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Gene |

Product(s) |

Expression|

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Standard Name	dcuS
Gene Synonym(s)	ECK4118, b4125, JW4086, yjdH^[1], yjdH
Product Desc.	sensory histidine kinase in two-component regulatory system with DcuR, regulator of anaerobic fumarate respiration^[1] C4-dicarboxylate regulation of anaerobic fumurate respiratory system; two-component system sensory histidine kinase^[2]
Product Synonyms(s)	B4125^[3]^[1], YjdH^[3]^[1], ECK4118, JW4086, yjdH, b4125
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): dcuSR^[3]
Regulation/Activity
Quick Links
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Notes

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dcuSR operon is repressed by nitrate via the NarXL system.^[2]

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	dcuS
Mnemonic	Dicarboxylate uptake
Synonyms	ECK4118, b4125, JW4086, yjdH^[1], yjdH
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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	93.71 minutes	MG1655: 4349685..4348054 <gbrowseImage> name=NC_000913:4348054..4349685 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
BW2952		NC_012759: 4286789..4288420 <gbrowseImage> name=NC_012759:4286789..4288420 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 4356340..4354709 <gbrowseImage> name=NC_007779:4354709..4356340 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 4450047..4448416 <gbrowseImage> name=NC_010473:4448416..4450047 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
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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
ΔdcuS (Keio:JW4086)	deletion	deletion			PMID:16738554	Shigen CGSC10942^[4]
ΔdcuS::kan	deletion		Biolog:respiration	unable to respire Succinate	PMID:16095938
ΔdcuS::kan	deletion		Biolog:respiration	unable to respire Bromosuccinate	PMID:16095938
ΔdcuS::kan	deletion		Biolog:respiration	unable to respire L-Asparagine	PMID:16095938
ΔdcuS::kan	deletion		Biolog:respiration	unable to respire L-Aspartate	PMID:16095938
ΔdcuS751::kan					PMID:16738554	CGSC:100550
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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
JW4086	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAGACATTCATTGCCCTACCG Primer 2:CCTCTGTTCGACCTCTCCCCGTC
5H2	Kohara Phage	Genobase	PMID:3038334
21H11	Kohara Phage	Genobase	PMID:3038334
zje-2241::Tn10	Linked marker	CAG18427 = CGSC7481^[4]	est. P1 cotransduction: 16% ^[5]
cadB2231::Tn10	Linked marker	CAG18488 = CGSC7479^[4]	est. P1 cotransduction: 75% ^[5] Synonyms:zjd-2231::Tn10
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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:G7827	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12465	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004324	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948639	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2358	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013509	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	DcuS
Synonyms	B4125^[3]^[1], YjdH^[3]^[1], ECK4118, JW4086, yjdH, b4125
Product description	sensory histidine kinase in two-component regulatory system with DcuR, regulator of anaerobic fumarate respiration^[1] C4-dicarboxylate regulation of anaerobic fumurate respiratory system; two-component system sensory histidine kinase^[2]
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:0000155	phosphorelay sensor kinase activity	PMID:12167640	IDA: Inferred from Direct Assay		F		complete
	GO:0006355	regulation of transcription, DNA-dependent	PMID:14996819	IDA: Inferred from Direct Assay		P		complete
	GO:0016021	integral to membrane	PMID:12907689	ISS: Inferred from Sequence or Structural Similarity	EcoliWiki:citA	C	NMR was used to determine the protein structure. It showed structural similarity to the CitA family of sensors.	complete
	GO:0005886	plasma membrane	PMID:11803016	IDA: Inferred from Direct Assay		C		complete
	GO:0000160	two-component signal transduction system (phosphorelay)	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016120	P	Seeded from EcoCyc (v14.0)	complete
	GO:0000160	two-component signal transduction system (phosphorelay)	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0902	P	Seeded from EcoCyc (v14.0)	complete
	GO:0000166	nucleotide binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0547	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004673	protein histidine kinase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005467	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004673	protein histidine kinase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:2.7.13.3	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005886	plasma membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0997	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005886	plasma membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-1003	C	Seeded from EcoCyc (v14.0)	complete
	GO:0006468	protein amino acid phosphorylation	PMID:12167640	IDA: Inferred from Direct Assay		P	Figure 1	complete
	GO:0006355	regulation of transcription, DNA-dependent	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR013767	P	Seeded from EcoCyc (v14.0)	complete
	GO:0004673	protein histidine kinase activity	PMID:12167640	IDA: Inferred from Direct Assay		F		complete
	GO:0007165	signal transduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000014	P	Seeded from EcoCyc (v14.0)	complete
	GO:0000160	two-component signal transduction system (phosphorelay)	PMID:12167640	IDA: Inferred from Direct Assay		P	with DcuR	complete
	GO:0007165	signal transduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005467	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016020	membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0472	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016021	integral to membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0812	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016021	integral to membrane	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-9909	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016301	kinase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0418	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016310	phosphorylation	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004358	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	sdhA		PMID:16606699	Experiment(s):EBI-1147500
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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
plasma membrane	C-terminus localized in the cytoplasm with 2 predicted transmembrane domains	Daley et al. (2005) ^[6]
plasma membrane
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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 MRHSLPYRML RKRPMKLSTT VILMVSAVLF SVLLVVHLIY FSQISDMTRD GLANKALAVA RTLADSPEIR QGLQKKPQES GIQAIAEAVR KRNDLLFIVV TDMQSLRYSH PEAQRIGQPF KGDDILKALN GEENVAINRG FLAQALRVFT PIYDENHKQI GVVAIGLELS RVTQQINDSR WSIIWSVLFG MLVGLIGTCI LVKVLKKILF GLEPYEISTL FEQRQAMLQS IKEGVVAVDD RGEVTLINDA AQELLNYRKS QDDEKLSTLS HSWSQVVDVS EVLRDGTPRR DEEITIKDRL LLINTVPVRS NGVIIGAIST FRDKTEVRKL MQRLDGLVNY ADALRERSHE FMNKLHVILG LLHLKSYKQL EDYILKTANN YQEEIGSLLG KIKSPVIAGF LISKINRATD LGHTLILNSE SQLPDSGSED QVATLITTLG NLIENALEAL GPEPGGEISV TLHYRHGWLH CEVNDDGPGI APDKIDHIFD KGVSTKGSER GVGLALVKQQ VENLGGSIAV ESEPGIFTQF FVQIPWDGER SNR
Length	543
Mol. Wt	60.552 kDa
pI	6.7 (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	References
Domain	430..537	PF02518 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase	PMID:19920124
Domain	222..324	PF00989 PAS fold	PMID:19920124
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<motif_map/>

