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P0AEB2 (DACA_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 93. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (5) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
D-alanyl-D-alanine carboxypeptidase DacA

Short name=DD-carboxypeptidase
Short name=DD-peptidase
EC=3.4.16.4
Alternative name(s):
Beta-lactamase
EC=3.5.2.6
Penicillin-binding protein 5
Short name=PBP-5
Gene names
Name:dacA
Synonyms:pfv
Ordered Locus Names:b0632, JW0627
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length403 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Removes C-terminal D-alanyl residues from sugar-peptide cell wall precursors.

Catalytic activity

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.

Pathway

Cell wall biogenesis; peptidoglycan biosynthesis.

Subcellular location

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

Sequence similarities

Belongs to the peptidase S11 family.

Sequence caution

The sequence AAB40832.1 differs from that shown. Reason: Erroneous initiation.

Binary interactions

With

Entry

#Exp.

IntAct

Notes

yfaYP778081EBI-548634,EBI-556720

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Signal peptide1 – 2929 Ref.9
Chain30 – 403374D-alanyl-D-alanine carboxypeptidase DacA
PRO_0000027231

Sites

Active site731Acyl-ester intermediate
Active site761Proton acceptor
Active site1391
Binding site2421Substrate

Natural variations

Natural variant1341G → 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. Ref.13 Ref.14

Experimental info

Mutagenesis101 – 12121Missing: Complete loss of enzyme activity. No effect on penicillin binding. Ref.14
Mutagenesis2131K → R: Complete loss of enzyme activity. No effect on penicillin binding. Ref.10
Mutagenesis2131K → X: Complete loss of activity. Ref.10

Secondary structure

.............................................................. 403
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P0AEB2 [UniParc].

Last modified March 20, 1987. Version 1.
Checksum: 7FAAB8E98452FF22

FASTA40344,444
        10         20         30         40         50         60 
MNTIFSARIM KRLALTTALC TAFISAAHAD DLNIKTMIPG VPQIDAESYI LIDYNSGKVL 

        70         80         90        100        110        120 
AEQNADVRRD PASLTKMMTS YVIGQAMKAG KFKETDLVTI GNDAWATGNP VFKGSSLMFL 

       130        140        150        160        170        180 
KPGMQVPVSQ LIRGINLQSG NDACVAMADF AAGSQDAFVG LMNSYVNALG LKNTHFQTVH 

       190        200        210        220        230        240 
GLDADGQYSS ARDMALIGQA LIRDVPNEYS IYKEKEFTFN GIRQLNRNGL LWDNSLNVDG 

       250        260        270        280        290        300 
IKTGHTDKAG YNLVASATEG QMRLISAVMG GRTFKGREAE SKKLLTWGFR FFETVNPLKV 

       310        320        330        340        350        360 
GKEFASEPVW FGDSDRASLG VDKDVYLTIP RGRMKDLKAS YVLNSSELHA PLQKNQVVGT 

       370        380        390        400 
INFQLDGKTI EQRPLVVLQE IPEGNFFGKI IDYIKLMFHH WFG 

« Hide

References

« Hide 'large scale' references
[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]"A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 12.7-28.0 min region on the linkage map."
Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K., Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S., Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K. expand/collapse author list , Mori H., Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G., Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M., Horiuchi T.
DNA Res. 3:137-155(1996) [PubMed] [Europe PMC] [Abstract]
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]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
PIRZPECP5. A28536.
RefSeqNP_415165.1. NC_000913.3.
YP_488923.1. NC_007779.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
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[»]
ProteinModelPortalP0AEB2.
SMRP0AEB2. Positions 32-386.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-47947N.
IntActP0AEB2. 8 interactions.
MINTMINT-1247273.
STRING511145.b0632.

Chemistry

ChEMBLCHEMBL2354204.

Protein family/group databases

MEROPSS11.008.

PTM databases

PhosSiteP0809377.

Proteomic databases

PaxDbP0AEB2.
PRIDEP0AEB2.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC73733; AAC73733; b0632.
BAA35275; BAA35275; BAA35275.
GeneID12931704.
945222.
KEGGecj:Y75_p0622.
eco:b0632.
PATRIC32116445. VBIEscCol129921_0662.

Organism-specific databases

EchoBASEEB0197.
EcoGeneEG10201. dacA.

Phylogenomic databases

eggNOGCOG1686.
HOGENOMHOG000086623.
KOK07258.
OMAYVIGQAV.
OrthoDBEOG6RJV2H.
PhylomeDBP0AEB2.

Enzyme and pathway databases

BioCycEcoCyc:EG10201-MONOMER.
ECOL316407:JW0627-MONOMER.
MetaCyc:EG10201-MONOMER.
UniPathwayUPA00219.

Gene expression databases

GenevestigatorP0AEB2.

Family and domain databases

Gene3D2.60.410.10. 1 hit.
3.40.710.10. 1 hit.
InterProIPR012338. Beta-lactam/transpept-like.
IPR015956. Peniciliin-bd_prot-assoc.
IPR018044. Peptidase_S11.
IPR012907. Peptidase_S11_C.
IPR001967. Peptidase_S11_N.
[Graphical view]
PfamPF07943. PBP5_C. 1 hit.
PF00768. Peptidase_S11. 1 hit.
[Graphical view]
PRINTSPR00725. DADACBPTASE1.
SMARTSM00936. PBP5_C. 1 hit.
[Graphical view]
SUPFAMSSF56601. SSF56601. 1 hit.
SSF69189. SSF69189. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceP0AEB2.
PROP0AEB2.

Entry information

Entry nameDACA_ECOLI
AccessionPrimary (citable) accession number: P0AEB2
Secondary accession number(s): P04287, P77106
Entry history
Integrated into UniProtKB/Swiss-Prot: March 20, 1987
Last sequence update: March 20, 1987
Last modified: July 9, 2014
This is version 93 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Peptidase families

Classification of peptidase families and list of entries

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene