P33013 (DACD_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

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

Alternative name(s):
Penicillin-binding protein 6b
Short name=PBP-6b

Gene names

Name:	dacD
Synonyms:	phsE, yeeC
Ordered Locus Names:	b2010, JW5329

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	388 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.
Pathway	Cell wall biogenesis; peptidoglycan biosynthesis.
Subcellular location	Cell inner membrane; Peripheral membrane protein Potential. Note: N-terminal lies in the periplasmic space Potential.
Sequence similarities	Belongs to the peptidase S11 family.
Sequence caution	The sequence AAA16416.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

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	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	peptidoglycan biosynthetic process Inferred from mutant phenotype Ref.1. Source: EcoCyc proteolysis Inferred from electronic annotation. Source: UniProtKB-KW regulation of cell shape Inferred from genetic interaction PubMed 11325933PubMed 12562782PubMed 15576782. Source: EcoCyc
Cellular_component	plasma membrane Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	carboxypeptidase activity Inferred from mutant phenotype Ref.1. Source: EcoCyc penicillin binding Inferred from direct assay Ref.1. Source: EcoCyc serine-type D-Ala-D-Ala carboxypeptidase activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Signal peptide	1 – 21	21	Potential
	Chain	22 – 388	367	D-alanyl-D-alanine carboxypeptidase DacD		PRO_0000027234
Sites
	Active site	63	1	Acyl-ester intermediate By similarity
	Active site	66	1	Proton acceptor By similarity
	Active site	129	1	By similarity
	Binding site	232	1	Substrate By similarity

Sequences

	Sequence		Length	Mass (Da)
	P33013 [UniParc]. Last modified July 15, 1998. Version 3. Checksum: 453FE18C21D207D0	FASTA	388	43,346
	10 20 30 40 50 60 MKRRLIIAAS LFVFNLSSGF AAENIPFSPQ PPEIHAGSWV LMDYTTGQIL TAGNEHQQRN 70 80 90 100 110 120 PASLTKLMTG YVVDRAIDSH RITPDDIVTV GRDAWAKDNP VFVGSSLMFL KEGDRVSVRD 130 140 150 160 170 180 LSRGLIVDSG NDACVALADY IAGGQRQFVE MMNNYAEKLH LKDTHFETVH GLDAPGQHSS 190 200 210 220 230 240 AYDLAVLSRA IIHGEPEFYH MYSEKSLTWN GITQQNRNGL LWDKTMNVDG LKTGHTSGAG 250 260 270 280 290 300 FNLIASAVDG QRRLIAVVMG ADSAKGREEE ARKLLRWGQQ NFTTVQILHR GKKVGTERIW 310 320 330 340 350 360 YGDKENIDLG TEQEFWMVLP KAEIPHIKAK YTLDGKELTA PISAHQRVGE IELYDRDKQV 370 380 AHWPLVTLES VGEGSMFSRL SDYFHHKA

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"dacD, an Escherichia coli gene encoding a novel penicillin-binding protein (PBP6b) with DD-carboxypeptidase activity." Baquero M.-R., Bouzon M., Quintela J.C., Ayala J.A., Moreno F. J. Bacteriol. 178:7106-7111(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], CHARACTERIZATION.
[2]	"Automated multiplex sequencing of the E.coli genome." Richterich P., Lakey N., Gryan G., Jaehn L., Mintz L., Robison K., Church G.M. Submitted (OCT-1993) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / BHB2600.
[3]	"A 460-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 40.1-50.0 min region on the linkage map." Itoh T., Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K., Kasai H., Kimura S., Kitakawa M., Kitagawa M., Makino K., Miki T., Mizobuchi K., Mori H., Mori T., Motomura K., Nakade S. , Nakamura Y., Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G., Seki Y., Sivasundaram S., Tagami H., Takeda J., Takemoto K., Wada C., Yamamoto Y., Horiuchi T. DNA Res. 3:379-392(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[4]	"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.
[5]	"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.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	U00009 Genomic DNA. Translation: AAA16416.1. Different initiation. U00096 Genomic DNA. Translation: AAC75071.2. AP009048 Genomic DNA. Translation: BAA15838.2.
PIR	A64966.
RefSeq	NP_416514.4. NC_000913.2. YP_490252.1. NC_007779.1.
3D structure databases
ProteinModelPortal	P33013.
SMR	P33013. Positions 29-375.
ModBase	Search...
Protein-protein interaction databases
STRING	511145.b2010.
Protein family/group databases
MEROPS	S11.009.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	AAC75071; AAC75071; b2010. BAA15838; BAA15838; BAA15838.
GeneID	12931419. 946518.
KEGG	ecj:Y75_p1972. eco:b2010.
PATRIC	32119355. VBIEscCol129921_2087.
Organism-specific databases
EchoBASE	EB1839.
EcoGene	EG11893. dacD.
Phylogenomic databases
eggNOG	COG1686.
HOGENOM	HOG000086623.
KO	K07258.
OMA	VAKSMWA.
ProtClustDB	PRK11397.
Enzyme and pathway databases
BioCyc	EcoCyc:RPOA-MONOMER. ECOL316407:JW5329-MONOMER. MetaCyc:RPOA-MONOMER.
UniPathway	UPA00219.
Gene expression databases
Genevestigator	P33013.
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	CHEMBL1990.

Entry information

Entry name

DACD_ECOLI

Accession

Primary (citable) accession number: P33013

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1994
Last sequence update:	July 15, 1998
Last modified:	May 1, 2013
This is version 122 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program