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Protein

D-alanyl-D-alanine carboxypeptidase DacB

Gene

dacB

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

Functioni

Not involved in transpeptidation but exclusively catalyzes a DD-carboxypeptidase and DD-endopeptidase reaction.1 Publication

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 sitei62Acyl-ester intermediate1
Active sitei65Proton acceptorBy similarity1
Active sitei306By similarity1
Binding sitei417SubstrateBy similarity1

GO - Molecular functioni

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

GO - Biological processi

  • cell wall macromolecule catabolic process Source: EcoCyc
  • cell wall organization Source: EcoCyc
  • FtsZ-dependent cytokinesis Source: EcoCyc
  • peptidoglycan biosynthetic process Source: UniProtKB-UniPathway
  • peptidoglycan catabolic process Source: EcoCyc
  • peptidoglycan metabolic process Source: EcoCyc
  • peptidoglycan turnover Source: EcoCyc
  • regulation of cell shape Source: EcoCyc
  • response to antibiotic Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Antibiotic resistance, Cell cycle, Cell division, Cell shape, Cell wall biogenesis/degradation, Peptidoglycan synthesis

Enzyme and pathway databases

BioCyciEcoCyc:EG10202-MONOMER.
ECOL316407:JW3149-MONOMER.
MetaCyc:EG10202-MONOMER.
BRENDAi3.4.16.4. 2165.
3.4.17.14. 2026.
UniPathwayiUPA00219.

Protein family/group databases

MEROPSiS13.001.
MoonProtiP24228.

Names & Taxonomyi

Protein namesi
Recommended name:
D-alanyl-D-alanine carboxypeptidase DacB (EC:3.4.16.4)
Short name:
DD-carboxypeptidase
Short name:
DD-peptidase
Alternative name(s):
D-alanyl-D-alanine endopeptidase (EC:3.4.21.-)
Short name:
DD-endopeptidase
Penicillin-binding protein 4
Short name:
PBP-4
Gene namesi
Name:dacB
Ordered Locus Names:b3182, JW3149
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10202. dacB.

Subcellular locationi

GO - Cellular componenti

  • outer membrane-bounded periplasmic space Source: EcoliWiki
Complete GO annotation...

Keywords - Cellular componenti

Periplasm

Pathology & Biotechi

Chemistry databases

ChEMBLiCHEMBL2354204.
DrugBankiDB01328. Cefonicid.
DB01329. Cefoperazone.
DB01331. Cefoxitin.
DB00303. Ertapenem.
DB04570. Latamoxef.
DB00760. Meropenem.
DB00417. Phenoxymethylpenicillin.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 201 PublicationAdd BLAST20
ChainiPRO_000002724121 – 477D-alanyl-D-alanine carboxypeptidase DacBAdd BLAST457

Proteomic databases

PaxDbiP24228.
PRIDEiP24228.

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
argGP0A6E42EBI-1131834,EBI-1120296

Protein-protein interaction databases

BioGridi4262437. 320 interactors.
IntActiP24228. 1 interactor.
STRINGi511145.b3182.

Structurei

Secondary structure

1477
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi23 – 27Combined sources5
Beta strandi35 – 42Combined sources8
Beta strandi49 – 53Combined sources5
Helixi61 – 63Combined sources3
Helixi64 – 75Combined sources12
Beta strandi83 – 93Combined sources11
Beta strandi96 – 104Combined sources9
Helixi113 – 125Combined sources13
Beta strandi130 – 133Combined sources4
Beta strandi135 – 138Combined sources4
Helixi153 – 155Combined sources3
Helixi159 – 161Combined sources3
Helixi170 – 172Combined sources3
Beta strandi173 – 179Combined sources7
Beta strandi189 – 191Combined sources3
Beta strandi199 – 207Combined sources9
Beta strandi209 – 211Combined sources3
Turni213 – 216Combined sources4
Beta strandi219 – 224Combined sources6
Helixi225 – 227Combined sources3
Beta strandi228 – 236Combined sources9
Beta strandi242 – 247Combined sources6
Helixi251 – 265Combined sources15
Beta strandi269 – 272Combined sources4
Beta strandi274 – 277Combined sources4
Beta strandi285 – 291Combined sources7
Helixi295 – 305Combined sources11
Helixi308 – 323Combined sources16
Helixi329 – 342Combined sources14
Beta strandi356 – 358Combined sources3
Helixi367 – 379Combined sources13
Helixi381 – 384Combined sources4
Helixi387 – 389Combined sources3
Turni393 – 395Combined sources3
Helixi397 – 399Combined sources3
Helixi403 – 407Combined sources5
Turni411 – 413Combined sources3
Beta strandi414 – 421Combined sources8
Beta strandi424 – 432Combined sources9
Beta strandi438 – 447Combined sources10
Helixi452 – 454Combined sources3
Turni455 – 457Combined sources3
Helixi460 – 475Combined sources16

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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[»]
ProteinModelPortaliP24228.
SMRiP24228.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP24228.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni90 – 263Absent in class-A beta-lactamasesAdd BLAST174

Sequence similaritiesi

Belongs to the peptidase S13 family.Curated

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiENOG4106HRJ. Bacteria.
COG2027. LUCA.
HOGENOMiHOG000279266.
InParanoidiP24228.
KOiK07259.
OMAiAHSKPMK.
PhylomeDBiP24228.

