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P0AEB2

- DACA_ECOLI

UniProt

P0AEB2 - DACA_ECOLI

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Protein

D-alanyl-D-alanine carboxypeptidase DacA

Gene

dacA

Organism
Escherichia coli (strain K12)
Status
Reviewed - 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.
A beta-lactam + H2O = a substituted beta-amino acid.

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei73 – 731Acyl-ester intermediate
Active sitei76 – 761Proton acceptor
Active sitei139 – 1391
Binding sitei242 – 2421Substrate

GO - Molecular functioni

  1. beta-lactamase activity Source: UniProtKB-EC
  2. carboxypeptidase activity Source: EcoCyc
  3. penicillin binding Source: EcoCyc
  4. serine-type D-Ala-D-Ala carboxypeptidase activity Source: CACAO

GO - Biological processi

  1. cell division Source: EcoCyc
  2. cell wall macromolecule metabolic process Source: EcoCyc
  3. cell wall organization Source: UniProtKB-KW
  4. peptidoglycan biosynthetic process Source: UniProtKB-UniPathway
  5. peptidoglycan metabolic process Source: EcoCyc
  6. 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:EG10201-MONOMER.
ECOL316407:JW0627-MONOMER.
MetaCyc:EG10201-MONOMER.
UniPathwayiUPA00219.

Protein family/group databases

MEROPSiS11.008.

Names & Taxonomyi

Protein namesi
Recommended name:
D-alanyl-D-alanine carboxypeptidase DacA (EC:3.4.16.4)
Short name:
DD-carboxypeptidase
Short name:
DD-peptidase
Alternative name(s):
Beta-lactamase (EC:3.5.2.6)
Penicillin-binding protein 5
Short name:
PBP-5
Gene namesi
Name:dacA
Synonyms:pfv
Ordered Locus Names:b0632, JW0627
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG10201. dacA.

Subcellular locationi

Cell inner membrane; Peripheral membrane protein; Cytoplasmic side
Note: N-terminal lies in the periplasmic space.

GO - Cellular componenti

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

Keywords - Cellular componenti

Cell inner membrane, Cell membrane, Membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi101 – 12121Missing: Complete loss of enzyme activity. No effect on penicillin binding. 1 PublicationAdd
BLAST
Mutagenesisi213 – 2131K → R: Complete loss of enzyme activity. No effect on penicillin binding. 1 Publication
Mutagenesisi213 – 2131K → X: Complete loss of activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 29291 PublicationAdd
BLAST
Chaini30 – 403374D-alanyl-D-alanine carboxypeptidase DacAPRO_0000027231Add
BLAST

Proteomic databases

PaxDbiP0AEB2.
PRIDEiP0AEB2.

PTM databases

PhosSiteiP0809377.

Expressioni

Gene expression databases

GenevestigatoriP0AEB2.

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
yfaYP778081EBI-548634,EBI-556720

Protein-protein interaction databases

DIPiDIP-47947N.
IntActiP0AEB2. 8 interactions.
MINTiMINT-1247273.
STRINGi511145.b0632.

Structurei

Secondary structure

1
403
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Turni33 – 353Combined sources
Beta strandi46 – 538Combined sources
Turni54 – 563Combined sources
Beta strandi59 – 646Combined sources
Helixi72 – 743Combined sources
Helixi75 – 8814Combined sources
Beta strandi97 – 993Combined sources
Helixi102 – 1043Combined sources
Helixi106 – 1083Combined sources
Helixi110 – 1123Combined sources
Beta strandi125 – 1273Combined sources
Helixi128 – 1369Combined sources
Helixi141 – 15212Combined sources
Helixi155 – 16814Combined sources
Beta strandi179 – 1835Combined sources
Helixi191 – 20414Combined sources
Helixi206 – 2094Combined sources
Helixi210 – 2134Combined sources
Beta strandi216 – 2194Combined sources
Beta strandi222 – 2254Combined sources
Helixi229 – 2324Combined sources
Beta strandi236 – 24611Combined sources
Turni247 – 2493Combined sources
Beta strandi250 – 25910Combined sources
Beta strandi262 – 27110Combined sources
Helixi274 – 2763Combined sources
Helixi279 – 29113Combined sources
Beta strandi292 – 2987Combined sources
Beta strandi304 – 32017Combined sources
Beta strandi325 – 3306Combined sources
Helixi334 – 3363Combined sources
Beta strandi338 – 35013Combined sources
Beta strandi357 – 3659Combined sources
Beta strandi368 – 37912Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1HD8X-ray2.30A30-386[»]
1NJ4X-ray1.90A30-392[»]
1NZOX-ray1.85A30-392[»]
1NZUX-ray2.00A30-392[»]
1SDNX-ray2.50A30-392[»]
1Z6FX-ray1.60A30-392[»]
3BEBX-ray2.00A30-386[»]
3BECX-ray1.60A30-386[»]
3MZDX-ray1.90A30-386[»]
3MZEX-ray2.10A30-386[»]
3MZFX-ray1.50A30-386[»]
ProteinModelPortaliP0AEB2.
SMRiP0AEB2. Positions 32-386.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0AEB2.

