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P0AEB2

- DACA_ECOLI

UniProt

P0AEB2 - DACA_ECOLI

Protein

D-alanyl-D-alanine carboxypeptidase DacA

Gene

dacA

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 94 (01 Oct 2014)
      Sequence version 1 (20 Mar 1987)
      Previous versions | rss
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    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.
    A beta-lactam + H2O = a substituted beta-amino acid.

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei73 – 731Acyl-ester intermediate
    Active sitei76 – 761Proton acceptor
    Active sitei139 – 1391
    Binding sitei242 – 2421Substrate

    GO - Molecular functioni

    1. beta-lactamase activity Source: UniProtKB-EC
    2. carboxypeptidase activity Source: EcoCyc
    3. penicillin binding Source: EcoCyc
    4. serine-type D-Ala-D-Ala carboxypeptidase activity Source: CACAO

    GO - Biological processi

    1. cell division Source: EcoCyc
    2. cell wall macromolecule metabolic process Source: EcoCyc
    3. peptidoglycan biosynthetic process Source: UniProtKB-UniPathway
    4. peptidoglycan metabolic process Source: EcoCyc
    5. regulation of cell shape Source: EcoCyc

    Keywords - Molecular functioni

    Carboxypeptidase, Hydrolase, Protease

    Keywords - Biological processi

    Cell shape, Cell wall biogenesis/degradation, Peptidoglycan synthesis

    Enzyme and pathway databases

    BioCyciEcoCyc:EG10201-MONOMER.
    ECOL316407:JW0627-MONOMER.
    MetaCyc:EG10201-MONOMER.
    UniPathwayiUPA00219.

    Protein family/group databases

    MEROPSiS11.008.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    D-alanyl-D-alanine carboxypeptidase DacA (EC:3.4.16.4)
    Short name:
    DD-carboxypeptidase
    Short name:
    DD-peptidase
    Alternative name(s):
    Beta-lactamase (EC:3.5.2.6)
    Penicillin-binding protein 5
    Short name:
    PBP-5
    Gene namesi
    Name:dacA
    Synonyms:pfv
    Ordered Locus Names:b0632, JW0627
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG10201. dacA.

    Subcellular locationi

    Cell inner membrane; Peripheral membrane protein; Cytoplasmic side
    Note: N-terminal lies in the periplasmic space.

    GO - Cellular componenti

    1. integral component of plasma membrane Source: EcoliWiki

    Keywords - Cellular componenti

    Cell inner membrane, Cell membrane, Membrane

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi101 – 12121Missing: Complete loss of enzyme activity. No effect on penicillin binding. 1 PublicationAdd
    BLAST
    Mutagenesisi213 – 2131K → R: Complete loss of enzyme activity. No effect on penicillin binding. 2 Publications
    Mutagenesisi213 – 2131K → X: Complete loss of activity. 2 Publications

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Signal peptidei1 – 29291 PublicationAdd
    BLAST
    Chaini30 – 403374D-alanyl-D-alanine carboxypeptidase DacAPRO_0000027231Add
    BLAST

    Proteomic databases

    PaxDbiP0AEB2.
    PRIDEiP0AEB2.

    PTM databases

    PhosSiteiP0809377.

    Expressioni

    Gene expression databases

    GenevestigatoriP0AEB2.

    Interactioni

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    yfaYP778081EBI-548634,EBI-556720

    Protein-protein interaction databases

    DIPiDIP-47947N.
    IntActiP0AEB2. 8 interactions.
    MINTiMINT-1247273.
    STRINGi511145.b0632.

