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P15555

- DAC_STRSR

UniProt

P15555 - DAC_STRSR

Protein

D-alanyl-D-alanine carboxypeptidase

Gene
N/A
Organism
Streptomyces sp. (strain R61)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 98 (01 Oct 2014)
      Sequence version 2 (01 Feb 1996)
      Previous versions | rss
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    Functioni

    Catalyzes distinct carboxypeptidation and transpeptidation reactions during the last stages of wall peptidoglycan synthesis. Mistaking a beta-lactam antibiotic molecule for a normal substrate (i.e. a D-alanyl-D-alanine-terminated peptide), it becomes immobilized in the form of a long-lived, serine-ester-linked acyl enzyme and thus behave as penicillin-binding protein (PBP).

    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.

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei93 – 931Acyl-ester intermediate
    Binding sitei316 – 3161Substrate

    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

    Keywords - Molecular functioni

    Carboxypeptidase, Hydrolase, Protease

    Keywords - Biological processi

    Cell shape, Cell wall biogenesis/degradation, Peptidoglycan synthesis

    Enzyme and pathway databases

    UniPathwayiUPA00219.

    Protein family/group databases

    MEROPSiS12.001.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    D-alanyl-D-alanine carboxypeptidase (EC:3.4.16.4)
    Short name:
    DD-carboxypeptidase
    Short name:
    DD-peptidase
    OrganismiStreptomyces sp. (strain R61)
    Taxonomic identifieri31952 [NCBI]
    Taxonomic lineageiBacteriaActinobacteriaActinobacteridaeActinomycetalesStreptomycineaeStreptomycetaceaeStreptomyces

    Subcellular locationi

    GO - Cellular componenti

    1. extracellular region Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Secreted

    Pathology & Biotechi

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Signal peptidei1 – 3131Add
    BLAST
    Chaini32 – 380349D-alanyl-D-alanine carboxypeptidasePRO_0000017050Add
    BLAST
    Propeptidei381 – 40626PRO_0000017051Add
    BLAST

    Structurei

    Secondary structure

    1
    406
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi39 – 5113
    Beta strandi55 – 639
    Beta strandi66 – 7510
    Turni77 – 793
    Beta strandi88 – 903
    Helixi92 – 943
    Helixi95 – 10814
    Helixi118 – 1214
    Beta strandi125 – 1273
    Helixi133 – 1375
    Helixi147 – 1504
    Beta strandi151 – 1533
    Helixi154 – 1618
    Helixi168 – 1769
    Beta strandi181 – 1833
    Helixi192 – 20615
    Helixi210 – 2178
    Turni218 – 2236
    Beta strandi238 – 2403
    Turni263 – 2653
    Helixi266 – 2683
    Helixi275 – 28612
    Helixi293 – 2997
    Beta strandi303 – 3064
    Beta strandi309 – 3113
    Beta strandi316 – 3194
    Beta strandi325 – 3339
    Beta strandi336 – 3427
    Beta strandi346 – 35813
    Helixi360 – 37415

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1CEFX-ray2.04A32-380[»]
    1CEGX-ray1.80A32-380[»]
    1HVBX-ray1.17A32-380[»]
    1IKGX-ray1.90A32-380[»]
    1IKIX-ray1.25A32-380[»]
    1MPLX-ray1.12A32-380[»]
    1PW1X-ray1.20A32-380[»]
    1PW8X-ray1.30A32-380[»]
    1PWCX-ray1.10A32-380[»]
    1PWDX-ray1.20A32-380[»]
    1PWGX-ray1.07A32-380[»]
    1SCWX-ray1.13A32-380[»]
    1SDEX-ray1.15A32-378[»]
    1YQSX-ray1.05A32-380[»]
    2PTEmodel-E32-380[»]
    3PTEX-ray1.60A32-380[»]
    ProteinModelPortaliP15555.
    SMRiP15555. Positions 32-378.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP15555.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni151 – 1544Substrate binding
    Regioni190 – 1923Substrate binding
    Regioni330 – 3323Substrate binding
    Regioni357 – 3582Substrate binding

    Sequence similaritiesi

    Belongs to the peptidase S12 family.Curated

    Keywords - Domaini

    Signal

    Family and domain databases

    Gene3Di3.40.710.10. 1 hit.
    InterProiIPR001466. Beta-lactam-related.
    IPR012338. Beta-lactam/transpept-like.
    [Graphical view]
    PfamiPF00144. Beta-lactamase. 1 hit.
    [Graphical view]
    SUPFAMiSSF56601. SSF56601. 1 hit.