Family & Domainsi

Sequence similaritiesi

Belongs to the peptidase S11 family.Curated

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiCOG1686.
HOGENOMiHOG000086623.
InParanoidiP0AEB2.
KOiK07258.
OMAiYVIGQAV.
OrthoDBiEOG6RJV2H.
PhylomeDBiP0AEB2.

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.

P0AEB2-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MNTIFSARIM KRLALTTALC TAFISAAHAD DLNIKTMIPG VPQIDAESYI
60 70 80 90 100
LIDYNSGKVL AEQNADVRRD PASLTKMMTS YVIGQAMKAG KFKETDLVTI
110 120 130 140 150
GNDAWATGNP VFKGSSLMFL KPGMQVPVSQ LIRGINLQSG NDACVAMADF
160 170 180 190 200
AAGSQDAFVG LMNSYVNALG LKNTHFQTVH GLDADGQYSS ARDMALIGQA
210 220 230 240 250
LIRDVPNEYS IYKEKEFTFN GIRQLNRNGL LWDNSLNVDG IKTGHTDKAG
260 270 280 290 300
YNLVASATEG QMRLISAVMG GRTFKGREAE SKKLLTWGFR FFETVNPLKV
310 320 330 340 350
GKEFASEPVW FGDSDRASLG VDKDVYLTIP RGRMKDLKAS YVLNSSELHA
360 370 380 390 400
PLQKNQVVGT INFQLDGKTI EQRPLVVLQE IPEGNFFGKI IDYIKLMFHH

WFG
Length:403
Mass (Da):44,444
Last modified:March 20, 1987 - v1
Checksum:i7FAAB8E98452FF22
GO

Sequence cautioni

The sequence AAB40832.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti134 – 1341G → D in mutant dacA11191; inactive but still binds penicillin. Blocked in the release of the bound penicilloyl moiety; the mutant also fails to catalyze the D-alanine carboxypeptidase reaction as the hydrolysis of the acyl-enzyme formed with substrate is also blocked and the acyl-enzyme accumulates.

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X06479 Genomic DNA. Translation: CAA29774.1.
M18276 Genomic DNA. Translation: AAA24553.1.
U82598 Genomic DNA. Translation: AAB40832.1. Different initiation.
U00096 Genomic DNA. Translation: AAC73733.1.
AP009048 Genomic DNA. Translation: BAA35275.1.
L07636 Genomic DNA. Translation: AAA66340.1.
PIRiA28536. ZPECP5.
RefSeqiNP_415165.1. NC_000913.3.
YP_488923.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC73733; AAC73733; b0632.
BAA35275; BAA35275; BAA35275.
GeneIDi12931704.
945222.
KEGGiecj:Y75_p0622.
eco:b0632.
PATRICi32116445. VBIEscCol129921_0662.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X06479 Genomic DNA. Translation: CAA29774.1 .
M18276 Genomic DNA. Translation: AAA24553.1 .
U82598 Genomic DNA. Translation: AAB40832.1 . Different initiation.
U00096 Genomic DNA. Translation: AAC73733.1 .
AP009048 Genomic DNA. Translation: BAA35275.1 .
L07636 Genomic DNA. Translation: AAA66340.1 .
PIRi A28536. ZPECP5.
RefSeqi NP_415165.1. NC_000913.3.
YP_488923.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1HD8 X-ray 2.30 A 30-386 [» ]
1NJ4 X-ray 1.90 A 30-392 [» ]
1NZO X-ray 1.85 A 30-392 [» ]
1NZU X-ray 2.00 A 30-392 [» ]
1SDN X-ray 2.50 A 30-392 [» ]
1Z6F X-ray 1.60 A 30-392 [» ]
3BEB X-ray 2.00 A 30-386 [» ]
3BEC X-ray 1.60 A 30-386 [» ]
3MZD X-ray 1.90 A 30-386 [» ]
3MZE X-ray 2.10 A 30-386 [» ]
3MZF X-ray 1.50 A 30-386 [» ]
ProteinModelPortali P0AEB2.
SMRi P0AEB2. Positions 32-386.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-47947N.
IntActi P0AEB2. 8 interactions.
MINTi MINT-1247273.
STRINGi 511145.b0632.

Chemistry

ChEMBLi CHEMBL2354204.
DrugBanki DB00274. Cefmetazole.
DB01329. Cefoperazone.
DB01331. Cefoxitin.

Protein family/group databases

MEROPSi S11.008.

PTM databases

PhosSitei P0809377.

