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P24228

- DACB_ECOLI

UniProt

P24228 - DACB_ECOLI

Protein

D-alanyl-D-alanine carboxypeptidase DacB

Gene

dacB

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 125 (01 Oct 2014)
      Sequence version 2 (01 Nov 1995)
      Previous versions | rss
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    Functioni

    Not involved in transpeptidation but exclusively catalyzes a DD-carboxypeptidase and DD-endopeptidase reaction.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.

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei62 – 621Acyl-ester intermediate
    Active sitei65 – 651Proton acceptorBy similarity
    Active sitei306 – 3061By similarity
    Binding sitei417 – 4171SubstrateBy similarity

    GO - Molecular functioni

    1. carboxypeptidase activity Source: EcoCyc
    2. endopeptidase activity Source: EcoCyc
    3. penicillin binding Source: EcoCyc
    4. protein binding Source: IntAct
    5. serine-type D-Ala-D-Ala carboxypeptidase activity Source: EcoliWiki

    GO - Biological processi

    1. cell wall macromolecule catabolic process Source: EcoCyc
    2. cell wall organization Source: EcoCyc
    3. FtsZ-dependent cytokinesis Source: EcoCyc
    4. peptidoglycan biosynthetic process Source: UniProtKB-UniPathway
    5. peptidoglycan catabolic process Source: EcoCyc
    6. peptidoglycan metabolic process Source: EcoCyc
    7. peptidoglycan turnover Source: EcoCyc
    8. regulation of cell shape Source: EcoCyc
    9. response to antibiotic Source: UniProtKB-KW

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Biological processi

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

    Enzyme and pathway databases

    BioCyciEcoCyc:EG10202-MONOMER.
    ECOL316407:JW3149-MONOMER.
    MetaCyc:EG10202-MONOMER.
    BRENDAi3.4.17.14. 2026.
    UniPathwayiUPA00219.

    Protein family/group databases

    MEROPSiS13.001.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    D-alanyl-D-alanine carboxypeptidase DacB (EC:3.4.16.4)
    Short name:
    DD-carboxypeptidase
    Short name:
    DD-peptidase
    Alternative name(s):
    D-alanyl-D-alanine endopeptidase (EC:3.4.21.-)
    Short name:
    DD-endopeptidase
    Penicillin-binding protein 4
    Short name:
    PBP-4
    Gene namesi
    Name:dacB
    Ordered Locus Names:b3182, JW3149
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG10202. dacB.

    Subcellular locationi

    Periplasm Curated

    GO - Cellular componenti

    1. outer membrane-bounded periplasmic space Source: EcoliWiki

    Keywords - Cellular componenti

    Periplasm

    Pathology & Biotechi

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Signal peptidei1 – 20201 PublicationAdd
    BLAST
    Chaini21 – 477457D-alanyl-D-alanine carboxypeptidase DacBPRO_0000027241Add
    BLAST

    Proteomic databases

    PaxDbiP24228.
    PRIDEiP24228.

    Expressioni

    Gene expression databases

    GenevestigatoriP24228.

    Interactioni

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    argGP0A6E42EBI-1131834,EBI-1120296

    Protein-protein interaction databases

    IntActiP24228. 1 interaction.
    STRINGi511145.b3182.

    Structurei

    Secondary structure

    1
    477
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi23 – 275
    Beta strandi35 – 428
    Beta strandi49 – 535
    Helixi61 – 633
    Helixi64 – 7512
    Beta strandi83 – 9311
    Beta strandi96 – 1049
    Helixi113 – 12513
    Beta strandi130 – 1334
    Beta strandi135 – 1384
    Helixi153 – 1553
    Helixi159 – 1613
    Helixi170 – 1723
    Beta strandi173 – 1797
    Beta strandi189 – 1913
    Beta strandi199 – 2079
    Beta strandi209 – 2113
    Turni213 – 2164
    Beta strandi219 – 2246
    Helixi225 – 2273
    Beta strandi228 – 2369
    Beta strandi242 – 2476
    Helixi251 – 26515
    Beta strandi269 – 2724
    Beta strandi274 – 2774
    Beta strandi285 – 2917
    Helixi295 – 30511
    Helixi308 – 32316
    Helixi329 – 34214
    Beta strandi356 – 3583
    Helixi367 – 37913
    Helixi381 – 3844
    Helixi387 – 3893
    Turni393 – 3953
    Helixi397 – 3993
    Helixi403 – 4075
    Turni411 – 4133
    Beta strandi414 – 4218
    Beta strandi424 – 4329
    Beta strandi438 – 44710
    Helixi452 – 4543
    Turni455 – 4573
    Helixi460 – 47516