    Structurei

    Secondary structure

    1
    403
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Turni33 – 353
    Beta strandi46 – 538
    Turni54 – 563
    Beta strandi59 – 646
    Helixi72 – 743
    Helixi75 – 8814
    Beta strandi97 – 993
    Helixi102 – 1043
    Helixi106 – 1083
    Helixi110 – 1123
    Beta strandi125 – 1273
    Helixi128 – 1369
    Helixi141 – 15212
    Helixi155 – 16814
    Beta strandi179 – 1835
    Helixi191 – 20414
    Helixi206 – 2094
    Helixi210 – 2134
    Beta strandi216 – 2194
    Beta strandi222 – 2254
    Helixi229 – 2324
    Beta strandi236 – 24611
    Turni247 – 2493
    Beta strandi250 – 25910
    Beta strandi262 – 27110
    Helixi274 – 2763
    Helixi279 – 29113
    Beta strandi292 – 2987
    Beta strandi304 – 32017
    Beta strandi325 – 3306
    Helixi334 – 3363
    Beta strandi338 – 35013
    Beta strandi357 – 3659
    Beta strandi368 – 37912

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1HD8X-ray2.30A30-386[»]
    1NJ4X-ray1.90A30-392[»]
    1NZOX-ray1.85A30-392[»]
    1NZUX-ray2.00A30-392[»]
    1SDNX-ray2.50A30-392[»]
    1Z6FX-ray1.60A30-392[»]
    3BEBX-ray2.00A30-386[»]
    3BECX-ray1.60A30-386[»]
    3MZDX-ray1.90A30-386[»]
    3MZEX-ray2.10A30-386[»]
    3MZFX-ray1.50A30-386[»]
    ProteinModelPortaliP0AEB2.
    SMRiP0AEB2. Positions 32-386.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP0AEB2.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the peptidase S11 family.Curated

    Keywords - Domaini

    Signal

    Phylogenomic databases

    eggNOGiCOG1686.
    HOGENOMiHOG000086623.
    KOiK07258.
    OMAiYVIGQAV.
    OrthoDBiEOG6RJV2H.
    PhylomeDBiP0AEB2.

    Family and domain databases

    Gene3Di2.60.410.10. 1 hit.
    3.40.710.10. 1 hit.
    InterProiIPR012338. Beta-lactam/transpept-like.
    IPR015956. Peniciliin-bd_prot-assoc.
    IPR018044. Peptidase_S11.
    IPR012907. Peptidase_S11_C.
    IPR001967. Peptidase_S11_N.
    [Graphical view]
    PfamiPF07943. PBP5_C. 1 hit.
    PF00768. Peptidase_S11. 1 hit.
    [Graphical view]
    PRINTSiPR00725. DADACBPTASE1.
    SMARTiSM00936. PBP5_C. 1 hit.
    [Graphical view]
    SUPFAMiSSF56601. SSF56601. 1 hit.
    SSF69189. SSF69189. 1 hit.

    Sequencei

    Sequence statusi: Complete.

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

    P0AEB2-1 [UniParc]FASTAAdd to Basket

    « Hide

    MNTIFSARIM KRLALTTALC TAFISAAHAD DLNIKTMIPG VPQIDAESYI    50
    LIDYNSGKVL AEQNADVRRD PASLTKMMTS YVIGQAMKAG KFKETDLVTI 100
    GNDAWATGNP VFKGSSLMFL KPGMQVPVSQ LIRGINLQSG NDACVAMADF 150
    AAGSQDAFVG LMNSYVNALG LKNTHFQTVH GLDADGQYSS ARDMALIGQA 200
    LIRDVPNEYS IYKEKEFTFN GIRQLNRNGL LWDNSLNVDG IKTGHTDKAG 250
    YNLVASATEG QMRLISAVMG GRTFKGREAE SKKLLTWGFR FFETVNPLKV 300
    GKEFASEPVW FGDSDRASLG VDKDVYLTIP RGRMKDLKAS YVLNSSELHA 350
    PLQKNQVVGT INFQLDGKTI EQRPLVVLQE IPEGNFFGKI IDYIKLMFHH 400
    WFG 403
    Length:403
    Mass (Da):44,444
    Last modified:March 20, 1987 - v1
    Checksum:i7FAAB8E98452FF22
    GO

    Sequence cautioni

    The sequence AAB40832.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti134 – 1341G → D in mutant dacA11191; inactive but still binds penicillin. Blocked in the release of the bound penicilloyl moiety; the mutant also fails to catalyze the D-alanine carboxypeptidase reaction as the hydrolysis of the acyl-enzyme formed with substrate is also blocked and the acyl-enzyme accumulates.

