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Protein

D-alanyl-D-alanine carboxypeptidase DacC

Gene

dacC

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes DD-carboxypeptidase and transpeptidation reactions.1 Publication

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 cephaloridine.1 Publication

Kineticsi

  1. KM=400 µM for N(alpha)-acetyl-L-Lys-D-Ala-D-thiolactate1 Publication
  2. KM=470 µM for benzoyl-Gly-thiogylcolate1 Publication
  3. KM=380 µM for benzoyl-D-Ala-thiogylcolate1 Publication

    pH dependencei

    Optimum pH is 12.1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Active sitei81Acyl-ester intermediate1
    Active sitei84Proton acceptor1
    Binding sitei174Substrate1
    Active sitei3281
    Binding sitei381Substrate1

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Biological processi

    Cell cycle, Cell division, Cell shape, Cell wall biogenesis/degradation, Peptidoglycan synthesis

    Enzyme and pathway databases

    BioCyciBSUB:BSU18350-MONOMER.
    BRENDAi3.4.16.4. 658.
    SABIO-RKP39844.

    Protein family/group databases

    MEROPSiS13.002.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    D-alanyl-D-alanine carboxypeptidase DacC (EC:3.4.16.4)
    Short name:
    DD-carboxypeptidase
    Short name:
    DD-peptidase
    Alternative name(s):
    Penicillin-binding protein 4a
    Short name:
    PBP-4a
    Gene namesi
    Name:dacC
    Synonyms:pbp
    Ordered Locus Names:BSU18350
    OrganismiBacillus subtilis (strain 168)
    Taxonomic identifieri224308 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
    Proteomesi
    • UP000001570 Componenti: Chromosome

    Subcellular locationi

    • Secreted 1 Publication

    • Note: May be anchored in the membrane via a C-terminal amphiphatic alpha helix.

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Secreted

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Signal peptidei1 – 291 PublicationAdd BLAST29
    ChainiPRO_000002724330 – 491D-alanyl-D-alanine carboxypeptidase DacCAdd BLAST462

    Proteomic databases

    PaxDbiP39844.

    Expressioni

    Developmental stagei

    Expression starts at the end of the exponential phase and peaks two hours into sporulation. There is no enzyme activity in spores.1 Publication

    Inductioni

    Expression is sigma H-dependent.1 Publication

    Interactioni

    Protein-protein interaction databases

    STRINGi224308.Bsubs1_010100010111.

    Structurei

    Secondary structure

    1491
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi35 – 46Combined sources12
    Helixi48 – 50Combined sources3
    Beta strandi54 – 61Combined sources8
    Turni62 – 64Combined sources3
    Beta strandi67 – 72Combined sources6
    Helixi80 – 83Combined sources4
    Helixi84 – 95Combined sources12
    Beta strandi102 – 109Combined sources8
    Beta strandi112 – 116Combined sources5
    Beta strandi120 – 124Combined sources5
    Helixi132 – 144Combined sources13
    Beta strandi149 – 152Combined sources4
    Beta strandi154 – 157Combined sources4
    Helixi172 – 174Combined sources3
    Helixi178 – 180Combined sources3
    Beta strandi198 – 204Combined sources7
    Beta strandi207 – 211Combined sources5
    Beta strandi214 – 219Combined sources6
    Beta strandi222 – 233Combined sources12
    Beta strandi242 – 245Combined sources4
    Beta strandi249 – 261Combined sources13
    Beta strandi265 – 270Combined sources6
    Helixi274 – 288Combined sources15
    Beta strandi292 – 295Combined sources4
    Beta strandi297 – 299Combined sources3
    Beta strandi306 – 313Combined sources8
    Helixi317 – 327Combined sources11
    Helixi330 – 344Combined sources15
    Helixi350 – 360Combined sources11
    Helixi361 – 364Combined sources4
    Helixi368 – 370Combined sources3
    Beta strandi376 – 378Combined sources3
    Helixi387 – 397Combined sources11
    Helixi403 – 409Combined sources7
    Helixi418 – 421Combined sources4
    Helixi422 – 424Combined sources3
    Beta strandi425 – 428Combined sources4
    Turni432 – 436Combined sources5
    Beta strandi437 – 444Combined sources8
    Beta strandi447 – 455Combined sources9
    Beta strandi457 – 459Combined sources3
    Beta strandi461 – 470Combined sources10
    Helixi474 – 476Combined sources3
    Helixi477 – 489Combined sources13

