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Protein

D-alanyl-D-alanine carboxypeptidase DacA

Gene

dacA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

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: peptidoglycan biosynthesis

This protein is involved in the pathway peptidoglycan biosynthesis, which is part of Cell wall biogenesis.
View all proteins of this organism that are known to be involved in the pathway peptidoglycan biosynthesis and in Cell wall biogenesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei73Acyl-ester intermediate1
Active sitei76Proton acceptor1
Active sitei1391
Binding sitei242Substrate1

GO - Molecular functioni

  • beta-lactamase activity Source: UniProtKB-EC
  • carboxypeptidase activity Source: EcoCyc
  • endopeptidase activity Source: GO_Central
  • penicillin binding Source: EcoCyc
  • serine-type D-Ala-D-Ala carboxypeptidase activity Source: CACAO

GO - Biological processi

  • cell wall macromolecule metabolic process Source: EcoCyc
  • cell wall organization Source: UniProtKB-KW
  • peptidoglycan biosynthetic process Source: GO_Central
  • peptidoglycan metabolic process Source: EcoCyc
  • regulation of cell shape Source: EcoCyc
Complete GO annotation...

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.
BRENDAi3.4.16.4. 2026.
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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10201. dacA.

Subcellular locationi

GO - Cellular componenti

  • integral component of plasma membrane Source: EcoliWiki
Complete GO annotation...

Keywords - Cellular componenti

Cell inner membrane, Cell membrane, Membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi101 – 121Missing : Complete loss of enzyme activity. No effect on penicillin binding. 1 PublicationAdd BLAST21
Mutagenesisi213K → R: Complete loss of enzyme activity. No effect on penicillin binding. 1 Publication1
Mutagenesisi213K → X: Complete loss of activity. 1 Publication1

Chemistry databases

ChEMBLiCHEMBL2354204.
DrugBankiDB00274. Cefmetazole.
DB01329. Cefoperazone.
DB01331. Cefoxitin.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 291 PublicationAdd BLAST29
ChainiPRO_000002723130 – 403D-alanyl-D-alanine carboxypeptidase DacAAdd BLAST374

Proteomic databases

EPDiP0AEB2.
PaxDbiP0AEB2.
PRIDEiP0AEB2.

Interactioni

Protein-protein interaction databases

BioGridi4260698. 250 interactors.
DIPiDIP-47947N.
IntActiP0AEB2. 8 interactors.
MINTiMINT-1247273.
STRINGi511145.b0632.

Structurei

Secondary structure

1403
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Turni33 – 35Combined sources3
Beta strandi46 – 53Combined sources8
Turni54 – 56Combined sources3
Beta strandi59 – 64Combined sources6
Helixi72 – 74Combined sources3
Helixi75 – 88Combined sources14
Beta strandi97 – 99Combined sources3
Helixi102 – 104Combined sources3
Helixi106 – 108Combined sources3
Helixi110 – 112Combined sources3
Beta strandi125 – 127Combined sources3
Helixi128 – 136Combined sources9
Helixi141 – 152Combined sources12
Helixi155 – 168Combined sources14
Beta strandi179 – 183Combined sources5
Helixi191 – 204Combined sources14
Helixi206 – 209Combined sources4
Helixi210 – 213Combined sources4
Beta strandi216 – 219Combined sources4
Beta strandi222 – 225Combined sources4
Helixi229 – 232Combined sources4
Beta strandi236 – 246Combined sources11
Turni247 – 249Combined sources3
Beta strandi250 – 259Combined sources10
Beta strandi262 – 271Combined sources10
Helixi274 – 276Combined sources3
Helixi279 – 291Combined sources13
Beta strandi292 – 298Combined sources7
Beta strandi304 – 320Combined sources17
Beta strandi325 – 330Combined sources6
Helixi334 – 336Combined sources3
Beta strandi338 – 350Combined sources13
Beta strandi357 – 365Combined sources9
Beta strandi368 – 379Combined sources12

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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[»]
5J8XX-ray2.53A30-392[»]
ProteinModelPortaliP0AEB2.
SMRiP0AEB2.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0AEB2.

