RegulonDB

Gene
Name:	dcuS
Synonym(s):	ECK4118, G7827, b4125, yjdH
Genome position(nucleotides):	4350031 <-- 4351662
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	49.94
External database links:

ASAP:	ABE-0013509
ECHOBASE:	EB2358
ECOLIHUB:	dcuS
OU-MICROARRAY:	b4125
STRING:	511145.b4125
COLOMBOS:	dcuS

Gene

Name:

dcuS

Synonym(s):

ECK4118, G7827, b4125, yjdH

Genome position(nucleotides):

4350031 <-- 4351662

Strand:

reverse

Sequence:

Get nucleotide sequence FastaFormat

GC content %:

49.94

External database links:

ASAP:

ECHOBASE:

ECOLIHUB:

OU-MICROARRAY:

STRING:

COLOMBOS:

Type

Positions

Sequence

Comment

21 -> 41

VILMVSAVLFSVLLVVHLIYF

46 -> 179

DMTRDGLANKALAVARTLADSPEIRQGLQKKPQESGIQAIAEAVRKRNDLLFIVVTDMQSLRYSHPEAQRIGQPFKGDDILKALNGEENVAINRGFLAQALRVFTPIYDENHKQIGVVAIGLELSRVTQQINDS

periplasmic domain forming a novel α-β fold

47 -> 179

MTRDGLANKALAVARTLADSPEIRQGLQKKPQESGIQAIAEAVRKRNDLLFIVVTDMQSLRYSHPEAQRIGQPFKGDDILKALNGEENVAINRGFLAQALRVFTPIYDENHKQIGVVAIGLELSRVTQQINDS

107 -> 141

RYSHPEAQRIGQPFKGDDILKALNGEENVAINRGF

putative ligand binding region

110 -> 110

UniProt: Abolishes the stimulation by fumarate to the same extent as complete deletion of the dcuS gene..

Type

Positions

Sequence

Comment

21 -> 41

VILMVSAVLFSVLLVVHLIYF

46 -> 179

DMTRDGLANKALAVARTLADSPEIRQGLQKKPQESGIQAIAEAVRKRNDLLFIVVTDMQSLRYSHPEAQRIGQPFKGDDILKALNGEENVAINRGFLAQALRVFTPIYDENHKQIGVVAIGLELSRVTQQINDS

periplasmic domain forming a novel α-β fold

47 -> 179

MTRDGLANKALAVARTLADSPEIRQGLQKKPQESGIQAIAEAVRKRNDLLFIVVTDMQSLRYSHPEAQRIGQPFKGDDILKALNGEENVAINRGFLAQALRVFTPIYDENHKQIGVVAIGLELSRVTQQINDS

107 -> 141

RYSHPEAQRIGQPFKGDDILKALNGEENVAINRGF

putative ligand binding region

110 -> 110

UniProt: Abolishes the stimulation by fumarate to the same extent as complete deletion of the dcuS gene..

120 -> 120

F &arr; A: no longer responds to fumarate and D-tartrate but is able to respond to L-malate, citrate and mesaconate (as measured by dcu-lacZ reporter expression)

140 -> 142

GFL

UniProt: (R)-malate binding; Sequence Annotation Type: region of interest.

147 -> 147

R → A: autophosphorylation no longer stimulated by C4 dicarboxylates but activation independent kinase activity (ie. autophosphorylation activity that occurs in the absence of C4 dicarboxylates) is unaffected; no longer responds to mesaconate, fumarate, citrate and D-tartrate but is able to respond to L-malate (as measured by dcu-lacZ reporter expression)

149 -> 149

F → K: no longer responds to mesaconate and citrate but is able to respond to L-malate, fumarate and D-tartrate (as measured by dcu-lacZ reporter expression)

182 -> 202

SIIWSVLFGMLVGLIGTCILV

UniProt: Helical.

212 -> 323

LEPYEISTLFEQRQAMLQSIKEGVVAVDDRGEVTLINDAAQELLNYRKSQDDEKLSTLSHSWSQVVDVSEVLRDGTPRRDEEITIKDRLLLINTVPVRSNGVIIGAISTFRD

UniProt: PAS.

220 -> 291

LFEQRQAMLQSIKEGVVAVDDRGEVTLINDAAQELLNYRKSQDDEKLSTLSHSWSQVVDVSEVLRDGTPRRD

UniProt: PAS;

222 -> 323

EQRQAMLQSIKEGVVAVDDRGEVTLINDAAQELLNYRKSQDDEKLSTLSHSWSQVVDVSEVLRDGTPRRDEEITIKDRLLLINTVPVRSNGVIIGAISTFRD

228 -> 228

L → A: classified as a type IIB 'on' mutation, results in constitutive expression of dcuB-lacZ reporter but does not effect PAS_c dimerization or interaction with DctA

233 -> 233

E → G: classified as a type IIA 'on' mutation, results in constitutive expression of dcuB-lacZ reporter, PAS_c dimerization unaffected but interaction of PAS_c with DctA is abolished

248 -> 248

UniProt: Causes constitutive active state of the kinase, leading to constitutive expression of a target gene, without addition of C4-dicarboxylates..