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2EX2X-ray1.55A21-477[»]
    2EX6X-ray1.60A21-477[»]
    2EX8X-ray1.60A21-477[»]
    2EX9X-ray1.65A21-477[»]
    2EXAX-ray1.70A21-477[»]
    2EXBX-ray1.75A21-477[»]
    ProteinModelPortaliP24228.
    SMRiP24228. Positions 22-477.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP24228.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni90 – 263174Absent in class-A beta-lactamasesAdd
    BLAST

    Sequence similaritiesi

    Belongs to the peptidase S13 family.Curated

    Keywords - Domaini

    Signal

    Phylogenomic databases

    eggNOGiCOG2027.
    HOGENOMiHOG000279266.
    KOiK07259.
    OMAiFRTIGHE.
    OrthoDBiEOG6NGVQ4.
    PhylomeDBiP24228.

    Family and domain databases

    Gene3Di3.40.710.10. 1 hit.
    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.

    P24228-1 [UniParc]FASTAAdd to Basket

    « Hide

    MRFSRFIIGL TSCIAFSVQA ANVDEYITQL PAGANLALMV QKVGASAPAI    50
    DYHSQQMALP ASTQKVITAL AALIQLGPDF RFTTTLETKG NVENGVLKGD 100
    LVARFGADPT LKRQDIRNMV ATLKKSGVNQ IDGNVLIDTS IFASHDKAPG 150
    WPWNDMTQCF SAPPAAAIVD RNCFSVSLYS APKPGDMAFI RVASYYPVTM 200
    FSQVRTLPRG SAEAQYCELD VVPGDLNRFT LTGCLPQRSE PLPLAFAVQD 250
    GASYAGAILK DELKQAGITW SGTLLRQTQV NEPGTVVASK QSAPLHDLLK 300
    IMLKKSDNMI ADTVFRMIGH ARFNVPGTWR AGSDAVRQIL RQQAGVDIGN 350
    TIIADGSGLS RHNLIAPATM MQVLQYIAQH DNELNFISML PLAGYDGSLQ 400
    YRAGLHQAGV DGKVSAKTGS LQGVYNLAGF ITTASGQRMA FVQYLSGYAV 450
    EPADQRNRRI PLVRFESRLY KDIYQNN 477
    Length:477
    Mass (Da):51,798
    Last modified:November 1, 1995 - v2
    Checksum:i4EF5E43D2BEC4E5B
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti261 – 2611D → Y(PubMed:16411754)Curated
    Sequence conflicti427 – 4271L → Q in CAA42643. (PubMed:2040429)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X59460 Genomic DNA. Translation: CAA42070.1.
    X60038 Genomic DNA. Translation: CAA42643.1.
    U01376 Genomic DNA. Translation: AAA97505.1.
    U18997 Genomic DNA. Translation: AAA57983.1.
    U00096 Genomic DNA. Translation: AAC76214.1.
    AP009048 Genomic DNA. Translation: BAE77226.1.
    PIRiA54535.
    RefSeqiNP_417649.1. NC_000913.3.
    YP_491367.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC76214; AAC76214; b3182.
    BAE77226; BAE77226; BAE77226.
    GeneIDi12933443.
    947693.
    KEGGiecj:Y75_p3102.
    eco:b3182.
    PATRICi32121782. VBIEscCol129921_3275.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X59460 Genomic DNA. Translation: CAA42070.1 .
    X60038 Genomic DNA. Translation: CAA42643.1 .
    U01376 Genomic DNA. Translation: AAA97505.1 .
    U18997 Genomic DNA. Translation: AAA57983.1 .
    U00096 Genomic DNA. Translation: AAC76214.1 .
    AP009048 Genomic DNA. Translation: BAE77226.1 .
    PIRi A54535.
    RefSeqi NP_417649.1. NC_000913.3.
    YP_491367.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2EX2 X-ray 1.55 A 21-477 [» ]
    2EX6 X-ray 1.60 A 21-477 [» ]
    2EX8 X-ray 1.60 A 21-477 [» ]
    2EX9 X-ray 1.65 A 21-477 [» ]
    2EXA X-ray 1.70 A 21-477 [» ]
    2EXB X-ray 1.75 A 21-477 [» ]
    ProteinModelPortali P24228.
    SMRi P24228. Positions 22-477.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    IntActi P24228. 1 interaction.
    STRINGi 511145.b3182.

