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Protein

D-alanyl-D-alanine carboxypeptidase DacD

Gene

dacD

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 sitei63Acyl-ester intermediateBy similarity1
Active sitei66Proton acceptorBy similarity1
Active sitei129By similarity1
Binding sitei232SubstrateBy 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
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:RPOA-MONOMER.
ECOL316407:JW5329-MONOMER.
MetaCyc:RPOA-MONOMER.
UniPathwayiUPA00219.

Protein family/group databases

MEROPSiS11.009.

Names & Taxonomyi

Protein namesi
Recommended name:
D-alanyl-D-alanine carboxypeptidase DacD (EC:3.4.16.4)
Short name:
DD-carboxypeptidase
Short name:
DD-peptidase
Alternative name(s):
Penicillin-binding protein 6b
Short name:
PBP-6b
Gene namesi
Name:dacD
Synonyms:phsE, yeeC
Ordered Locus Names:b2010, JW5329
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11893. dacD.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cell inner membrane, Cell membrane, Membrane

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 21Sequence analysisAdd BLAST21
ChainiPRO_000002723422 – 388D-alanyl-D-alanine carboxypeptidase DacDAdd BLAST367

Proteomic databases

PaxDbiP33013.
PRIDEiP33013.

Interactioni

Protein-protein interaction databases

BioGridi4260413. 257 interactors.
STRINGi511145.b2010.

Structurei

Secondary structure

1388
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi36 – 43Combined sources8
Turni44 – 46Combined sources3
Beta strandi49 – 54Combined sources6
Helixi62 – 64Combined sources3
Helixi65 – 78Combined sources14
Beta strandi87 – 89Combined sources3
Helixi92 – 94Combined sources3
Turni100 – 104Combined sources5
Beta strandi115 – 117Combined sources3
Helixi118 – 126Combined sources9
Helixi131 – 142Combined sources12
Helixi145 – 158Combined sources14
Beta strandi168 – 171Combined sources4
Helixi181 – 192Combined sources12
Helixi196 – 200Combined sources5
Helixi201 – 203Combined sources3
Beta strandi206 – 209Combined sources4
Beta strandi212 – 215Combined sources4
Helixi219 – 222Combined sources4
Beta strandi226 – 228Combined sources3
Beta strandi232 – 235Combined sources4
Beta strandi241 – 249Combined sources9
Beta strandi252 – 263Combined sources12
Helixi264 – 281Combined sources18
Beta strandi282 – 291Combined sources10
Beta strandi315 – 320Combined sources6
Helixi321 – 326Combined sources6
Beta strandi327 – 332Combined sources6
Beta strandi349 – 355Combined sources7
Beta strandi358 – 365Combined sources8

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5FSRX-ray2.40A/B22-374[»]
ProteinModelPortaliP33013.
SMRiP33013.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the peptidase S11 family.Curated

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiENOG4105DZ1. Bacteria.
COG1686. LUCA.
HOGENOMiHOG000086623.
InParanoidiP33013.
KOiK07258.
OMAiTNTHFET.
PhylomeDBiP33013.

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.

P33013-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKRRLIIAAS LFVFNLSSGF AAENIPFSPQ PPEIHAGSWV LMDYTTGQIL
60 70 80 90 100
TAGNEHQQRN PASLTKLMTG YVVDRAIDSH RITPDDIVTV GRDAWAKDNP
110 120 130 140 150
VFVGSSLMFL KEGDRVSVRD LSRGLIVDSG NDACVALADY IAGGQRQFVE
160 170 180 190 200
MMNNYAEKLH LKDTHFETVH GLDAPGQHSS AYDLAVLSRA IIHGEPEFYH
210 220 230 240 250
MYSEKSLTWN GITQQNRNGL LWDKTMNVDG LKTGHTSGAG FNLIASAVDG
260 270 280 290 300
QRRLIAVVMG ADSAKGREEE ARKLLRWGQQ NFTTVQILHR GKKVGTERIW
310 320 330 340 350
YGDKENIDLG TEQEFWMVLP KAEIPHIKAK YTLDGKELTA PISAHQRVGE
360 370 380
IELYDRDKQV AHWPLVTLES VGEGSMFSRL SDYFHHKA
Length:388
Mass (Da):43,346
Last modified:July 15, 1998 - v3
Checksum:i453FE18C21D207D0
GO

Sequence cautioni

The sequence AAA16416 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00009 Genomic DNA. Translation: AAA16416.1. Different initiation.
U00096 Genomic DNA. Translation: AAC75071.2.
AP009048 Genomic DNA. Translation: BAA15838.2.
PIRiA64966.
RefSeqiNP_416514.4. NC_000913.3.
WP_000830156.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC75071; AAC75071; b2010.
BAA15838; BAA15838; BAA15838.
GeneIDi946518.
KEGGiecj:JW5329.
eco:b2010.
PATRICi32119355. VBIEscCol129921_2087.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00009 Genomic DNA. Translation: AAA16416.1. Different initiation.
U00096 Genomic DNA. Translation: AAC75071.2.
AP009048 Genomic DNA. Translation: BAA15838.2.
PIRiA64966.
RefSeqiNP_416514.4. NC_000913.3.
WP_000830156.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5FSRX-ray2.40A/B22-374[»]
ProteinModelPortaliP33013.
SMRiP33013.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4260413. 257 interactors.
STRINGi511145.b2010.

Protein family/group databases

MEROPSiS11.009.

Proteomic databases

PaxDbiP33013.
PRIDEiP33013.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75071; AAC75071; b2010.
BAA15838; BAA15838; BAA15838.
GeneIDi946518.
KEGGiecj:JW5329.
eco:b2010.
PATRICi32119355. VBIEscCol129921_2087.

Organism-specific databases

EchoBASEiEB1839.
EcoGeneiEG11893. dacD.

Phylogenomic databases

eggNOGiENOG4105DZ1. Bacteria.
COG1686. LUCA.
HOGENOMiHOG000086623.
InParanoidiP33013.
KOiK07258.
OMAiTNTHFET.
PhylomeDBiP33013.

Enzyme and pathway databases

UniPathwayiUPA00219.
BioCyciEcoCyc:RPOA-MONOMER.
ECOL316407:JW5329-MONOMER.
MetaCyc:RPOA-MONOMER.

Miscellaneous databases

PROiP33013.

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 nameiDACD_ECOLI
AccessioniPrimary (citable) accession number: P33013
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1994
Last sequence update: July 15, 1998
Last modified: November 2, 2016
This is version 143 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, 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.