RegulonDB

Gene
Name:	dacA
Synonym(s):	ECK0625, EG10201, b0632, pfv
Genome position(nucleotides):	662752 <-- 663963
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	49.34
Reference(s):	[1] Broome-Smith JK., et al., 1988
External database links:

ASAP:	ABE-0002168
CGSC:	886
ECHOBASE:	EB0197
ECOLIHUB:	dacA
OU-MICROARRAY:	b0632
STRING:	511145.b0632
COLOMBOS:	dacA

Gene

Name:

dacA

Synonym(s):

ECK0625, EG10201, b0632, pfv

Genome position(nucleotides):

662752 <-- 663963

Strand:

reverse

Sequence:

Get nucleotide sequence FastaFormat

GC content %:

49.34

Reference(s):

[1] Broome-Smith JK., et al., 1988

External database links:

ASAP:

CGSC:

ECHOBASE:

ECOLIHUB:

OU-MICROARRAY:

STRING:

COLOMBOS:

Type

Positions

Sequence

Comment

1 -> 29

MNTIFSARIMKRLALTTALCTAFISAAHA

30 -> 403

DDLNIKTMIPGVPQIDAESYILIDYNSGKVLAEQNADVRRDPASLTKMMTSYVIGQAMKAGKFKETDLVTIGNDAWATGNPVFKGSSLMFLKPGMQVPVSQLIRGINLQSGNDACVAMADFAAGSQDAFVGLMNSYVNALGLKNTHFQTVHGLDADGQYSSARDMALIGQALIRDVPNEYSIYKEKEFTFNGIRQLNRNGLLWDNSLNVDGIKTGHTDKAGYNLVASATEGQMRLISAVMGGRTFKGREAESKKLLTWGFRFFETVNPLKVGKEFASEPVWFGDSDRASLGVDKDVYLTIPRGRMKDLKASYVLNSSELHAPLQKNQVVGTINFQLDGKTIEQRPLVVLQEIPEGNFFGKIIDYIKLMFHHWFG

UniProt: D-alanyl-D-alanine carboxypeptidase DacA.

38 -> 272

IPGVPQIDAESYILIDYNSGKVLAEQNADVRRDPASLTKMMTSYVIGQAMKAGKFKETDLVTIGNDAWATGNPVFKGSSLMFLKPGMQVPVSQLIRGINLQSGNDACVAMADFAAGSQDAFVGLMNSYVNALGLKNTHFQTVHGLDADGQYSSARDMALIGQALIRDVPNEYSIYKEKEFTFNGIRQLNRNGLLWDNSLNVDGIKTGHTDKAGYNLVASATEGQMRLISAVMGGR

73 -> 73

S → C/G: loss of function mutation; inactive with benzyl penicillin and bisacetyl-L-Lys-D-Ala-D-Ala

76 -> 76

K → R: loss of DD-carboxypeptidase activity; able to bind and hydrolyse penicillin at a reduced rate

Type

Positions

Sequence

Comment

1 -> 29

MNTIFSARIMKRLALTTALCTAFISAAHA

30 -> 403

UniProt: D-alanyl-D-alanine carboxypeptidase DacA.

38 -> 272

73 -> 73

S → C/G: loss of function mutation; inactive with benzyl penicillin and bisacetyl-L-Lys-D-Ala-D-Ala

76 -> 76

K → R: loss of DD-carboxypeptidase activity; able to bind and hydrolyse penicillin at a reduced rate

101 -> 121

GNDAWATGNPVFKGSSLMFLK

UniProt: Complete loss of enzyme activity. No effect on penicillin binding..

115 -> 115

S→A: significant decrease in DD-carboxypeptidase activity; no significant effect on interaction with penicillin G

116 -> 116

S→A: significant decrease in DD-carboxypeptidase activity; no significant effect on interaction with penicillin G

134 -> 134

UniProt: 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..

139 -> 139

S→A/E/T: loss of DD-carboxypeptiase activity but retains residual penicillin binding activity

141 -> 141

N→T/S: reduced DD-carboxypeptidase activity and varying effects on penicillin binding and hydrolysis

144 -> 144

C→S/A: no significant effect on DD-carboxypeptidase activity or interaction with penicillin

182 -> 182

L→E: significant reduction in the ability to restore normal morphology in strain CS703-1 (ΔPBP1, 4, 5, 6, 7, AmpC and AmpH); poor DD-carboxypeptidase activity in vitro; reduced rate of penicillin binding but no significant effect on dissociation; disrupts conformation of active site

204 -> 204

D→N: loss of DD-carboxypeptidase activity; acylation of pencillin strongly reduced but deacylation unaffected

213 -> 213

UniProt: Complete loss of enzyme activity. No effect on penicillin binding..