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X06479 Genomic DNA. Translation: CAA29774.1.
    M18276 Genomic DNA. Translation: AAA24553.1.
    U82598 Genomic DNA. Translation: AAB40832.1. Different initiation.
    U00096 Genomic DNA. Translation: AAC73733.1.
    AP009048 Genomic DNA. Translation: BAA35275.1.
    L07636 Genomic DNA. Translation: AAA66340.1.
    PIRiA28536. ZPECP5.
    RefSeqiNP_415165.1. NC_000913.3.
    YP_488923.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC73733; AAC73733; b0632.
    BAA35275; BAA35275; BAA35275.
    GeneIDi12931704.
    945222.
    KEGGiecj:Y75_p0622.
    eco:b0632.
    PATRICi32116445. VBIEscCol129921_0662.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X06479 Genomic DNA. Translation: CAA29774.1 .
    M18276 Genomic DNA. Translation: AAA24553.1 .
    U82598 Genomic DNA. Translation: AAB40832.1 . Different initiation.
    U00096 Genomic DNA. Translation: AAC73733.1 .
    AP009048 Genomic DNA. Translation: BAA35275.1 .
    L07636 Genomic DNA. Translation: AAA66340.1 .
    PIRi A28536. ZPECP5.
    RefSeqi NP_415165.1. NC_000913.3.
    YP_488923.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1HD8 X-ray 2.30 A 30-386 [» ]
    1NJ4 X-ray 1.90 A 30-392 [» ]
    1NZO X-ray 1.85 A 30-392 [» ]
    1NZU X-ray 2.00 A 30-392 [» ]
    1SDN X-ray 2.50 A 30-392 [» ]
    1Z6F X-ray 1.60 A 30-392 [» ]
    3BEB X-ray 2.00 A 30-386 [» ]
    3BEC X-ray 1.60 A 30-386 [» ]
    3MZD X-ray 1.90 A 30-386 [» ]
    3MZE X-ray 2.10 A 30-386 [» ]
    3MZF X-ray 1.50 A 30-386 [» ]
    ProteinModelPortali P0AEB2.
    SMRi P0AEB2. Positions 32-386.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-47947N.
    IntActi P0AEB2. 8 interactions.
    MINTi MINT-1247273.
    STRINGi 511145.b0632.

    Chemistry

    ChEMBLi CHEMBL2354204.

    Protein family/group databases

    MEROPSi S11.008.

    PTM databases

    PhosSitei P0809377.

    Proteomic databases

    PaxDbi P0AEB2.
    PRIDEi P0AEB2.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC73733 ; AAC73733 ; b0632 .
    BAA35275 ; BAA35275 ; BAA35275 .
    GeneIDi 12931704.
    945222.
    KEGGi ecj:Y75_p0622.
    eco:b0632.
    PATRICi 32116445. VBIEscCol129921_0662.

    Organism-specific databases

    EchoBASEi EB0197.
    EcoGenei EG10201. dacA.

    Phylogenomic databases

    eggNOGi COG1686.
    HOGENOMi HOG000086623.
    KOi K07258.
    OMAi YVIGQAV.
    OrthoDBi EOG6RJV2H.
    PhylomeDBi P0AEB2.

    Enzyme and pathway databases

    UniPathwayi UPA00219 .
    BioCyci EcoCyc:EG10201-MONOMER.
    ECOL316407:JW0627-MONOMER.
    MetaCyc:EG10201-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P0AEB2.
    PROi P0AEB2.

    Gene expression databases

    Genevestigatori P0AEB2.

