMsiTIGR00666. PBP4. 1 hit.

    Sequencei

    Sequence statusi: Complete.

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

    P39045-1 [UniParc]FASTAAdd to Basket

    « Hide

    MKQSSPEPLR PRRTGGRGGA RRAAALVTIP LLPMTLLGAS PALADASGAR    50
    LTELREDIDA ILEDPALEGA VSGVVVVDTA TGEELYSRDG GEQLLPASNM 100
    KLFTAAAALE VLGADHSFGT EVAAESAPGR RGEVQDLYLV GRGDPTLSAE 150
    DLDAMAAEVA ASGVRTVRGD LYADDTWFDS ERLVDDWWPE DEPYAYSAQI 200
    SALTVAHGER FDTGVTEVSV TPAAEGEPAD VDLGAAEGYA ELDNRAVTGA 250
    AGSANTLVID RPVGTNTIAV TGSLPADAAP VTALRTVDEP AALAGHLFEE 300
    ALESNGVTVK GDVGLGGVPA DWQDAEVLAD HTSAELSEIL VPFMKFSNNG 350
    HAEMLVKSIG QETAGAGTWD AGLVGVEEAL SGLGVDTAGL VLNDGSGLSR 400
    GNLVTADTVV DLLGQAGSAP WAQTWSASLP VAGESDPFVG GTLANRMRGT 450
    AAEGVVEAKT GTMSGVSALS GYVPGPEGEL AFSIVNNGHS GPAPLAVQDA 500
    IAVRLAEYAG HQAPEGARMM RGPVQGSGEL ECSWVQAC 538
    Length:538
    Mass (Da):54,974
    Last modified:February 1, 1995 - v1
    Checksum:i58A8300C32802E7B
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti100 – 1012MK → GV AA sequence (PubMed:7305936)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X64790 Genomic DNA. Translation: CAA46023.1.
    PIRiS22409.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X64790 Genomic DNA. Translation: CAA46023.1 .
    PIRi S22409.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1W79 X-ray 1.80 A/B/C/D 50-538 [» ]
    1W8Q X-ray 2.85 A/B/C/D 50-538 [» ]
    1W8Y X-ray 2.40 A/B/C/D 50-538 [» ]
    2VGJ X-ray 2.40 A/B/C/D 50-538 [» ]
    2VGK X-ray 2.25 A/B/C/D 50-538 [» ]
    2WKE X-ray 2.20 A/B/C/D 50-515 [» ]
    2XDM X-ray 2.40 A/B/C/D 50-515 [» ]
    2XK1 X-ray 2.80 A/B/C/D 50-515 [» ]
    2XLN X-ray 2.40 A/B/C/D 50-538 [» ]
    2Y4A X-ray 2.70 A/B/C/D 50-515 [» ]
    2Y55 X-ray 2.60 A/B/C/D 50-515 [» ]
    2Y59 X-ray 2.50 A/B/C/D 50-515 [» ]
    3ZCZ X-ray 2.60 A/B/C/D 50-516 [» ]
    3ZVT X-ray 3.10 A/B/C/D 50-515 [» ]
    3ZVW X-ray 2.00 A/B/C/D 50-515 [» ]
    4B4X X-ray 2.65 A/B/C/D 50-515 [» ]
    4B4Z X-ray 2.20 A/B/C/D 50-515 [» ]
    4BEN X-ray 2.15 A/B/C/D 50-515 [» ]
    ProteinModelPortali P39045.
    SMRi P39045. Positions 50-515.
    ModBasei Search...
    MobiDBi Search...

    Chemistry

    BindingDBi P39045.
    ChEMBLi CHEMBL6016.

    Protein family/group databases

    MEROPSi S13.002.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Enzyme and pathway databases

    UniPathwayi UPA00219 .
    SABIO-RK P39045.

    Miscellaneous databases

    EvolutionaryTracei P39045.

    Family and domain databases

    Gene3Di 3.40.710.10. 2 hits.
    InterProi IPR012338. Beta-lactam/transpept-like.
    IPR000667. Peptidase_S13.
    [Graphical view ]
    Pfami PF02113. Peptidase_S13. 1 hit.
    [Graphical view ]
    PRINTSi PR00922. DADACBPTASE3.
    SUPFAMi SSF56601. SSF56601. 1 hit.
    TIGRFAMsi TIGR00666. PBP4. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "Primary and predicted secondary structures of the Actinomadura R39 extracellular DD-peptidase, a penicillin-binding protein (PBP) related to the Escherichia coli PBP4."
      Granier B., Duez C., Lepage S., Englebert S., Dusart J., Dideberg O., van Beeumen J., Frere J.-M., Ghuysen J.-M.
      Biochem. J. 282:781-788(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 50-87.
    2. "The penicillin-binding site in the exocellular DD-carboxypeptidase-transpeptidase of Actinomadura R39."
      Duez C., Joris B., Frere J.-M., Ghuysen J.-M., van Beeumen J.
      Biochem. J. 193:83-86(1981) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 95-101, SUBSTRATE-BINDING SITE.
    3. "Purification and characterization of PBP4a, a new low-molecular-weight penicillin-binding protein from Bacillus subtilis."
      Duez C., Vanhove M., Gallet X., Bouillenne F., Docquier J.-D., Brans A., Frere J.-M.
      J. Bacteriol. 183:1595-1599(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: ENZYME REGULATION.
    4. "Crystal structure of the Actinomadura R39 DD-peptidase reveals new domains in penicillin-binding proteins."
      Sauvage E., Herman R., Petrella S., Duez C., Bouillenne F., Frere J.-M., Charlier P.
      J. Biol. Chem. 280:31249-31256(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 50-515 OF APOENZYME AND COMPLEX WITH NITROCEFIN, PROCESSING OF C-TERMINUS.

    Entry informationi

    Entry nameiDAC_ACTSP
    AccessioniPrimary (citable) accession number: P39045
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1995
    Last sequence update: February 1, 1995
    Last modified: October 1, 2014
    This is version 88 of the entry and version 1 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. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    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

    External Data

    Dasty 3