    Chemistry

    ChEMBLi CHEMBL2354204.
    DrugBanki DB00303. Ertapenem.
    DB00760. Meropenem.

    Protein family/group databases

    MEROPSi S13.001.

    Proteomic databases

    PaxDbi P24228.
    PRIDEi P24228.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC76214 ; AAC76214 ; b3182 .
    BAE77226 ; BAE77226 ; BAE77226 .
    GeneIDi 12933443.
    947693.
    KEGGi ecj:Y75_p3102.
    eco:b3182.
    PATRICi 32121782. VBIEscCol129921_3275.

    Organism-specific databases

    EchoBASEi EB0198.
    EcoGenei EG10202. dacB.

    Phylogenomic databases

    eggNOGi COG2027.
    HOGENOMi HOG000279266.
    KOi K07259.
    OMAi FRTIGHE.
    OrthoDBi EOG6NGVQ4.
    PhylomeDBi P24228.

    Enzyme and pathway databases

    UniPathwayi UPA00219 .
    BioCyci EcoCyc:EG10202-MONOMER.
    ECOL316407:JW3149-MONOMER.
    MetaCyc:EG10202-MONOMER.
    BRENDAi 3.4.17.14. 2026.

    Miscellaneous databases

    EvolutionaryTracei P24228.
    PROi P24228.

    Gene expression databases

    Genevestigatori P24228.

    Family and domain databases

    Gene3Di 3.40.710.10. 1 hit.
    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. "Penicillin-binding protein 4 of Escherichia coli shows a novel type of primary structure among penicillin-interacting proteins."
      Mottl H., Terpstra P., Keck W.
      FEMS Microbiol. Lett. 62:213-220(1991) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 21-31.
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    2. Wang R., Kushner S.R.
      Submitted (SEP-1993) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: K12.
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    4. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
      Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
      Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    5. "Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, both in the native form and covalently linked to various antibiotics."
      Kishida H., Unzai S., Roper D.I., Lloyd A., Park S.-Y., Tame J.R.H.
      Biochemistry 45:783-792(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: PARTIAL NUCLEOTIDE SEQUENCE [GENOMIC DNA], X-RAY CRYSTALLOGRAPHY (1.55 ANGSTROMS) OF 21-477 OF APOENZYME AND IN COMPLEX WITH PENICILLIN ANTIBIOTICS.
      Strain: K12.
    6. "Penicillin-binding protein 4 of Escherichia coli: molecular cloning of the dacB gene, controlled overexpression, and alterations in murein composition."
      Korat B., Mottl H., Keck W.
      Mol. Microbiol. 5:675-684(1991) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.

    Entry informationi

    Entry nameiDACB_ECOLI
    AccessioniPrimary (citable) accession number: P24228
    Secondary accession number(s): Q2M930
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: March 1, 1992
    Last sequence update: November 1, 1995
    Last modified: October 1, 2014
    This is version 125 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    In E.coli there are three murein endopeptidases: two are penicillin sensitive (DacB and PbpG), the other (MepA) not.

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. Peptidase families
      Classification of peptidase families and list of entries
    5. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3