Proteomic databases

PaxDbi P0AEB2.
PRIDEi P0AEB2.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAC73733 ; AAC73733 ; b0632 .
BAA35275 ; BAA35275 ; BAA35275 .
GeneIDi 12931704.
945222.
KEGGi ecj:Y75_p0622.
eco:b0632.
PATRICi 32116445. VBIEscCol129921_0662.

Organism-specific databases

EchoBASEi EB0197.
EcoGenei EG10201. dacA.

Phylogenomic databases

eggNOGi COG1686.
HOGENOMi HOG000086623.
InParanoidi P0AEB2.
KOi K07258.
OMAi YVIGQAV.
OrthoDBi EOG6RJV2H.
PhylomeDBi P0AEB2.

Enzyme and pathway databases

UniPathwayi UPA00219 .
BioCyci EcoCyc:EG10201-MONOMER.
ECOL316407:JW0627-MONOMER.
MetaCyc:EG10201-MONOMER.

Miscellaneous databases

EvolutionaryTracei P0AEB2.
PROi P0AEB2.

Gene expression databases

Genevestigatori P0AEB2.

Family and domain databases

Gene3Di 2.60.410.10. 1 hit.
3.40.710.10. 1 hit.
InterProi IPR012338. Beta-lactam/transpept-like.
IPR015956. Peniciliin-bd_prot-assoc.
IPR018044. Peptidase_S11.
IPR012907. Peptidase_S11_C.
IPR001967. Peptidase_S11_N.
[Graphical view ]
Pfami PF07943. PBP5_C. 1 hit.
PF00768. Peptidase_S11. 1 hit.
[Graphical view ]
PRINTSi PR00725. DADACBPTASE1.
SMARTi SM00936. PBP5_C. 1 hit.
[Graphical view ]
SUPFAMi SSF56601. SSF56601. 1 hit.
SSF69189. SSF69189. 1 hit.
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. Broome-Smith J.K.
    Submitted (APR-1984) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "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.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  4. "Sequence of minutes 4-25 of Escherichia coli."
    Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M., Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D., Namath A., Oefner P., Roberts D., Schramm S., Davis R.W.
    Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  5. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  6. "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.
  7. "An amino acid substitution that blocks the deacylation step in the enzyme mechanism of penicillin-binding protein 5 of Escherichia coli."
    Broome-Smith J.K., Spratt B.G.
    FEBS Lett. 165:185-189(1984) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 108-336, MUTANT DACA11191.
  8. "Genes encoding two lipoproteins in the leuS-dacA region of the Escherichia coli chromosome."
    Takase I., Ishino F., Wachi M., Kamata H., Doi M., Asoh S., Matsuzawa H., Ohta T., Matsuhashi M.
    J. Bacteriol. 169:5692-5699(1987) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-39.
    Strain: K12.
  9. "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 30-57.
  10. "Substitution of lysine 213 with arginine in penicillin-binding protein 5 of Escherichia coli abolishes D-alanine carboxypeptidase activity without affecting penicillin binding."
    Malhotra K.T., Nicholas R.A.
    J. Biol. Chem. 267:11386-11391(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF LYS-213.
  11. "Domain organization of penicillin-binding protein 5 from Escherichia coli analysed by C-terminal truncation."
    van der Linden M.P.G., de Haan L., Keck W.
    Biochem. J. 289:593-598(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: DOMAINS.
  12. "Escherichia coli proteome analysis using the gene-protein database."
    VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.
    Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY 2D-GEL.
  13. "Crystal structure of a deacylation-defective mutant of penicillin-binding protein 5 at 2.3-A resolution."
    Davies C., White S.W., Nicholas R.A.
    J. Biol. Chem. 276:616-623(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 30-386 OF MUTANT ASP-134.
  14. "Crystal structure of wild-type penicillin-binding protein 5 from Escherichia coli. Implications for deacylation of the acyl-enzyme complex."
    Nicholas R.A., Krings S., Tomberg J., Nicola G., Davies C.
    J. Biol. Chem. 278:52826-52833(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS) OF 30-386 OF WILD-TYPE AND MUTANT ASP-134, MUTAGENESIS OF 101-GLY--LYS-121.
  15. "Crystal structure of Escherichia coli penicillin-binding protein 5 bound to a tripeptide boronic acid inhibitor: a role for Ser-110 in deacylation."
    Nicola G., Peddi S., Stefanova M., Nicholas R.A., Gutheil W.G., Davies C.
    Biochemistry 44:8207-8217(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) OF 30-386 IN COMPLEX WITH SUBSTRATE ANALOG, REACTION MECHANISM.

Entry informationi

Entry nameiDACA_ECOLI
AccessioniPrimary (citable) accession number: P0AEB2
Secondary accession number(s): P04287, P77106
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 20, 1987
Last sequence update: March 20, 1987
Last modified: November 26, 2014
This is version 96 of the entry and version 1 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

External Data

Dasty 3