Family & Domainsi

Sequence similaritiesi

Belongs to the peptidase S11 family.Curated

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiENOG4105DZ1. Bacteria.
COG1686. LUCA.
HOGENOMiHOG000086623.
InParanoidiP0AEB2.
KOiK07258.
OMAiGKIHQDD.
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

        10         20         30         40         50
MNTIFSARIM KRLALTTALC TAFISAAHAD DLNIKTMIPG VPQIDAESYI
60 70 80 90 100
LIDYNSGKVL AEQNADVRRD PASLTKMMTS YVIGQAMKAG KFKETDLVTI
110 120 130 140 150
GNDAWATGNP VFKGSSLMFL KPGMQVPVSQ LIRGINLQSG NDACVAMADF
160 170 180 190 200
AAGSQDAFVG LMNSYVNALG LKNTHFQTVH GLDADGQYSS ARDMALIGQA
210 220 230 240 250
LIRDVPNEYS IYKEKEFTFN GIRQLNRNGL LWDNSLNVDG IKTGHTDKAG
260 270 280 290 300
YNLVASATEG QMRLISAVMG GRTFKGREAE SKKLLTWGFR FFETVNPLKV
310 320 330 340 350
GKEFASEPVW FGDSDRASLG VDKDVYLTIP RGRMKDLKAS YVLNSSELHA
360 370 380 390 400
PLQKNQVVGT INFQLDGKTI EQRPLVVLQE IPEGNFFGKI IDYIKLMFHH

WFG
Length:403
Mass (Da):44,444
Last modified:March 20, 1987 - v1
Checksum:i7FAAB8E98452FF22
GO

Sequence cautioni

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

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural varianti134G → 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. 1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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.
WP_001092082.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC73733; AAC73733; b0632.
BAA35275; BAA35275; BAA35275.
GeneIDi945222.
KEGGiecj:JW0627.
eco:b0632.
PATRICi32116445. VBIEscCol129921_0662.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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.
WP_001092082.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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[»]
5J8XX-ray2.53A30-392[»]
ProteinModelPortaliP0AEB2.
SMRiP0AEB2.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4260698. 250 interactors.
DIPiDIP-47947N.
IntActiP0AEB2. 8 interactors.
MINTiMINT-1247273.
STRINGi511145.b0632.

Chemistry databases

ChEMBLiCHEMBL2354204.
DrugBankiDB00274. Cefmetazole.
DB01329. Cefoperazone.
DB01331. Cefoxitin.

Protein family/group databases

MEROPSiS11.008.

Proteomic databases

EPDiP0AEB2.
PaxDbiP0AEB2.
PRIDEiP0AEB2.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73733; AAC73733; b0632.
BAA35275; BAA35275; BAA35275.
GeneIDi945222.
KEGGiecj:JW0627.
eco:b0632.
PATRICi32116445. VBIEscCol129921_0662.

Organism-specific databases

EchoBASEiEB0197.
EcoGeneiEG10201. dacA.

Phylogenomic databases

eggNOGiENOG4105DZ1. Bacteria.
COG1686. LUCA.
HOGENOMiHOG000086623.
InParanoidiP0AEB2.
KOiK07258.
OMAiGKIHQDD.
PhylomeDBiP0AEB2.

Enzyme and pathway databases

UniPathwayiUPA00219.
BioCyciEcoCyc:EG10201-MONOMER.
ECOL316407:JW0627-MONOMER.
MetaCyc:EG10201-MONOMER.
BRENDAi3.4.16.4. 2026.

Miscellaneous databases

EvolutionaryTraceiP0AEB2.
PROiP0AEB2.

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.
ProtoNetiSearch...

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: November 2, 2016
This is version 113 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

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.