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1W5DX-ray2.10A30-491[»]
    2J9PX-ray2.80A/B30-491[»]
    ProteinModelPortaliP39844.
    SMRiP39844.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP39844.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni328 – 330Substrate binding3
    Regioni441 – 445Substrate binding5

    Sequence similaritiesi

    Belongs to the peptidase S13 family.Curated

    Keywords - Domaini

    Signal

    Phylogenomic databases

    eggNOGiENOG4107RVU. Bacteria.
    COG2027. LUCA.
    HOGENOMiHOG000253754.
    InParanoidiP39844.
    KOiK07259.
    OMAiAHSKPMK.
    PhylomeDBiP39844.

    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.

    P39844-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MKKSIKLYVA VLLLFVVASV PYMHQAALAA EKQDALSGQI DKILADHPAL
    60 70 80 90 100
    EGAMAGITVR SAETGAVLYE HSGDTRMRPA SSLKLLTAAA ALSVLGENYS
    110 120 130 140 150
    FTTEVRTDGT LKGKKLNGNL YLKGKGDPTL LPSDFDKMAE ILKHSGVKVI
    160 170 180 190 200
    KGNLIGDDTW HDDMRLSPDM PWSDEYTYYG APISALTASP NEDYDAGTVI
    210 220 230 240 250
    VEVTPNQKEG EEPAVSVSPK TDYITIKNDA KTTAAGSEKD LTIEREHGTN
    260 270 280 290 300
    TITIEGSVPV DANKTKEWIS VWEPAGYALD LFKQSLKKQG ITVKGDIKTG
    310 320 330 340 350
    EAPSSSDVLL SHRSMPLSKL FVPFMKLSNN GHAEVLVKEM GKVKKGEGSW
    360 370 380 390 400
    EKGLEVLNST LPEFGVDSKS LVLRDGSGIS HIDAVSSDQL SQLLYDIQDQ
    410 420 430 440 450
    SWFSAYLNSL PVAGNPDRMV GGTLRNRMKG TPAQGKVRAK TGSLSTVSSL
    460 470 480 490
    SGYAETKSGK KLVFSILLNG LIDEEDGKDI EDQIAVILAN Q
    Length:491
    Mass (Da):52,891
    Last modified:February 1, 1995 - v1
    Checksum:iE442E5A227B7D080
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    Z34883 Genomic DNA. Translation: CAA84366.1.
    AL009126 Genomic DNA. Translation: CAB13718.1.
    PIRiI40455.
    RefSeqiNP_389717.1. NC_000964.3.
    WP_004399303.1. NZ_JNCM01000036.1.

    Genome annotation databases

    EnsemblBacteriaiCAB13718; CAB13718; BSU18350.
    GeneIDi939990.
    KEGGibsu:BSU18350.
    PATRICi18975507. VBIBacSub10457_1945.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    Z34883 Genomic DNA. Translation: CAA84366.1.
    AL009126 Genomic DNA. Translation: CAB13718.1.
    PIRiI40455.
    RefSeqiNP_389717.1. NC_000964.3.
    WP_004399303.1. NZ_JNCM01000036.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1W5DX-ray2.10A30-491[»]
    2J9PX-ray2.80A/B30-491[»]
    ProteinModelPortaliP39844.
    SMRiP39844.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi224308.Bsubs1_010100010111.

    Protein family/group databases

    MEROPSiS13.002.

    Proteomic databases

    PaxDbiP39844.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiCAB13718; CAB13718; BSU18350.
    GeneIDi939990.
    KEGGibsu:BSU18350.
    PATRICi18975507. VBIBacSub10457_1945.

    Phylogenomic databases

    eggNOGiENOG4107RVU. Bacteria.
    COG2027. LUCA.
    HOGENOMiHOG000253754.
    InParanoidiP39844.
    KOiK07259.
    OMAiAHSKPMK.
    PhylomeDBiP39844.

    Enzyme and pathway databases

    BioCyciBSUB:BSU18350-MONOMER.
    BRENDAi3.4.16.4. 658.
    SABIO-RKP39844.

    Miscellaneous databases

    EvolutionaryTraceiP39844.

    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.
    ProtoNetiSearch...

    Entry informationi

    Entry nameiDACC_BACSU
    AccessioniPrimary (citable) accession number: P39844
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1995
    Last sequence update: February 1, 1995
    Last modified: November 2, 2016
    This is version 114 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, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. Bacillus subtilis
      Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
    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.