dacB:Gene Product(s)

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Nomenclature Function Interactions Localization Sequence Domains Structure Resources Accessions Links References Suggestions

Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name

DacB

Synonyms

D-alanyl-D-alanine carboxypeptidase[1], B3182[2][1], DacB[2][1], D-alanyl-D-alanine carboxypeptidase, fraction B; penicillin-binding protein 4[2][1] , ECK3171, JW3149, b3182

Product description

EG10202[2][3]

D-alanine D-alanine carboxypeptidase PBP4; penicillin-binding protein 4[4]

EC number (for enzymes)
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Notes

Function

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<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier GO ID GO term name Reference Evidence Code with/from Aspect Notes Status
GO:0030288

outer membrane-bounded periplasmic space

PMID:331322[5]

IMP: Inferred from Mutant Phenotype

C

Seeded from Riley et al 2006 [1].

complete

GO:0006508

proteolysis

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000667

P

Seeded from EcoCyc (v14.0)

complete

GO:0007049

cell cycle

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0131

P

Seeded from EcoCyc (v14.0)

complete

GO:0009002

serine-type D-Ala-D-Ala carboxypeptidase activity

PMID:331322[5]

IMP: Inferred from Mutant Phenotype

F

complete

GO:0008360

regulation of cell shape

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0133

P

Seeded from EcoCyc (v14.0)

complete

GO:0009002

serine-type D-Ala-D-Ala carboxypeptidase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:3.4.16.4

F

Seeded from EcoCyc (v14.0)

complete

GO:0009252

peptidoglycan biosynthetic process

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0573

P

Seeded from EcoCyc (v14.0)

complete

GO:0010382

cellular cell wall macromolecule metabolic process

PMID:2046551[6]

IDA: Inferred from Direct Assay

P

Seeded from EcoCyc (v14.0)

complete

GO:0046677

response to antibiotic

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0046

P

Seeded from EcoCyc (v14.0)

complete

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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type Partner Notes References Evidence

Protein

argG

PMID:16606699[7]

Experiment(s):EBI-1145060
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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment Description Evidence Reference/Source Notes

Periplasm

PMID:16411754[8], PMID:15576782[9]

EchoLocation:dacB


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Notes

Structure and Physical Properties

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<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence

at EcoCyc 

MRFSRFIIGL TSCIAFSVQA ANVDEYITQL PAGANLALMV QKVGASAPAI DYHSQQMALP
ASTQKVITAL AALIQLGPDF RFTTTLETKG NVENGVLKGD LVARFGADPT LKRQDIRNMV
ATLKKSGVNQ IDGNVLIDTS IFASHDKAPG WPWNDMTQCF SAPPAAAIVD RNCFSVSLYS
APKPGDMAFI RVASYYPVTM FSQVRTLPRG SAEAQYCELD VVPGDLNRFT LTGCLPQRSE
PLPLAFAVQD GASYAGAILK DELKQAGITW SGTLLRQTQV NEPGTVVASK QSAPLHDLLK
IMLKKSDNMI ADTVFRMIGH ARFNVPGTWR AGSDAVRQIL RQQAGVDIGN TIIADGSGLS
RHNLIAPATM MQVLQYIAQH DNELNFISML PLAGYDGSLQ YRAGLHQAGV DGKVSAKTGS
LQGVYNLAGF ITTASGQRMA FVQYLSGYAV EPADQRNRRI PLVRFESRLY KDIYQNN
Length

477

Mol. Wt

51.798 kDa

pI

9.0 (calculated)

Extinction coefficient

44,350 - 44,975 (calc based on 15 Y, 4 W, and 5 C residues)

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Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type Residues Description Notes References

motif

1-20

UniProt Manual:Signal Peptides

UniProt:P24228

Domain

60..446

PF02113 D-Ala-D-Ala carboxypeptidase 3 (S13) family

PMID:19920124[10]

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Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=dacB taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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Notes

Gene Product Resources

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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type Source Notes/Reference
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:16131072

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947693

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010458

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P24228

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10202

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10202

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947693

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000196

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0198

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 2.3 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. ↑ 5.0 5.1 Matsuhashi, M et al. (1977) Mutants of Escherichia coli lacking in highly penicillin-sensitive D-alanine carboxypeptidase activity. Proc. Natl. Acad. Sci. U.S.A. 74 2976-9 PubMed
  6. ↑ Korat, B et al. (1991) Penicillin-binding protein 4 of Escherichia coli: molecular cloning of the dacB gene, controlled overexpression, and alterations in murein composition. Mol. Microbiol. 5 675-84 PubMed
  7. ↑ Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  8. ↑ Kishida, H et al. (2006) Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, both in the native form and covalently linked to various antibiotics. Biochemistry 45 783-92 PubMed
  9. ↑ Meberg, BM et al. (2004) Endopeptidase penicillin-binding proteins 4 and 7 play auxiliary roles in determining uniform morphology of Escherichia coli. J. Bacteriol. 186 8326-36 PubMed
  10. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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