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Protein

D-alanyl-D-alanine carboxypeptidase DacC

Gene

dacC

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.

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)LengthDescriptionGraphical viewFeature identifierActions
Active sitei66 – 661Acyl-ester intermediateBy similarity
Active sitei69 – 691Proton acceptorBy similarity
Active sitei132 – 1321By similarity
Binding sitei235 – 2351SubstrateBy similarity

GO - Molecular functioni

  • carboxypeptidase activity Source: EcoCyc
  • endopeptidase activity Source: GO_Central
  • penicillin binding Source: EcoCyc
  • serine-type D-Ala-D-Ala carboxypeptidase activity Source: GO_Central

GO - Biological processi

  • cell wall organization Source: UniProtKB-KW
  • peptidoglycan biosynthetic process Source: EcoCyc
  • regulation of cell shape Source: EcoCyc
  • response to drug 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:EG10203-MONOMER.
ECOL316407:JW0823-MONOMER.
MetaCyc:EG10203-MONOMER.
UniPathwayiUPA00219.

Protein family/group databases

MEROPSiS11.003.

Names & Taxonomyi

Protein namesi
Recommended name:
D-alanyl-D-alanine carboxypeptidase DacC (EC:3.4.16.4)
Short name:
DD-carboxypeptidase
Short name:
DD-peptidase
Alternative name(s):
Penicillin-binding protein 6
Short name:
PBP-6
Gene namesi
Name:dacC
Ordered Locus Names:b0839, JW0823
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10203. dacC.

Subcellular locationi

  • Cell inner membrane 1 Publication; Peripheral membrane protein 1 Publication; Periplasmic side 1 Publication

  • Note: N-terminus lies in the periplasmic space, targeted there by the C-terminal amphiphilic helix (PMID:3330754).

GO - Cellular componenti

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

Keywords - Cellular componenti

Cell inner membrane, Cell membrane, Membrane

Pathology & Biotechi

Chemistry

ChEMBLiCHEMBL2354204.
DrugBankiDB00274. Cefmetazole.
DB01329. Cefoperazone.
DB01331. Cefoxitin.
DB00430. Cefpiramide.
DB00303. Ertapenem.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 27271 PublicationAdd
BLAST
Chaini28 – 400373D-alanyl-D-alanine carboxypeptidase DacCPRO_0000027233Add
BLAST

Proteomic databases

EPDiP08506.
PaxDbiP08506.
PRIDEiP08506.

Interactioni

Protein-protein interaction databases

BioGridi4262825. 212 interactions.
IntActiP08506. 2 interactions.
MINTiMINT-6478097.
STRINGi511145.b0839.

Structurei

Secondary structure

1
400
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi39 – 468Combined sources
Turni47 – 493Combined sources
Beta strandi52 – 576Combined sources
Helixi65 – 673Combined sources
Helixi68 – 8114Combined sources
Beta strandi90 – 923Combined sources
Helixi95 – 973Combined sources
Turni99 – 1013Combined sources
Helixi103 – 1053Combined sources
Beta strandi118 – 1203Combined sources
Helixi121 – 1299Combined sources
Helixi134 – 14512Combined sources
Helixi148 – 16114Combined sources
Beta strandi171 – 1733Combined sources
Helixi184 – 19714Combined sources
Helixi199 – 2024Combined sources
Helixi203 – 2064Combined sources
Beta strandi209 – 2124Combined sources
Beta strandi215 – 2184Combined sources
Helixi222 – 2254Combined sources
Beta strandi230 – 23910Combined sources
Turni240 – 2423Combined sources
Beta strandi243 – 25210Combined sources
Beta strandi255 – 26612Combined sources
Helixi267 – 28418Combined sources
Beta strandi285 – 2884Combined sources
Beta strandi297 – 31317Combined sources
Helixi315 – 3173Combined sources
Beta strandi320 – 3234Combined sources
Helixi327 – 3293Combined sources
Beta strandi330 – 34314Combined sources
Beta strandi350 – 3589Combined sources
Beta strandi361 – 37010Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3IT9X-ray2.10A/B/C/D28-378[»]
3ITAX-ray1.80A/B/C/D28-378[»]
3ITBX-ray1.80A/B/C/D28-378[»]
ProteinModelPortaliP08506.
SMRiP08506. Positions 28-378.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP08506.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni383 – 40018Required for inner membrane bindingAdd
BLAST

Domaini

The C-terminus forms an amphiphilic helix that targets the protein to the periplasmic side of the inner cell membrane.1 Publication

Sequence similaritiesi

Belongs to the peptidase S11 family.Curated

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiENOG4105DZ1. Bacteria.
COG1686. LUCA.
HOGENOMiHOG000086623.
InParanoidiP08506.
KOiK07258.
OMAiGTIDFKL.
OrthoDBiEOG6RJV2H.
PhylomeDBiP08506.

