D-alanyl-D-alanine carboxypeptidase dacB precursor

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P24228 (DACB_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 103. History...

Clusters with 100%, 90%, 50% identity |

Documents (5) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

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

Alternative name(s):
D-alanyl-D-alanine endopeptidase
Short name=DD-endopeptidase
EC=3.4.21.-
Penicillin-binding protein 4
Short name=PBP-4

Gene names

Name:	dacB
Ordered Locus Names:	b3182, JW3149

Organism

Escherichia coli (strain K12)

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	477 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	Not involved in transpeptidation but exclusively catalyzes a DD-carboxypeptidase and DD-endopeptidase reaction. Ref.6
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	Periplasm Potential.
Miscellaneous	In E.coli there are three murein endopeptidases: two are penicillin sensitive (dacB and pbpG), the other (mepA) not.
Sequence similarities	Belongs to the peptidase S13 family.

Ontologies

Keywords
Biological process	Antibiotic resistance Cell cycle Cell division Cell shape Cell wall biogenesis/degradation Peptidoglycan synthesis
Cellular component	Periplasm
Domain	Signal
Molecular function	Hydrolase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological process	cell cycle Inferred from electronic annotation. Source: UniProtKB-KW cell division Inferred from electronic annotation. Source: UniProtKB-KW cell wall macromolecule catabolic process Inferred from direct assay Ref.6. Source: EcoCyc cellular cell wall organization Inferred from direct assay Ref.6. Source: EcoCyc peptidoglycan biosynthetic process Inferred from electronic annotation. Source: UniProtKB-KW peptidoglycan catabolic process Inferred from direct assay Ref.6. Source: EcoCyc peptidoglycan turnover Inferred from direct assay Ref.6. Source: EcoCyc proteolysis Inferred from electronic annotation. Source: InterPro regulation of cell shape Inferred from electronic annotation. Source: UniProtKB-KW response to antibiotic Inferred from electronic annotation. Source: UniProtKB-KW response to drug Inferred from mutant phenotype. Source: EcoliWiki
Cellular component	outer membrane-bounded periplasmic space Inferred from mutant phenotype. Source: EcoliWiki
Molecular function	endopeptidase activity Inferred from direct assay Ref.6. Source: EcoCyc penicillin binding Inferred from direct assay. Source: EcoCyc serine-type D-Ala-D-Ala carboxypeptidase activity Inferred from mutant phenotype. Source: EcoliWiki
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
argG	P0A6E4	1	EBI-1131834,EBI-1120296

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Signal peptide

1 – 20

Ref.1

Chain

21 – 477

457

D-alanyl-D-alanine carboxypeptidase dacB

PRO_0000027241

Regions

Region

90 – 263

174

Absent in class-A beta-lactamases

Sites

Active site

Acyl-ester intermediate

Active site

Proton acceptor By similarity

Active site

306

By similarity

Binding site

417

Substrate By similarity

Experimental info

Sequence conflict

261

D → Y Ref.5

Sequence conflict

427

L → Q in CAA42643. Ref.1

Secondary structure

477

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P24228 [UniParc].

Last modified November 1, 1995. Version 2.
Checksum: 4EF5E43D2BEC4E5B
Show »

FASTA

477

51,798

        10         20         30         40         50         60 
MRFSRFIIGL TSCIAFSVQA ANVDEYITQL PAGANLALMV QKVGASAPAI DYHSQQMALP 

        70         80         90        100        110        120 
ASTQKVITAL AALIQLGPDF RFTTTLETKG NVENGVLKGD LVARFGADPT LKRQDIRNMV 

       130        140        150        160        170        180 
ATLKKSGVNQ IDGNVLIDTS IFASHDKAPG WPWNDMTQCF SAPPAAAIVD RNCFSVSLYS 

       190        200        210        220        230        240 
APKPGDMAFI RVASYYPVTM FSQVRTLPRG SAEAQYCELD VVPGDLNRFT LTGCLPQRSE 

       250        260        270        280        290        300 
PLPLAFAVQD GASYAGAILK DELKQAGITW SGTLLRQTQV NEPGTVVASK QSAPLHDLLK 

       310        320        330        340        350        360 
IMLKKSDNMI ADTVFRMIGH ARFNVPGTWR AGSDAVRQIL RQQAGVDIGN TIIADGSGLS 

       370        380        390        400        410        420 
RHNLIAPATM MQVLQYIAQH DNELNFISML PLAGYDGSLQ YRAGLHQAGV DGKVSAKTGS 

       430        440        450        460        470 
LQGVYNLAGF ITTASGQRMA FVQYLSGYAV EPADQRNRRI PLVRFESRLY KDIYQNN

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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: 2040429] [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]	"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: 9278503] [Abstract] 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: 16738553] [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: 16411754] [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: 2046551] [Abstract] Cited for: FUNCTION.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

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.

PIR

A54535.

RefSeq

NP_417649.1. NC_000913.2.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2EX2	X-ray	1.55	A	21-477	[»]
2EX6	X-ray	1.60	A	21-477	[»]
2EX8	X-ray	1.60	A	21-477	[»]
2EX9	X-ray	1.65	A	21-477	[»]
2EXA	X-ray	1.70	A	21-477	[»]
2EXB	X-ray	1.75	A	21-477	[»]

ProteinModelPortal

P24228.

SMR

P24228. Positions 22-477.

ModBase

Search...

Protein-protein interaction databases

IntAct

P24228. 1 interaction.

Protein family/group databases

MEROPS

S13.001.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

EBESCT00000003389; EBESCP00000003389; EBESCG00000002777.
EBESCT00000018009; EBESCP00000017300; EBESCG00000017065.

GeneID

947693.

GenomeReviews

Gene locus JW3149 in contig AP009048_GR.
Gene locus b3182 in contig U00096_GR.

KEGG

ecj:JW3149.
eco:b3182.

PATRIC

32121782. VBIEscCol129921_3275.

Organism-specific databases

EchoBASE

EB0198.

EcoGene

EG10202. dacB.

Phylogenomic databases

eggNOG

COG2027.

GeneTree

EBGT00050000010654.

HOGENOM

HBG432869.

OMA

LYKDLYQ.

PhylomeDB

P24228.

ProtClustDB

PRK11113.

Enzyme and pathway databases

BioCyc

EcoCyc:EG10202-MONOMER.
MetaCyc:EG10202-MONOMER.

BRENDA

3.4.17.14. 2026.

Gene expression databases

Genevestigator

P24228.

Family and domain databases

InterPro

IPR012338. Beta-lactam/transpept-like.
IPR000667. Peptidase_S13.
[Graphical view]

Gene3D

G3DSA:3.40.710.10. G3DSA:3.40.710.10. 2 hits.

K07259.

Pfam

PF02113. Peptidase_S13. 1 hit.
[Graphical view]

PRINTS

PR00922. DADACBPTASE3.

SUPFAM

SSF56601. PBP_transp_fold. 1 hit.

TIGRFAMs

TIGR00666. PBP4. 1 hit.

ProtoNet

Search...

Other

DrugBank

DB00303. Ertapenem.
DB00760. Meropenem.

Entry information

Entry name

DACB_ECOLI

Accession

Primary (citable) accession number: P24228
Secondary accession number(s): Q2M930

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 1, 1992
Last sequence update:	November 1, 1995
Last modified:	January 25, 2012
This is version 103 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Peptidase families

Classification of peptidase families and list of entries

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene

PATHWAY comments

Index of metabolic and biosynthesis pathways

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Regions

Sites

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Protein family/group databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents