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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)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei81 – 811Acyl-ester intermediate
    Active sitei84 – 841Proton acceptor
    Binding sitei174 – 1741Substrate
    Active sitei328 – 3281
    Binding sitei381 – 3811Substrate

    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)LengthDescriptionGraphical viewFeature identifierActions
    Signal peptidei1 – 29291 PublicationAdd
    BLAST
    Chaini30 – 491462D-alanyl-D-alanine carboxypeptidase DacCPRO_0000027243Add
    BLAST

    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

    1
    491
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi35 – 4612Combined sources
    Helixi48 – 503Combined sources
    Beta strandi54 – 618Combined sources
    Turni62 – 643Combined sources
    Beta strandi67 – 726Combined sources
    Helixi80 – 834Combined sources
    Helixi84 – 9512Combined sources
    Beta strandi102 – 1098Combined sources
    Beta strandi112 – 1165Combined sources
    Beta strandi120 – 1245Combined sources
    Helixi132 – 14413Combined sources
    Beta strandi149 – 1524Combined sources
    Beta strandi154 – 1574Combined sources
    Helixi172 – 1743Combined sources
    Helixi178 – 1803Combined sources
    Beta strandi198 – 2047Combined sources
    Beta strandi207 – 2115Combined sources
    Beta strandi214 – 2196Combined sources
    Beta strandi222 – 23312Combined sources
    Beta strandi242 – 2454Combined sources
    Beta strandi249 – 26113Combined sources
    Beta strandi265 – 2706Combined sources
    Helixi274 – 28815Combined sources
    Beta strandi292 – 2954Combined sources
    Beta strandi297 – 2993Combined sources
    Beta strandi306 – 3138Combined sources
    Helixi317 – 32711Combined sources
    Helixi330 – 34415Combined sources
    Helixi350 – 36011Combined sources
    Helixi361 – 3644Combined sources
    Helixi368 – 3703Combined sources
    Beta strandi376 – 3783Combined sources
    Helixi387 – 39711Combined sources
    Helixi403 – 4097Combined sources
    Helixi418 – 4214Combined sources
    Helixi422 – 4243Combined sources
    Beta strandi425 – 4284Combined sources
    Turni432 – 4365Combined sources
    Beta strandi437 – 4448Combined sources
    Beta strandi447 – 4559Combined sources
    Beta strandi457 – 4593Combined sources
    Beta strandi461 – 47010Combined sources
    Helixi474 – 4763Combined sources
    Helixi477 – 48913Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1W5DX-ray2.10A30-491[»]
    2J9PX-ray2.80A/B30-491[»]
    ProteinModelPortaliP39844.
    SMRiP39844. Positions 34-491.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP39844.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni328 – 3303Substrate binding
    Regioni441 – 4455Substrate binding

    Sequence similaritiesi

    Belongs to the peptidase S13 family.Curated

    Keywords - Domaini

    Signal

    Phylogenomic databases

    eggNOGiENOG4107RVU. Bacteria.
    COG2027. LUCA.
    HOGENOMiHOG000253754.
    InParanoidiP39844.
    KOiK07259.
    OMAiAHSKPMK.
    OrthoDBiEOG6NGVQ4.
    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
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1W5DX-ray2.10A30-491[»]
    2J9PX-ray2.80A/B30-491[»]
    ProteinModelPortaliP39844.
    SMRiP39844. Positions 34-491.
    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.
    OrthoDBiEOG6NGVQ4.
    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...

    Publicationsi

    « Hide 'large scale' publications
    1. "A putative new peptide synthase operon in Bacillus subtilis: partial characterization."
      Tognoni A., Franchi E., Magistrelli C., Colombo E., Cosmina P., Grandi G.
      Microbiology 141:645-648(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: 168.
    2. "The complete genome sequence of the Gram-positive bacterium Bacillus subtilis."
      Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V.
      , Caldwell B., Capuano V., Carter N.M., Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J., Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C., Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S., Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B., Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S., Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K., Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E., Yoshikawa H., Danchin A.
      Nature 390:249-256(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: 168.
    3. "Characterization of dacC, which encodes a new low-molecular-weight penicillin-binding protein in Bacillus subtilis."
      Pedersen L.B., Murray T., Popham D.L., Setlow P.
      J. Bacteriol. 180:4967-4973(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 30-34, SUBCELLULAR LOCATION, DEVELOPMENTAL STAGE, INDUCTION.
      Strain: 168 / PS832.
    4. "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: FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, ENZYME REGULATION.
      Strain: 168 / BGSC1A1.
    5. "Crystal structure of the Bacillus subtilis penicillin-binding protein 4a, and its complex with a peptidoglycan mimetic peptide."
      Sauvage E., Duez C., Herman R., Kerff F., Petrella S., Anderson J.W., Adediran S.A., Pratt R.F., Frere J.-M., Charlier P.
      J. Mol. Biol. 371:528-539(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 30-491 OF APOENZYME AND IN COMPLEX WITH SUBSTRATE ANALOG, REACTION MECHANISM.

    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: February 17, 2016
    This is version 111 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.