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P24228 (DACB_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 122. 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 DacB

Short name=DD-carboxypeptidase
Short name=DD-peptidase
EC=3.4.16.4
Alternative name(s):
D-alanyl-D-alanine endopeptidase
Short name=DD-endopeptidase
EC=3.4.21.-
Penicillin-binding protein 4
Short name=PBP-4
Gene names
Name:dacB
Ordered Locus Names:b3182, JW3149
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length477 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Not involved in transpeptidation but exclusively catalyzes a DD-carboxypeptidase and DD-endopeptidase reaction. Ref.6

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.

Pathway

Cell wall biogenesis; peptidoglycan biosynthesis.

Subcellular location

Periplasm Potential.

Miscellaneous

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

Sequence similarities

Belongs to the peptidase S13 family.

Ontologies

Keywords
   Biological processAntibiotic resistance
Cell cycle
Cell division
Cell shape
Cell wall biogenesis/degradation
Peptidoglycan synthesis
   Cellular componentPeriplasm
   DomainSignal
   Molecular functionHydrolase
   Technical term3D-structure
Complete proteome
Direct protein sequencing
Reference proteome
Gene Ontology (GO)
   Biological_processcell wall macromolecule catabolic process

Inferred from direct assay Ref.6. Source: EcoCyc

cell wall organization

Inferred from direct assay Ref.6. Source: EcoCyc

cytokinesis by binary fission

Inferred from genetic interaction PubMed 12399477. Source: EcoCyc

peptidoglycan biosynthetic process

Inferred from electronic annotation. Source: UniProtKB-UniPathway

peptidoglycan catabolic process

Inferred from direct assay Ref.6. Source: EcoCyc

peptidoglycan metabolic process

Inferred from direct assay Ref.6. Source: EcoCyc

peptidoglycan turnover

Inferred from direct assay Ref.6. Source: EcoCyc

proteolysis

Inferred from electronic annotation. Source: InterPro

regulation of cell shape

Inferred from genetic interaction PubMed 11325933PubMed 15466028PubMed 15576782. Source: EcoCyc

response to antibiotic

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentouter membrane-bounded periplasmic space

Inferred from mutant phenotype PubMed 331322. Source: EcoliWiki

   Molecular_functioncarboxypeptidase activity

Inferred from mutant phenotype PubMed 331322PubMed 345275. Source: EcoCyc

endopeptidase activity

Inferred from direct assay Ref.6. Source: EcoCyc

penicillin binding

Inferred from direct assay PubMed 319999. Source: EcoCyc

serine-type D-Ala-D-Ala carboxypeptidase activity

Inferred from mutant phenotype PubMed 331322. Source: EcoliWiki

Complete GO annotation...

Binary interactions

With

Entry

#Exp.

IntAct

Notes

argGP0A6E42EBI-1131834,EBI-1120296

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Signal peptide1 – 2020 Ref.1
Chain21 – 477457D-alanyl-D-alanine carboxypeptidase DacB
PRO_0000027241

Regions

Region90 – 263174Absent in class-A beta-lactamases

Sites

Active site621Acyl-ester intermediate
Active site651Proton acceptor By similarity
Active site3061 By similarity
Binding site4171Substrate By similarity

Experimental info

Sequence conflict2611D → Y Ref.5
Sequence conflict4271L → Q in CAA42643. Ref.1

Secondary structure

................................................................................. 477
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P24228 [UniParc].

Last modified November 1, 1995. Version 2.
Checksum: 4EF5E43D2BEC4E5B

FASTA47751,798
        10         20         30         40         50         60 
MRFSRFIIGL TSCIAFSVQA ANVDEYITQL PAGANLALMV QKVGASAPAI DYHSQQMALP 

        70         80         90        100        110        120 
ASTQKVITAL AALIQLGPDF RFTTTLETKG NVENGVLKGD LVARFGADPT LKRQDIRNMV 

       130        140        150        160        170        180 
ATLKKSGVNQ IDGNVLIDTS IFASHDKAPG WPWNDMTQCF SAPPAAAIVD RNCFSVSLYS 

       190        200        210        220        230        240 
APKPGDMAFI RVASYYPVTM FSQVRTLPRG SAEAQYCELD VVPGDLNRFT LTGCLPQRSE 

       250        260        270        280        290        300 
PLPLAFAVQD GASYAGAILK DELKQAGITW SGTLLRQTQV NEPGTVVASK QSAPLHDLLK 

       310        320        330        340        350        360 
IMLKKSDNMI ADTVFRMIGH ARFNVPGTWR AGSDAVRQIL RQQAGVDIGN TIIADGSGLS 

       370        380        390        400        410        420 
RHNLIAPATM MQVLQYIAQH DNELNFISML PLAGYDGSLQ YRAGLHQAGV DGKVSAKTGS 

       430        440        450        460        470 
LQGVYNLAGF ITTASGQRMA FVQYLSGYAV EPADQRNRRI PLVRFESRLY KDIYQNN 

« Hide

References

« Hide 'large scale' references
[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]"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.
[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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
PIRA54535.
RefSeqNP_417649.1. NC_000913.3.
YP_491367.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj
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[»]
ProteinModelPortalP24228.
SMRP24228. Positions 22-477.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

IntActP24228. 1 interaction.
STRING511145.b3182.

Chemistry

ChEMBLCHEMBL2354204.
DrugBankDB00303. Ertapenem.
DB00760. Meropenem.

Protein family/group databases

MEROPSS13.001.

Proteomic databases

PaxDbP24228.
PRIDEP24228.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC76214; AAC76214; b3182.
BAE77226; BAE77226; BAE77226.
GeneID12933443.
947693.
KEGGecj:Y75_p3102.
eco:b3182.
PATRIC32121782. VBIEscCol129921_3275.

Organism-specific databases

EchoBASEEB0198.
EcoGeneEG10202. dacB.

Phylogenomic databases

eggNOGCOG2027.
HOGENOMHOG000279266.
KOK07259.
OMAFRTIGHE.
OrthoDBEOG6NGVQ4.
PhylomeDBP24228.
ProtClustDBPRK11113.

Enzyme and pathway databases

BioCycEcoCyc:EG10202-MONOMER.
ECOL316407:JW3149-MONOMER.
MetaCyc:EG10202-MONOMER.
BRENDA3.4.17.14. 2026.
UniPathwayUPA00219.

Gene expression databases

GenevestigatorP24228.

Family and domain databases

Gene3D3.40.710.10. 1 hit.
InterProIPR012338. Beta-lactam/transpept-like.
IPR000667. Peptidase_S13.
[Graphical view]
PfamPF02113. Peptidase_S13. 1 hit.
[Graphical view]
PRINTSPR00922. DADACBPTASE3.
SUPFAMSSF56601. SSF56601. 1 hit.
TIGRFAMsTIGR00666. PBP4. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceP24228.
PROP24228.

Entry information

Entry nameDACB_ECOLI
AccessionPrimary (citable) accession number: P24228
Secondary accession number(s): Q2M930
Entry history
Integrated into UniProtKB/Swiss-Prot: March 1, 1992
Last sequence update: November 1, 1995
Last modified: April 16, 2014
This is version 122 of the entry and version 2 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