Family and domain databases

Gene3Di3.40.710.10. 1 hit.
InterProiIPR012338. Beta-lactam/transpept-like.
IPR000667. Peptidase_S13.
[Graphical view]
PfamiPF02113. Peptidase_S13. 1 hit.
[Graphical view]
PRINTSiPR00922. DADACBPTASE3.
SUPFAMiSSF56601. SSF56601. 1 hit.
TIGRFAMsiTIGR00666. PBP4. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P24228-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRFSRFIIGL TSCIAFSVQA ANVDEYITQL PAGANLALMV QKVGASAPAI
60 70 80 90 100
DYHSQQMALP ASTQKVITAL AALIQLGPDF RFTTTLETKG NVENGVLKGD
110 120 130 140 150
LVARFGADPT LKRQDIRNMV ATLKKSGVNQ IDGNVLIDTS IFASHDKAPG
160 170 180 190 200
WPWNDMTQCF SAPPAAAIVD RNCFSVSLYS APKPGDMAFI RVASYYPVTM
210 220 230 240 250
FSQVRTLPRG SAEAQYCELD VVPGDLNRFT LTGCLPQRSE PLPLAFAVQD
260 270 280 290 300
GASYAGAILK DELKQAGITW SGTLLRQTQV NEPGTVVASK QSAPLHDLLK
310 320 330 340 350
IMLKKSDNMI ADTVFRMIGH ARFNVPGTWR AGSDAVRQIL RQQAGVDIGN
360 370 380 390 400
TIIADGSGLS RHNLIAPATM MQVLQYIAQH DNELNFISML PLAGYDGSLQ
410 420 430 440 450
YRAGLHQAGV DGKVSAKTGS LQGVYNLAGF ITTASGQRMA FVQYLSGYAV
460 470
EPADQRNRRI PLVRFESRLY KDIYQNN
Length:477
Mass (Da):51,798
Last modified:November 1, 1995 - v2
Checksum:i4EF5E43D2BEC4E5B
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti261D → Y (PubMed:16411754).Curated1
Sequence conflicti427L → Q in CAA42643 (PubMed:2040429).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
PIRiA54535.
RefSeqiNP_417649.1. NC_000913.3.
WP_001212619.1. NZ_CP014272.1.

Genome annotation databases

EnsemblBacteriaiAAC76214; AAC76214; b3182.
BAE77226; BAE77226; BAE77226.
GeneIDi947693.
KEGGiecj:JW3149.
eco:b3182.
PATRICi32121782. VBIEscCol129921_3275.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
PIRiA54535.
RefSeqiNP_417649.1. NC_000913.3.
WP_001212619.1. NZ_CP014272.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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[»]
ProteinModelPortaliP24228.
SMRiP24228.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4262437. 320 interactors.
IntActiP24228. 1 interactor.
STRINGi511145.b3182.

Chemistry databases

ChEMBLiCHEMBL2354204.
DrugBankiDB01328. Cefonicid.
DB01329. Cefoperazone.
DB01331. Cefoxitin.
DB00303. Ertapenem.
DB04570. Latamoxef.
DB00760. Meropenem.
DB00417. Phenoxymethylpenicillin.

Protein family/group databases

MEROPSiS13.001.
MoonProtiP24228.

Proteomic databases

PaxDbiP24228.
PRIDEiP24228.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC76214; AAC76214; b3182.
BAE77226; BAE77226; BAE77226.
GeneIDi947693.
KEGGiecj:JW3149.
eco:b3182.
PATRICi32121782. VBIEscCol129921_3275.

Organism-specific databases

EchoBASEiEB0198.
EcoGeneiEG10202. dacB.

Phylogenomic databases

eggNOGiENOG4106HRJ. Bacteria.
COG2027. LUCA.
HOGENOMiHOG000279266.
InParanoidiP24228.
KOiK07259.
OMAiAHSKPMK.
PhylomeDBiP24228.

Enzyme and pathway databases

UniPathwayiUPA00219.
BioCyciEcoCyc:EG10202-MONOMER.
ECOL316407:JW3149-MONOMER.
MetaCyc:EG10202-MONOMER.
BRENDAi3.4.16.4. 2165.
3.4.17.14. 2026.

Miscellaneous databases

EvolutionaryTraceiP24228.
PROiP24228.

Family and domain databases

Gene3Di3.40.710.10. 1 hit.
InterProiIPR012338. Beta-lactam/transpept-like.
IPR000667. Peptidase_S13.
[Graphical view]
PfamiPF02113. Peptidase_S13. 1 hit.
[Graphical view]
PRINTSiPR00922. DADACBPTASE3.
SUPFAMiSSF56601. SSF56601. 1 hit.
TIGRFAMsiTIGR00666. PBP4. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiDACB_ECOLI
AccessioniPrimary (citable) accession number: P24228
Secondary accession number(s): Q2M930
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 1, 1992
Last sequence update: November 1, 1995
Last modified: November 2, 2016
This is version 139 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

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

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.