    Sequencei

    Sequence statusi: Complete.

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

    P15555-1 [UniParc]FASTAAdd to Basket

    « Hide

    MVSGTVGRGT ALGAVLLALL AVPAQAGTAA AADLPAPDDT GLQAVLHTAL    50
    SQGAPGAMVR VDDNGTIHQL SEGVADRATG RAITTTDRFR VGSVTKSFSA 100
    VVLLQLVDEG KLDLDASVNT YLPGLLPDDR ITVRQVMSHR SGLYDYTNDM 150
    FAQTVPGFES VRNKVFSYQD LITLSLKHGV TNAPGAAYSY SNTNFVVAGM 200
    LIEKLTGHSV ATEYQNRIFT PLNLTDTFYV HPDTVIPGTH ANGYLTPDEA 250
    GGALVDSTEQ TVSWAQSAGA VISSTQDLDT FFSALMSGQL MSAAQLAQMQ 300
    QWTTVNSTQG YGLGLRRRDL SCGISVYGHT GTVQGYYTYA FASKDGKRSV 350
    TALANTSNNV NVLNTMARTL ESAFCGKPTT AKLRSATSSA TTVERHEDIA 400
    PGIARD 406
    Length:406
    Mass (Da):42,917
    Last modified:February 1, 1996 - v2
    Checksum:iC2C77B53A29099E9
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X05109 Genomic DNA. Translation: CAA28756.1.
    X55810 Genomic DNA. Translation: CAB97254.1.
    PIRiS48220.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X05109 Genomic DNA. Translation: CAA28756.1 .
    X55810 Genomic DNA. Translation: CAB97254.1 .
    PIRi S48220.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1CEF X-ray 2.04 A 32-380 [» ]
    1CEG X-ray 1.80 A 32-380 [» ]
    1HVB X-ray 1.17 A 32-380 [» ]
    1IKG X-ray 1.90 A 32-380 [» ]
    1IKI X-ray 1.25 A 32-380 [» ]
    1MPL X-ray 1.12 A 32-380 [» ]
    1PW1 X-ray 1.20 A 32-380 [» ]
    1PW8 X-ray 1.30 A 32-380 [» ]
    1PWC X-ray 1.10 A 32-380 [» ]
    1PWD X-ray 1.20 A 32-380 [» ]
    1PWG X-ray 1.07 A 32-380 [» ]
    1SCW X-ray 1.13 A 32-380 [» ]
    1SDE X-ray 1.15 A 32-378 [» ]
    1YQS X-ray 1.05 A 32-380 [» ]
    2PTE model - E 32-380 [» ]
    3PTE X-ray 1.60 A 32-380 [» ]
    ProteinModelPortali P15555.
    SMRi P15555. Positions 32-378.
    ModBasei Search...
    MobiDBi Search...

    Chemistry

    ChEMBLi CHEMBL3350.
    DrugBanki DB00456. Cefalotin.

    Protein family/group databases

    MEROPSi S12.001.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Enzyme and pathway databases

    UniPathwayi UPA00219 .

    Miscellaneous databases

    EvolutionaryTracei P15555.

