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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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei62 – 621Acyl-ester intermediate
Active sitei65 – 651Proton acceptorBy similarity
Active sitei306 – 3061By similarity
Binding sitei417 – 4171SubstrateBy similarity

GO - Molecular functioni

  1. carboxypeptidase activity Source: EcoCyc
  2. endopeptidase activity Source: EcoCyc
  3. penicillin binding Source: EcoCyc
  4. serine-type D-Ala-D-Ala carboxypeptidase activity Source: EcoliWiki

GO - Biological processi

  1. cell wall macromolecule catabolic process Source: EcoCyc
  2. cell wall organization Source: EcoCyc
  3. FtsZ-dependent cytokinesis Source: EcoCyc
  4. peptidoglycan biosynthetic process Source: UniProtKB-UniPathway
  5. peptidoglycan catabolic process Source: EcoCyc
  6. peptidoglycan metabolic process Source: EcoCyc
  7. peptidoglycan turnover Source: EcoCyc
  8. regulation of cell shape Source: EcoCyc
  9. 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.
BRENDAi3.4.17.14. 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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG10202. dacB.

Subcellular locationi

Periplasm Curated

GO - Cellular componenti

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

Keywords - Cellular componenti

Periplasm

Pathology & Biotechi

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 20201 PublicationAdd
BLAST
Chaini21 – 477457D-alanyl-D-alanine carboxypeptidase DacBPRO_0000027241Add
BLAST

Proteomic databases

PaxDbiP24228.
PRIDEiP24228.

Expressioni

Gene expression databases

GenevestigatoriP24228.

Interactioni

Binary interactionsi

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

Protein-protein interaction databases

IntActiP24228. 1 interaction.
STRINGi511145.b3182.

Structurei

Secondary structure

1
477
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi23 – 275Combined sources
Beta strandi35 – 428Combined sources
Beta strandi49 – 535Combined sources
Helixi61 – 633Combined sources
Helixi64 – 7512Combined sources
Beta strandi83 – 9311Combined sources
Beta strandi96 – 1049Combined sources
Helixi113 – 12513Combined sources
Beta strandi130 – 1334Combined sources
Beta strandi135 – 1384Combined sources
Helixi153 – 1553Combined sources
Helixi159 – 1613Combined sources
Helixi170 – 1723Combined sources
Beta strandi173 – 1797Combined sources
Beta strandi189 – 1913Combined sources
Beta strandi199 – 2079Combined sources
Beta strandi209 – 2113Combined sources
Turni213 – 2164Combined sources
Beta strandi219 – 2246Combined sources
Helixi225 – 2273Combined sources
Beta strandi228 – 2369Combined sources
Beta strandi242 – 2476Combined sources
Helixi251 – 26515Combined sources
Beta strandi269 – 2724Combined sources
Beta strandi274 – 2774Combined sources
Beta strandi285 – 2917Combined sources
Helixi295 – 30511Combined sources
Helixi308 – 32316Combined sources
Helixi329 – 34214Combined sources
Beta strandi356 – 3583Combined sources
Helixi367 – 37913Combined sources
Helixi381 – 3844Combined sources
Helixi387 – 3893Combined sources
Turni393 – 3953Combined sources
Helixi397 – 3993Combined sources
Helixi403 – 4075Combined sources
Turni411 – 4133Combined sources
Beta strandi414 – 4218Combined sources
Beta strandi424 – 4329Combined sources
Beta strandi438 – 44710Combined sources
Helixi452 – 4543Combined sources
Turni455 – 4573Combined sources
Helixi460 – 47516Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 22-477.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP24228.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni90 – 263174Absent in class-A beta-lactamasesAdd
BLAST

Sequence similaritiesi

Belongs to the peptidase S13 family.Curated

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiCOG2027.
HOGENOMiHOG000279266.
InParanoidiP24228.
KOiK07259.
OMAiFRTIGHE.
OrthoDBiEOG6NGVQ4.
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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti261 – 2611D → Y(PubMed:16411754)Curated
Sequence conflicti427 – 4271L → Q in CAA42643. (PubMed:2040429)Curated

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.
YP_491367.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC76214; AAC76214; b3182.
BAE77226; BAE77226; BAE77226.
GeneIDi12933443.
947693.
KEGGiecj:Y75_p3102.
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.
YP_491367.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 22-477.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiP24228. 1 interaction.
STRINGi511145.b3182.

Chemistry

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

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.
GeneIDi12933443.
947693.
KEGGiecj:Y75_p3102.
eco:b3182.
PATRICi32121782. VBIEscCol129921_3275.

Organism-specific databases

EchoBASEiEB0198.
EcoGeneiEG10202. dacB.

Phylogenomic databases

eggNOGiCOG2027.
HOGENOMiHOG000279266.
InParanoidiP24228.
KOiK07259.
OMAiFRTIGHE.
OrthoDBiEOG6NGVQ4.
PhylomeDBiP24228.

Enzyme and pathway databases

UniPathwayiUPA00219.
BioCyciEcoCyc:EG10202-MONOMER.
ECOL316407:JW3149-MONOMER.
MetaCyc:EG10202-MONOMER.
BRENDAi3.4.17.14. 2026.

Miscellaneous databases

EvolutionaryTraceiP24228.
PROiP24228.

Gene expression databases

GenevestigatoriP24228.

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...

Publicationsi

« Hide 'large scale' publications
  1. "Penicillin-binding protein 4 of Escherichia coli shows a novel type of primary structure among penicillin-interacting proteins."
    Mottl H., Terpstra P., Keck W.
    FEMS Microbiol. Lett. 62:213-220(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 21-31.
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  2. Wang R., Kushner S.R.
    Submitted (SEP-1993) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12.
  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. "Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, both in the native form and covalently linked to various antibiotics."
    Kishida H., Unzai S., Roper D.I., Lloyd A., Park S.-Y., Tame J.R.H.
    Biochemistry 45:783-792(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: PARTIAL NUCLEOTIDE SEQUENCE [GENOMIC DNA], X-RAY CRYSTALLOGRAPHY (1.55 ANGSTROMS) OF 21-477 OF APOENZYME AND IN COMPLEX WITH PENICILLIN ANTIBIOTICS.
    Strain: K12.
  6. "Penicillin-binding protein 4 of Escherichia coli: molecular cloning of the dacB gene, controlled overexpression, and alterations in murein composition."
    Korat B., Mottl H., Keck W.
    Mol. Microbiol. 5:675-684(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.

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: January 7, 2015
This is version 128 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

External Data

Dasty 3

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 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.