    Family and domain databases

    Gene3Di 2.60.410.10. 1 hit.
    3.40.710.10. 1 hit.
    InterProi IPR012338. Beta-lactam/transpept-like.
    IPR015956. Peniciliin-bd_prot-assoc.
    IPR018044. Peptidase_S11.
    IPR012907. Peptidase_S11_C.
    IPR001967. Peptidase_S11_N.
    [Graphical view ]
    Pfami PF07943. PBP5_C. 1 hit.
    PF00768. Peptidase_S11. 1 hit.
    [Graphical view ]
    PRINTSi PR00725. DADACBPTASE1.
    SMARTi SM00936. PBP5_C. 1 hit.
    [Graphical view ]
    SUPFAMi SSF56601. SSF56601. 1 hit.
    SSF69189. SSF69189. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. Broome-Smith J.K.
      Submitted (APR-1984) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "Nucleotide sequences of the penicillin-binding protein 5 and 6 genes of Escherichia coli."
      Broome-Smith J.K., Ioannidis I., Edelman A., Spratt B.G.
      Nucleic Acids Res. 16:1617-1617(1988) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: K12.
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    4. "Sequence of minutes 4-25 of Escherichia coli."
      Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M., Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D., Namath A., Oefner P., Roberts D., Schramm S., Davis R.W.
      Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    5. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    6. "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.
    7. "An amino acid substitution that blocks the deacylation step in the enzyme mechanism of penicillin-binding protein 5 of Escherichia coli."
      Broome-Smith J.K., Spratt B.G.
      FEBS Lett. 165:185-189(1984) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 108-336, MUTANT DACA11191.
    8. "Genes encoding two lipoproteins in the leuS-dacA region of the Escherichia coli chromosome."
      Takase I., Ishino F., Wachi M., Kamata H., Doi M., Asoh S., Matsuzawa H., Ohta T., Matsuhashi M.
      J. Bacteriol. 169:5692-5699(1987) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-39.
      Strain: K12.
    9. "Amino acid sequence homologies between Escherichia coli penicillin-binding protein 5 and class A beta-lactamases."
      Waxman D.J., Amanuma H., Strominger J.L.
      FEBS Lett. 139:159-163(1982) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 30-57.
    10. "Substitution of lysine 213 with arginine in penicillin-binding protein 5 of Escherichia coli abolishes D-alanine carboxypeptidase activity without affecting penicillin binding."
      Malhotra K.T., Nicholas R.A.
      J. Biol. Chem. 267:11386-11391(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS OF LYS-213.
    11. "Domain organization of penicillin-binding protein 5 from Escherichia coli analysed by C-terminal truncation."
      van der Linden M.P.G., de Haan L., Keck W.
      Biochem. J. 289:593-598(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: DOMAINS.
    12. "Escherichia coli proteome analysis using the gene-protein database."
      VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.
      Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY 2D-GEL.
    13. "Crystal structure of a deacylation-defective mutant of penicillin-binding protein 5 at 2.3-A resolution."
      Davies C., White S.W., Nicholas R.A.
      J. Biol. Chem. 276:616-623(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 30-386 OF MUTANT ASP-134.
    14. "Crystal structure of wild-type penicillin-binding protein 5 from Escherichia coli. Implications for deacylation of the acyl-enzyme complex."
      Nicholas R.A., Krings S., Tomberg J., Nicola G., Davies C.
      J. Biol. Chem. 278:52826-52833(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS) OF 30-386 OF WILD-TYPE AND MUTANT ASP-134, MUTAGENESIS OF 101-GLY--LYS-121.
    15. "Crystal structure of Escherichia coli penicillin-binding protein 5 bound to a tripeptide boronic acid inhibitor: a role for Ser-110 in deacylation."
      Nicola G., Peddi S., Stefanova M., Nicholas R.A., Gutheil W.G., Davies C.
      Biochemistry 44:8207-8217(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) OF 30-386 IN COMPLEX WITH SUBSTRATE ANALOG, REACTION MECHANISM.

    Entry informationi

    Entry nameiDACA_ECOLI
    AccessioniPrimary (citable) accession number: P0AEB2
    Secondary accession number(s): P04287, P77106
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: March 20, 1987
    Last sequence update: March 20, 1987
    Last modified: October 1, 2014
    This is version 94 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. 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