230 -> 248

LLWDNSLNVDGIKTGHTDK

'morphology maintenance domain'

242 -> 242

K→H: loss of DD-carboxypeptidase activity; retains residual penicillin binding activity

245 -> 245

H→S: affects DD-carboxypeptidase activity but not the interaction with penicillin

246 -> 246

T→S/A/P: varying affects on DD-carboxypeptidase activity and on the interaction with penicillin

292 -> 383

FETVNPLKVGKEFASEPVWFGDSDRASLGVDKDVYLTIPRGRMKDLKASYVLNSSELHAPLQKNQVVGTINFQLDGKTIEQRPLVVLQEIPE

386 -> 403

FFGKIIDYIKLMFHHWFG

PBP5CΔ18: mutant protein lacking its membrane anchor; retains DD-carboxypeptidase activity but is unable to to restore normal morphology in strain CS703-1 (ΔPBP1, 4, 5, 6, 7, AmpC and AmpH) and does not localize properly

Multifun Terms (GenProtEC)

1 - metabolism --> 1.6 - biosynthesis of macromolecules (cellular constituents) --> 1.6.7 - murein (peptidoglycan)

5 - cell processes --> 5.1 - cell division

5 - cell processes --> 5.6 - protection --> 5.6.4 - drug resistance/sensitivity

Gene Ontology Terms (GO)

cellular_component

GO:1990914 - integral component of periplasmic side of plasma membrane
GO:0016020 - membrane
GO:0030288 - outer membrane-bounded periplasmic space
GO:0005886 - plasma membrane
GO:0005887 - integral component of plasma membrane

molecular_function

GO:0005515 - protein binding
GO:0008233 - peptidase activity
GO:0016787 - hydrolase activity
GO:0004180 - carboxypeptidase activity
GO:0008800 - beta-lactamase activity
GO:0009002 - serine-type D-Ala-D-Ala carboxypeptidase activity
GO:0008658 - penicillin binding
GO:0042803 - protein homodimerization activity

biological_process

GO:0000270 - peptidoglycan metabolic process
GO:0051301 - cell division
GO:0006508 - proteolysis
GO:0009252 - peptidoglycan biosynthetic process
GO:0008360 - regulation of cell shape
GO:0071555 - cell wall organization

Type	Name	Post Left	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
promoter	lipBp3	662399	reverse	nd	[COMP-AINF]	[2]
promoter	lipBp2	662401	reverse	nd	[COMP-AINF]	[2]
promoter	TSS_754 (cluster)	662704	reverse	nd	[RS-EPT-CBR]	[3]
promoter	dacAp2	663967	reverse	nd	[COMP-AINF]	[2]
promoter	dacAp3	664001	reverse	nd	[COMP-AINF], [RS-EPT-CBR]	[2], [3]

Type

Name

Post Left

Post Right

Strand

Notes

Evidence (Confirmed, Strong, Weak)

References

promoter

lipBp3

662399

reverse

[COMP-AINF]

[2]

promoter

lipBp2

662401

reverse

[COMP-AINF]

[2]

promoter

TSS_754 (cluster)

662704

reverse

[RS-EPT-CBR]

[3]

promoter

dacAp2

663967

reverse

[COMP-AINF]

[2]

promoter

dacAp3

664001

reverse

[COMP-AINF], [RS-EPT-CBR]

[2], [3]

Evidence
[COMP-AINF] Inferred computationally without human oversight
[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

Evidence

[COMP-AINF] Inferred computationally without human oversight

[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

Reference(s)
[1] Broome-Smith JK., Ioannidis I., Edelman A., Spratt BG., 1988, Nucleotide sequences of the penicillin-binding protein 5 and 6 genes of Escherichia coli., Nucleic Acids Res 16(4):1617
[2] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78
[3] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

Reference(s)

[1] Broome-Smith JK., Ioannidis I., Edelman A., Spratt BG., 1988, Nucleotide sequences of the penicillin-binding protein 5 and 6 genes of Escherichia coli., Nucleic Acids Res 16(4):1617

[2] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

[3] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.