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On One Page

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Gene |

Product(s) |

Expression|

Evolution |

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Standard Name	dacA
Gene Synonym(s)	ECK0625, b0632, JW0627, pbp, pfv^[1], pfv
Product Desc.	D-alanyl-D-alanine carboxypeptidase, fraction A; penicillin-binding protein 5^[2]^[3] D-alanine D-alanine carboxypeptidase PBP5, cell morphology; penicillin-binding protein 5; beta-lactamase activity^[4]
Product Synonyms(s)	D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 5)^[1], B0632^[2]^[1], Pfv^[2]^[1], DacA^[2]^[1], PBP5, ECK0625, JW0627, pfv, b0632
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): dacA^[2]
Regulation/Activity
Quick Links
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Notes

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A dacA deletion suppresses ftsK (Ts). DacA-deficient cells have a branching growth pattern and biofilm defect.^[4]

Gene

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Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name	dacA
Mnemonic	D-Alanine carboxypeptidase
Synonyms	ECK0625, b0632, JW0627, pbp, pfv^[1], pfv
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Notes

Location(s) and DNA Sequence

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<protect> See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain	Map location	Genome coordinates	Genome browsers	Sequence links
MG1655	14.27 minutes	MG1655: 663186..661975 <gbrowseImage> name=NC_000913:661975..663186 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 646546..645335 <gbrowseImage> name=NC_012967:645335..646546 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 564735..565946 <gbrowseImage> name=NC_012759:564735..565946 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 664385..663174 <gbrowseImage> name=NC_007779:663174..664385 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 602518..601307 <gbrowseImage> name=NC_010473:601307..602518 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
DH10B		DH10B: 715778..714567 <gbrowseImage> name=NC_010473:714567..715778 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type	Strain	Genomic Location	Evidence	Reference	Notes
Coding Start (SO:0000323)	MG1655	661978	Edman degradation	PMID:7042389
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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele	Nt change(s)	AA change(s)	Phenotype: Type	Phenotype: Description	Reference	Availability	Comments
dacAK213X		K213X		Complete loss of activity			seeded from UniProt:P0AEB2
dacA							Deletion
dacAK213R		K213R		Complete loss of enzyme activity. No effect on penicillin binding			seeded from UniProt:P0AEB2
dacAG134D		G134D		(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)			Strain variation; seeded from UniProt:P0AEB2
ΔdacA (Keio:JW0627)	deletion	deletion			PMID:16738554	Shigen CGSC8733^[5]
dacA::Tn5KAN-2 (FB20215)	Insertion at nt 263 in Minus orientation				PMID:15262929	E. coli Genome Project:FB20215	does not contain pKD46
ΔdacA::kan	deletion		Biolog:respiration	unable to respire D-Mannose	PMID:16095938
ΔdacA::kan	deletion		Biolog:respiration	unable to respire a-Ketoglutarate	PMID:16095938
dacA1191(ts)				temperature sensitive		CGSC:7490
ΔdacA771::kan					PMID:16738554	CGSC:100516
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Notes

Genetic Interactions

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Interactor	Interaction	Allele	Score(s)	Reference(s)	Accessions	Notes
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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource	Resource Type	Source	Notes/Reference
JW0627	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAATACCATTTTTTCCGCTCG Primer 2:CCACCAAACCAGTGATGGAACAT
1G6	Kohara Phage	Genobase	PMID:3038334
15D7	Kohara Phage	Genobase	PMID:3038334
crcA280::Tn10	Linked marker	CAG12077 = CGSC7347^[5]	est. P1 cotransduction: 77% ^[6] Synonyms:zbe-280::Tn10
asnB3057::Tn10	Linked marker	CAG18433 = CGSC7349^[5]	est. P1 cotransduction: 20% ^[6] Synonyms:zbf-3057::Tn10 nnnThe Tn10 in CAG18433 is inserted in the asnB regulatory region, 4 bp before the start of the asnB ORF.
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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
EcoCyc	EcoCyc:EG10201	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10201	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000195	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945222	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0197	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002168	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Product(s)