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.

P08506-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTQYSSLLRG LAAGSAFLFL FAPTAFAAEQ TVEAPSVDAR AWILMDYASG
60 70 80 90 100
KVLAEGNADE KLDPASLTKI MTSYVVGQAL KADKIKLTDM VTVGKDAWAT
110 120 130 140 150
GNPALRGSSV MFLKPGDQVS VADLNKGVII QSGNDACIAL ADYVAGSQES
160 170 180 190 200
FIGLMNGYAK KLGLTNTTFQ TVHGLDAPGQ FSTARDMALL GKALIHDVPE
210 220 230 240 250
EYAIHKEKEF TFNKIRQPNR NRLLWSSNLN VDGMKTGTTA GAGYNLVASA
260 270 280 290 300
TQGDMRLISV VLGAKTDRIR FNESEKLLTW GFRFFETVTP IKPDATFVTQ
310 320 330 340 350
RVWFGDKSEV NLGAGEAGSV TIPRGQLKNL KASYTLTEPQ LTAPLKKGQV
360 370 380 390 400
VGTIDFQLNG KSIEQRPLIV MENVEEGGFF GRVWDFVMMK FHQWFGSWFS
Length:400
Mass (Da):43,609
Last modified:November 1, 1997 - v2
Checksum:i4D7F3BDCEA64C775
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti231 – 2311V → E in CAA29775 (PubMed:3279397).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X06480 Genomic DNA. Translation: CAA29775.1.
U00096 Genomic DNA. Translation: AAC73926.1.
AP009048 Genomic DNA. Translation: BAA35542.1.
PIRiG64821.
RefSeqiNP_415360.1. NC_000913.3.
WP_001300708.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC73926; AAC73926; b0839.
BAA35542; BAA35542; BAA35542.
GeneIDi945455.
KEGGiecj:JW0823.
eco:b0839.
PATRICi32116881. VBIEscCol129921_0866.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X06480 Genomic DNA. Translation: CAA29775.1.
U00096 Genomic DNA. Translation: AAC73926.1.
AP009048 Genomic DNA. Translation: BAA35542.1.
PIRiG64821.
RefSeqiNP_415360.1. NC_000913.3.
WP_001300708.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3IT9X-ray2.10A/B/C/D28-378[»]
3ITAX-ray1.80A/B/C/D28-378[»]
3ITBX-ray1.80A/B/C/D28-378[»]
ProteinModelPortaliP08506.
SMRiP08506. Positions 28-378.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4262825. 212 interactions.
IntActiP08506. 2 interactions.
MINTiMINT-6478097.
STRINGi511145.b0839.

Chemistry

ChEMBLiCHEMBL2354204.
DrugBankiDB00274. Cefmetazole.
DB01329. Cefoperazone.
DB01331. Cefoxitin.
DB00430. Cefpiramide.
DB00303. Ertapenem.

Protein family/group databases

MEROPSiS11.003.

Proteomic databases

EPDiP08506.
PaxDbiP08506.
PRIDEiP08506.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73926; AAC73926; b0839.
BAA35542; BAA35542; BAA35542.
GeneIDi945455.
KEGGiecj:JW0823.
eco:b0839.
PATRICi32116881. VBIEscCol129921_0866.

Organism-specific databases

EchoBASEiEB0199.
EcoGeneiEG10203. dacC.

Phylogenomic databases

eggNOGiENOG4105DZ1. Bacteria.
COG1686. LUCA.
HOGENOMiHOG000086623.
InParanoidiP08506.
KOiK07258.
OMAiGTIDFKL.
OrthoDBiEOG6RJV2H.
PhylomeDBiP08506.

Enzyme and pathway databases

UniPathwayiUPA00219.
BioCyciEcoCyc:EG10203-MONOMER.
ECOL316407:JW0823-MONOMER.
MetaCyc:EG10203-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP08506.
PROiP08506.

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...

Publicationsi

« Hide 'large scale' publications
  1. "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.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  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. "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 28-52.
  6. "An 18 amino acid amphiphilic helix forms the membrane-anchoring domain of the Escherichia coli penicillin-binding protein 5."
    Jackson M.E., Pratt J.M.
    Mol. Microbiol. 1:23-28(1987) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION, DOMAIN.

Entry informationi

Entry nameiDACC_ECOLI
AccessioniPrimary (citable) accession number: P08506
Secondary accession number(s): P77287
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1988
Last sequence update: November 1, 1997
Last modified: April 13, 2016
This is version 154 of the entry and version 2 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.