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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)DescriptionActionsGraphical viewLength
Active sitei66Acyl-ester intermediateBy similarity1
Active sitei69Proton acceptorBy similarity1
Active sitei132By similarity1
Binding sitei235SubstrateBy similarity1

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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
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 databases

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

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 271 PublicationAdd BLAST27
ChainiPRO_000002723328 – 400D-alanyl-D-alanine carboxypeptidase DacCAdd BLAST373

Proteomic databases

EPDiP08506.
PaxDbiP08506.
PRIDEiP08506.

Interactioni

Protein-protein interaction databases

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

Structurei

Secondary structure

1400
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi39 – 46Combined sources8
Turni47 – 49Combined sources3
Beta strandi52 – 57Combined sources6
Helixi65 – 67Combined sources3
Helixi68 – 81Combined sources14
Beta strandi90 – 92Combined sources3
Helixi95 – 97Combined sources3
Turni99 – 101Combined sources3
Helixi103 – 105Combined sources3
Beta strandi118 – 120Combined sources3
Helixi121 – 129Combined sources9
Helixi134 – 145Combined sources12
Helixi148 – 161Combined sources14
Beta strandi171 – 173Combined sources3
Helixi184 – 197Combined sources14
Helixi199 – 202Combined sources4
Helixi203 – 206Combined sources4
Beta strandi209 – 212Combined sources4
Beta strandi215 – 218Combined sources4
Helixi222 – 225Combined sources4
Beta strandi230 – 239Combined sources10
Turni240 – 242Combined sources3
Beta strandi243 – 252Combined sources10
Beta strandi255 – 266Combined sources12
Helixi267 – 284Combined sources18
Beta strandi285 – 288Combined sources4
Beta strandi297 – 313Combined sources17
Helixi315 – 317Combined sources3
Beta strandi320 – 323Combined sources4
Helixi327 – 329Combined sources3
Beta strandi330 – 343Combined sources14
Beta strandi350 – 358Combined sources9
Beta strandi361 – 370Combined sources10

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP08506.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni383 – 400Required for inner membrane bindingAdd BLAST18

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.
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)DescriptionActionsGraphical viewLength
Sequence conflicti231V → E in CAA29775 (PubMed:3279397).Curated1

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
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

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

Chemistry databases

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.
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...

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: November 2, 2016
This is version 157 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.