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Nomenclature

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

Standard name	DacA
Synonyms	D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 5)^[1], B0632^[2]^[1], Pfv^[2]^[1], DacA^[2]^[1], PBP5, ECK0625, JW0627, pfv, b0632
Product description	D-alanyl-D-alanine carboxypeptidase, fraction A; penicillin-binding protein 5^[2]^[3] D-alanine D-alanine carboxypeptidase PBP5, cell morphology; penicillin-binding protein 5; beta-lactamase activity^[4]
EC number (for enzymes)	3.4.16.4^[1]
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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				C	Seeded from Riley et al 2006 ^[1].	Missing: evidence, reference
	GO:0009002	serine-type D-Ala-D-Ala carboxypeptidase activity	PMID:368033	IMP: Inferred from Mutant Phenotype		F		complete
	GO:0009002	serine-type D-Ala-D-Ala carboxypeptidase activity	PMID:1740130	IDA: Inferred from Direct Assay		F		complete
	GO:0006508	proteolysis	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001967	P	Seeded from EcoCyc (v14.0)	complete
	GO:0005887	integral to plasma membrane	PMID:319999	IDA: Inferred from Direct Assay		C		complete
	GO:0006508	proteolysis	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012907	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006508	proteolysis	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR015956	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006508	proteolysis	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR018044	P	Seeded from EcoCyc (v14.0)	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:0008800	beta-lactamase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:3.5.2.6	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009002	serine-type D-Ala-D-Ala carboxypeptidase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001967	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009002	serine-type D-Ala-D-Ala carboxypeptidase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012907	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009002	serine-type D-Ala-D-Ala carboxypeptidase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR018044	F	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
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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	glpD		PMID:19402753	LCMS(ID Probability):99.6
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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
Inner membrane		PMID:3279397, PMID:8424800, PMID:8486152	EchoLocation:dacA	Membrane anchored
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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 MNTIFSARIM KRLALTTALC TAFISAAHAD DLNIKTMIPG VPQIDAESYI LIDYNSGKVL AEQNADVRRD PASLTKMMTS YVIGQAMKAG KFKETDLVTI GNDAWATGNP VFKGSSLMFL KPGMQVPVSQ LIRGINLQSG NDACVAMADF AAGSQDAFVG LMNSYVNALG LKNTHFQTVH GLDADGQYSS ARDMALIGQA LIRDVPNEYS IYKEKEFTFN GIRQLNRNGL LWDNSLNVDG IKTGHTDKAG YNLVASATEG QMRLISAVMG GRTFKGREAE SKKLLTWGFR FFETVNPLKV GKEFASEPVW FGDSDRASLG VDKDVYLTIP RGRMKDLKAS YVLNSSELHA PLQKNQVVGT INFQLDGKTI EQRPLVVLQE IPEGNFFGKI IDYIKLMFHH WFG
Length	403
Mol. Wt	44.445 kDa
pI	8.5 (calculated)
Extinction coefficient	43,890 - 44,140 (calc based on 11 Y, 5 W, and 2 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	1-29	UniProt Manual:Signal Peptides	UniProt:P0AEB2
Modification Site	345	phosphorylation site at S345	probability greater than 75%	PMID:17938405
Domain	35..273	PF00768 D-alanyl-D-alanine carboxypeptidase		PMID:19920124
Domain	292..383	PF07943 Penicillin-binding protein 5, C-terminal domain		PMID:19920124
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<motif_map/>

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

Structures

<beststructure> gene=dacA 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:16128615	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945222	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002168	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0AEB2	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10201	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10201	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945222	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000195	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0197	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Expression

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Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Cellular Levels

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See Help:Cellular levels

Molecule	Organism or Strain	Value	Units	Experimental Conditions	Assay used	Notes	Reference(s)
Protein	E. coli K-12 MC4100	6.29E+02	molecules/cell	Medium: median data from rich and minimal media Temperature (°C): 37 Doubling time (min): Growth Rate(min): Growth phase: other:	emPAI		PMID:18304323
Protein	Ecoli K-12	5.122+/-0.073	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.089182494	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		by RNA_Seq	PMID:20671182
Protein	E. coli K-12 MG1655	4143	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling		PMID: 24766808
Protein	E. coli K-12 MG1655	1180	molecules/cell/generation	Medium: MOPS Minimal Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling		PMID: 24766808
Protein	E. coli K-12 MG1655	2135	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling		PMID: 24766808
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Notes

Transcription and Transcriptional Regulation

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

Transcription unit(s)
dacA
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Figure courtesy of RegulonDB

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Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

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<protect><gbrowseImage> name=NC_000913:663166..663206 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

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Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

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<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name	Mutation	Phenotype	Reference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type	Reference	Notes
microarray	GEO Profiles:b0632 (EcoliWiki Page)	NCBI GEO profiles for dacA
microarray	GenExpDB:b0632 (EcoliWiki Page)	Summary of data for dacA from multiple microarray studies
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Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name	Resource Type	Description	Source	Notes
	GFP Fusion	Intergenic region (663090..663382) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ11; Well:B10^[7]
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Notes

Accessions Related to dacA Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10201	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0197	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0632
EcoGene	EcoGene:EG10201	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000195	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002168	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Evolution

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Homologs in Other Organisms

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

Organism	Homologs (Statistics)	Comments
Xenopus tropicalis	ENSXETP00000051393 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	DACA	From SHIGELLACYC
E. coli O157	DACA	From ECOO157CYC
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Do-It-Yourself Web Tools

Notes

Families

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

Database	Accession	Notes
Superfamily (EcoliWiki Page)	SUPERFAMILY:56601
Superfamily (EcoliWiki Page)	SUPERFAMILY:69189
Pfam (EcoliWiki Page)	PF00768 D-alanyl-D-alanine carboxypeptidase
Pfam (EcoliWiki Page)	PF07943 Penicillin-binding protein 5, C-terminal domain
EcoCyc	EcoCyc:EG10201	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10201	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000195	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0197	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002168	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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References

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

↑ ^1.00 ^1.01 ^1.02 ^1.03 ^1.04 ^1.05 ^1.06 ^1.07 ^1.08 ^1.09 ^1.10 ^1.11 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.0 ^2.1 ^2.2 ^2.3 ^2.4 ^2.5 ^2.6 ^2.7 ^2.8 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 ^4.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^5.0 ^5.1 ^5.2 CGSC: The Coli Genetics Stock Center
↑ ^6.0 ^6.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

dacA:On One Page

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Notes

Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

Notes

Accessions in Other Databases

Notes

Links

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

Expression

Overview

Cellular Levels

Notes

Transcription and Transcriptional Regulation

Notes

Translation and Regulation of Translation

Notes

Turnover and Regulation of Turnover

Notes

Experimental

Notes

Accessions Related to dacA Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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