P24228 (DACB_ECOLI) Reviewed, UniProtKB/Swiss-Prot

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) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

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

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 wall macromolecule catabolic process Inferred from direct assay Ref.6. Source: EcoCyc cell wall organization Inferred from direct assay Ref.6. Source: EcoCyc cytokinesis by binary fission Inferred from genetic interaction PubMed 12399477. Source: EcoCyc peptidoglycan biosynthetic process Inferred from electronic annotation. Source: UniProtKB-UniPathway 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 genetic interaction PubMed 11325933PubMed 15466028PubMed 15576782. Source: EcoCyc response to antibiotic Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	outer membrane-bounded periplasmic space Inferred from mutant phenotype PubMed 331322. Source: EcoliWiki
Molecular_function	endopeptidase activity Inferred from direct assay Ref.6. Source: EcoCyc penicillin binding Inferred from direct assay PubMed 319999. Source: EcoCyc serine-type D-Ala-D-Ala carboxypeptidase activity Inferred from mutant phenotype PubMed 331322. 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

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

62

1

Acyl-ester intermediate

Active site

65

1

Proton acceptor By similarity

Active site

306

1

By similarity

Binding site

417

1

Substrate By similarity

Experimental info

Sequence conflict

261

1

D → Y Ref.5

Sequence conflict

427

1

L → Q in CAA42643. Ref.1

Secondary structure

1

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477

Helix Strand Turn

Details...

Helix

23 – 27

5

Beta strand

35 – 42

8

Beta strand

49 – 53

5

Helix

61 – 63

3

Helix

64 – 75

12

Beta strand

83 – 93

11

Beta strand

96 – 104

9

Helix

113 – 125

13

Beta strand

130 – 133

4

Beta strand

135 – 138

4

Helix

153 – 155

3

Helix

159 – 161

3

Helix

170 – 172

3

Beta strand

173 – 179

7

Beta strand

189 – 191

3

Beta strand

199 – 207

9

Beta strand

209 – 211

3

Turn

213 – 216

4

Beta strand

219 – 224

6

Helix

225 – 227

3

Beta strand

228 – 236

9

Beta strand

242 – 247

6

Helix

251 – 265

15

Beta strand

269 – 272

4

Beta strand

274 – 277

4

Beta strand

285 – 291

7

Helix

295 – 305

11

Helix

308 – 323

16

Helix

329 – 342

14

Beta strand

356 – 358

3

Helix

367 – 379

13

Helix

381 – 384

4

Helix

387 – 389

3

Turn

393 – 395

3

Helix

397 – 399

3

Helix

403 – 407

5

Turn

411 – 413

3

Beta strand

414 – 421

8

Beta strand

424 – 432

9

Beta strand

438 – 447

10

Helix

452 – 454

3

Turn

455 – 457

3

Helix

460 – 475

16

Sequences

	Sequence		Length	Mass (Da)
	P24228 [UniParc]. Last modified November 1, 1995. Version 2. Checksum: 4EF5E43D2BEC4E5B	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

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] [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]	"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.
[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.
+	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.
YP_491367.1. NC_007779.1.

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.

STRING

511145.b3182.

Protein family/group databases

MEROPS

S13.001.

Proteomic databases

PaxDb

P24228.

PRIDE

P24228.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC76214; AAC76214; b3182.
BAE77226; BAE77226; BAE77226.

GeneID

12933443.
947693.

KEGG

ecj:Y75_p3102.
eco:b3182.

PATRIC

32121782. VBIEscCol129921_3275.

Organism-specific databases

EchoBASE

EB0198.

EcoGene

EG10202. dacB.

Phylogenomic databases

eggNOG

COG2027.

HOGENOM

HOG000279266.

KO

K07259.

OMA

FRTIGHE.

ProtClustDB

PRK11113.

Enzyme and pathway databases

BioCyc

EcoCyc:EG10202-MONOMER.
ECOL316407:JW3149-MONOMER.
MetaCyc:EG10202-MONOMER.

BRENDA

3.4.17.14. 2026.

UniPathway

UPA00219.

Gene expression databases

Genevestigator

P24228.

Family and domain databases

Gene3D

3.40.710.10. 1 hit.

InterPro

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

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

ChEMBL

CHEMBL1779.

DrugBank

DB00303. Ertapenem.
DB00760. Meropenem.

EvolutionaryTrace

P24228.

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:	May 1, 2013
This is version 115 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program