P0AEB2 (DACA_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
D-alanyl-D-alanine carboxypeptidase DacA
Short name=DD-carboxypeptidase
Short name=DD-peptidase
EC=3.4.16.4

Alternative name(s):
Beta-lactamase
EC=3.5.2.6
Penicillin-binding protein 5
Short name=PBP-5

Gene names

Name:	dacA
Synonyms:	pfv
Ordered Locus Names:	b0632, JW0627

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	403 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Removes C-terminal D-alanyl residues from sugar-peptide cell wall precursors.
Catalytic activity	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.
Pathway	Cell wall biogenesis; peptidoglycan biosynthesis.
Subcellular location	Cell inner membrane; Peripheral membrane protein; Cytoplasmic side. Note: N-terminal lies in the periplasmic space.
Sequence similarities	Belongs to the peptidase S11 family.
Sequence caution	The sequence AAB40832.1 differs from that shown. Reason: Erroneous initiation.

Ontologies

Keywords
Biological process	Cell shape Cell wall biogenesis/degradation Peptidoglycan synthesis
Cellular component	Cell inner membrane Cell membrane Membrane
Domain	Signal
Molecular function	Carboxypeptidase Hydrolase Protease
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	cell division Inferred from genetic interaction PubMed 2254246. Source: EcoCyc cell wall macromolecule metabolic process Inferred from direct assay PubMed 7002918. Source: EcoCyc peptidoglycan biosynthetic process Inferred from electronic annotation. Source: UniProtKB-UniPathway peptidoglycan metabolic process Inferred from direct assay PubMed 7002918. Source: EcoCyc proteolysis Inferred from electronic annotation. Source: UniProtKB-KW regulation of cell shape Inferred from genetic interaction PubMed 9324260. Source: EcoCyc
Cellular_component	integral to plasma membrane Inferred from direct assay PubMed 319999. Source: EcoliWiki
Molecular_function	beta-lactamase activity Inferred from electronic annotation. Source: EC penicillin binding Inferred from direct assay PubMed 7002918. Source: EcoCyc serine-type D-Ala-D-Ala carboxypeptidase activity Inferred from direct assay PubMed 14750804. Source: EcoCyc
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
yfaY	P77808	1	EBI-548634,EBI-556720

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Signal peptide

1 – 29

29

Ref.9

Chain

30 – 403

374

D-alanyl-D-alanine carboxypeptidase DacA

PRO_0000027231

Sites

Active site

73

1

Acyl-ester intermediate

Active site

76

1

Proton acceptor

Active site

139

1

Binding site

242

1

Substrate

Natural variations

Natural variant

134

1

G → 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. Ref.13 Ref.14

Experimental info

Mutagenesis

101 – 121

21

Missing: Complete loss of enzyme activity. No effect on penicillin binding. Ref.14

Mutagenesis

213

1

K → R: Complete loss of enzyme activity. No effect on penicillin binding. Ref.10

Mutagenesis

213

1

K → X: Complete loss of activity. Ref.10

Secondary structure

1

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403

Helix Strand Turn

Details...