276 -> 276

V → A: classified as an 'off' mutation, results in a low level reporter gene (dcuB-lacZ) expression even in the presence of fumarate, does not affect dimerization

300 -> 300

L → A: classified as an 'off' mutation, results in a low level reporter gene (dcuB-lacZ) expression even in the presence of fumarate, does not affect dimerization

304 -> 304

N → D: classified as a type IIB 'on' mutation, results in constitutive expression of dcuB-lacZ reporter but does not effect PAS_c dimerization or interaction with DctA

321 -> 321

F → A: classified as a type IIA 'on' mutation, results in constitutive expression of dcuB-lacZ reporter, PAS_c dimerization unaffected but interaction of PAS_c with DctA is abolished

322 -> 322

R → A: classified as a type IIB 'on' mutation, results in constitutive expression of dcuB-lacZ reporter but does not effect PAS_c dimerization or interaction with DctA

339 -> 384

NYADALRERSHEFMNKLHVILGLLHLKSYKQLEDYILKTANNYQEE

346 -> 538

ERSHEFMNKLHVILGLLHLKSYKQLEDYILKTANNYQEEIGSLLGKIKSPVIAGFLISKINRATDLGHTLILNSESQLPDSGSEDQVATLITTLGNLIENALEALGPEPGGEISVTLHYRHGWLHCEVNDDGPGIAPDKIDHIFDKGVSTKGSERGVGLALVKQQVENLGGSIAVESEPGIFTQFFVQIPWDG

UniProt: Histidine kinase;

435 -> 535

LITTLGNLIENALEALGPEPGGEISVTLHYRHGWLHCEVNDDGPGIAPDKIDHIFDKGVSTKGSERGVGLALVKQQVENLGGSIAVESEPGIFTQFFVQIP

Multifun Terms (GenProtEC)

1 - metabolism --> 1.3 - energy metabolism, carbon --> 1.3.7 - anaerobic respiration

2 - information transfer --> 2.3 - protein related --> 2.3.3 - posttranslational modification

3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.4 - complex regulation --> 3.1.2.4.3 - two component regulatory systems (external signal)

3 - regulation --> 3.1 - type of regulation --> 3.1.3 - posttranscriptional --> 3.1.3.2 - covalent modification, demodification, maturation

Gene Ontology Terms (GO)

cellular_component

GO:0009365 - protein histidine kinase complex
GO:0005829 - cytosol
GO:0016020 - membrane
GO:0030288 - outer membrane-bounded periplasmic space
GO:0005886 - plasma membrane
GO:0005887 - integral component of plasma membrane
GO:0016021 - integral component of membrane

molecular_function

GO:0005515 - protein binding
GO:0016740 - transferase activity
GO:0016772 - transferase activity, transferring phosphorus-containing groups
GO:0016301 - kinase activity
GO:0000166 - nucleotide binding
GO:0005524 - ATP binding
GO:0000155 - phosphorelay sensor kinase activity
GO:0004673 - protein histidine kinase activity
GO:0042802 - identical protein binding

biological_process

GO:0006355 - regulation of transcription, DNA-templated
GO:0006468 - protein phosphorylation
GO:0016310 - phosphorylation
GO:0000160 - phosphorelay signal transduction system
GO:0007165 - signal transduction
GO:0046777 - protein autophosphorylation
GO:0018106 - peptidyl-histidine phosphorylation

Transcriptional Regulation
	Display Regulation
Activated by:	FNR
Repressed by:	NarL

Transcriptional Regulation

Display Regulation

Activated by:

FNR

Repressed by:

NarL

Type	Name	Post Left	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
promoter	TSS_4923 (cluster)	4347981	reverse	nd	[RS-EPT-CBR]	[1]
promoter	TSS_4924	4348786	reverse	nd	[RS-EPT-CBR]	[1]
promoter	TSS_4925	4348841	reverse	nd	[RS-EPT-CBR]	[1]
promoter	TSS_4927	4351813	forward	nd	[RS-EPT-CBR]	[1]

Type

Name

Post Left

Post Right

Strand

Notes

Evidence (Confirmed, Strong, Weak)

References

promoter

TSS_4923 (cluster)

4347981

reverse

[RS-EPT-CBR]

[1]

promoter

TSS_4924

4348786

reverse

[RS-EPT-CBR]

[1]

promoter

TSS_4925

4348841

reverse

[RS-EPT-CBR]

[1]

promoter

TSS_4927

4351813

forward

[RS-EPT-CBR]

[1]

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

Evidence

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

Reference(s)
[1] 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] 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.