    Family and domain databases

    Gene3Di 3.40.710.10. 1 hit.
    InterProi IPR001466. Beta-lactam-related.
    IPR012338. Beta-lactam/transpept-like.
    [Graphical view ]
    Pfami PF00144. Beta-lactamase. 1 hit.
    [Graphical view ]
    SUPFAMi SSF56601. SSF56601. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "Primary structure of the Streptomyces R61 extracellular DD-peptidase. 1. Cloning into Streptomyces lividans and nucleotide sequence of the gene."
      Duez C., Piron-Fraipont C., Joris B., Dusart J., Urdea M.S., Martial J.A., Frere J.-M., Ghuysen J.-M.
      Eur. J. Biochem. 162:509-518(1987) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "Primary structure of the Streptomyces R61 extracellular DD-peptidase. 1. Cloning into Streptomyces lividans and nucleotide sequence of the gene."
      Duez C., Piron-Fraipont C., Joris B., Dusart J., Urdea M.S., Martial J.A., Frere J.-M., Ghuysen J.-M.
      Eur. J. Biochem. 224:1079-1079(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], SEQUENCE REVISION.
    3. "Primary structure of the Streptomyces R61 extracellular DD-peptidase. 2. Amino acid sequence data."
      Joris B., Jacques P., Frere J.-M., Ghuysen J.-M., van Beeumen J.
      Eur. J. Biochem. 162:519-524(1987) [PubMed] [Europe PMC] [Abstract]
      Cited for: PARTIAL PROTEIN SEQUENCE.
    4. "Transcriptional analysis of the DD-peptidase/penicillin-binding protein-encoding dac gene of Streptomyces R61: use of the promoter and signal sequences in a secretion vector."
      Piron-Fraipont C., Lenzini M.V., Dusart J., Ghuysen J.-M.
      Mol. Gen. Genet. 223:114-120(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-91.
    5. "Different modes of vancomycin and D-alanyl-D-alanine peptidase binding to cell wall peptide and a possible role for the vancomycin resistance protein."
      Knox J.R., Pratt R.F.
      Antimicrob. Agents Chemother. 34:1342-1347(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: 3D-STRUCTURE MODELING.
    6. "2.8-A structure of penicillin-sensitive D-alanyl carboxypeptidase-transpeptidase from Streptomyces R61 and complexes with beta-lactams."
      Kelly J.A., Knox J.R., Moews P.C., Hite G.J., Bartolone J.B., Zhao H., Joris B., Frere J.-M., Ghuysen J.-M.
      J. Biol. Chem. 260:6449-6458(1985) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS).
    7. "The refined crystallographic structure of a DD-peptidase penicillin-target enzyme at 1.6-A resolution."
      Kelly J.A., Kuzin A.P.
      J. Mol. Biol. 254:223-236(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS).
    8. "Structures of two kinetic intermediates reveal species specificity of penicillin-binding proteins."
      McDonough M.A., Anderson J.W., Silvaggi N.R., Pratt R.F., Knox J.R., Kelly J.A.
      J. Mol. Biol. 322:111-122(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.25 ANGSTROMS) OF 32-380 IN COMPLEX WITH SUBSTRATES.
    9. "The crystal structure of phosphonate-inhibited D-Ala-D-Ala peptidase reveals an analogue of a tetrahedral transition state."
      Silvaggi N.R., Anderson J.W., Brinsmade S.R., Pratt R.F., Kelly J.A.
      Biochemistry 42:1199-1208(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.12 ANGSTROMS) OF 32-380 IN COMPLEX WITH SUBSTRATES.
    10. "Crystal structures of complexes between the R61 DD-peptidase and peptidoglycan-mimetic beta-lactams: a non-covalent complex with a 'perfect penicillin'."
      Silvaggi N.R., Josephine H.R., Kuzin A.P., Nagarajan R., Pratt R.F., Kelly J.A.
      J. Mol. Biol. 345:521-533(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.07 ANGSTROMS) OF 32-380 IN COMPLEX WITH SUBSTRATE ANALOG.

    Entry informationi

    Entry nameiDAC_STRSR
    AccessioniPrimary (citable) accession number: P15555
    Secondary accession number(s): Q06656
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 1, 1990
    Last sequence update: February 1, 1996
    Last modified: October 1, 2014
    This is version 98 of the entry and version 2 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