Turn

33 – 35

3

Beta strand

46 – 53

8

Turn

54 – 56

3

Beta strand

59 – 64

6

Helix

72 – 74

3

Helix

75 – 88

14

Beta strand

97 – 99

3

Helix

102 – 104

3

Helix

106 – 108

3

Helix

110 – 112

3

Beta strand

125 – 127

3

Helix

128 – 136

9

Helix

141 – 152

12

Helix

155 – 168

14

Beta strand

179 – 183

5

Helix

191 – 204

14

Helix

206 – 209

4

Helix

210 – 213

4

Beta strand

216 – 219

4

Beta strand

222 – 225

4

Helix

229 – 232

4

Beta strand

236 – 246

11

Turn

247 – 249

3

Beta strand

250 – 259

10

Beta strand

262 – 271

10

Helix

274 – 276

3

Helix

279 – 291

13

Beta strand

292 – 298

7

Beta strand

304 – 320

17

Beta strand

325 – 330

6

Helix

334 – 336

3

Beta strand

338 – 350

13

Beta strand

357 – 365

9

Beta strand

368 – 379

12

Sequences

	Sequence		Length	Mass (Da)
	P0AEB2 [UniParc]. Last modified March 20, 1987. Version 1. Checksum: 7FAAB8E98452FF22	FASTA	403	44,444
	10 20 30 40 50 60 MNTIFSARIM KRLALTTALC TAFISAAHAD DLNIKTMIPG VPQIDAESYI LIDYNSGKVL 70 80 90 100 110 120 AEQNADVRRD PASLTKMMTS YVIGQAMKAG KFKETDLVTI GNDAWATGNP VFKGSSLMFL 130 140 150 160 170 180 KPGMQVPVSQ LIRGINLQSG NDACVAMADF AAGSQDAFVG LMNSYVNALG LKNTHFQTVH 190 200 210 220 230 240 GLDADGQYSS ARDMALIGQA LIRDVPNEYS IYKEKEFTFN GIRQLNRNGL LWDNSLNVDG 250 260 270 280 290 300 IKTGHTDKAG YNLVASATEG QMRLISAVMG GRTFKGREAE SKKLLTWGFR FFETVNPLKV 310 320 330 340 350 360 GKEFASEPVW FGDSDRASLG VDKDVYLTIP RGRMKDLKAS YVLNSSELHA PLQKNQVVGT 370 380 390 400 INFQLDGKTI EQRPLVVLQE IPEGNFFGKI IDYIKLMFHH WFG

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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]	"A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 12.7-28.0 min region on the linkage map." Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K., Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S., Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K. , Mori H., Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G., Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M., Horiuchi T. DNA Res. 3:137-155(1996) [PubMed] [Europe PMC] [Abstract] 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]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract] 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.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

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.

PIR

ZPECP5. A28536.

RefSeq

NP_415165.1. NC_000913.2.
YP_488923.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1HD8	X-ray	2.30	A	30-386	[»]
1NJ4	X-ray	1.90	A	30-386	[»]
1NZO	X-ray	1.85	A	30-386	[»]
1NZU	X-ray	2.00	A	30-386	[»]
1SDN	X-ray	2.50	A	30-386	[»]
1Z6F	X-ray	1.60	A	30-386	[»]
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	[»]

ProteinModelPortal

P0AEB2.

SMR

P0AEB2. Positions 32-386.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-47947N.

IntAct

P0AEB2. 8 interactions.

MINT

MINT-1247273.

STRING

511145.b0632.

Protein family/group databases

MEROPS

S11.008.

PTM databases

PhosSite

P0809377.

Proteomic databases

PaxDb

P0AEB2.

PRIDE

P0AEB2.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC73733; AAC73733; b0632.
BAA35275; BAA35275; BAA35275.

GeneID

12931704.
945222.

KEGG

ecj:Y75_p0622.
eco:b0632.

PATRIC

32116445. VBIEscCol129921_0662.

Organism-specific databases

EchoBASE

EB0197.

EcoGene

EG10201. dacA.

Phylogenomic databases

eggNOG

COG1686.

HOGENOM

HOG000086623.

KO

K07258.

OMA

KTMIPAV.

ProtClustDB

PRK10793.

Enzyme and pathway databases

BioCyc

EcoCyc:EG10201-MONOMER.
ECOL316407:JW0627-MONOMER.
MetaCyc:EG10201-MONOMER.

UniPathway

UPA00219.

Gene expression databases

Genevestigator

P0AEB2.

Family and domain databases

Gene3D

2.60.410.10. 1 hit.
3.40.710.10. 1 hit.

InterPro

IPR012338. Beta-lactam/transpept-like.
IPR015956. Peniciliin-bd_prot-assoc.
IPR018044. Peptidase_S11.
IPR012907. Peptidase_S11_C.
IPR001967. Peptidase_S11_N.
[Graphical view]

Pfam

PF07943. PBP5_C. 1 hit.
PF00768. Peptidase_S11. 1 hit.
[Graphical view]

PRINTS

PR00725. DADACBPTASE1.

SMART

SM00936. PBP5_C. 1 hit.
[Graphical view]

SUPFAM

SSF56601. PBP_transp_fold. 1 hit.
SSF69189. Peniciliin-bd_prot-assoc. 1 hit.

ProtoNet

Search...

Other

ChEMBL

CHEMBL1816.

EvolutionaryTrace

P0AEB2.

Entry information

Entry name

DACA_ECOLI

Accession

Primary (citable) accession number: P0AEB2
Secondary accession number(s): P04287, P77106

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 20, 1987
Last sequence update:	March 20, 1987
Last modified:	May 1, 2013
This is version 84 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program