Click the image to view raw output from TMHMM.

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

Structures

<beststructure> gene=dcuS 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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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:16131951	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948639	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013509	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0AEC8	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G7827	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12465	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948639	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004324	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2358	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	Reference(s)
Protein	E. coli K-12 MG1655	79	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	21	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	43	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)
dcuSR
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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_000913:4349665..4349705 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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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:b4125 (EcoliWiki Page)	NCBI GEO profiles for dcuS
microarray	GenExpDB:b4125 (EcoliWiki Page)	Summary of data for dcuS 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 (4349145..4349425) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ04; Well:B11^[7]
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Notes

Accessions Related to dcuS Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G7827	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2358	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b4125
EcoGene	EcoGene:EG12465	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004324	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013509	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
Shigella flexneri	YJDH	From SHIGELLACYC
E. coli O157	YJDH	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
Pfam (EcoliWiki Page)	PF02518 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
Panther (EcoliWiki Page)	PTHR24423:SF74
Superfamily (EcoliWiki Page)	SUPERFAMILY:55785
Superfamily (EcoliWiki Page)	SUPERFAMILY:55874
Superfamily (EcoliWiki Page)	SUPERFAMILY:103190
Pfam (EcoliWiki Page)	PF00989 PAS fold
EcoCyc	EcoCyc:G7827	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12465	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004324	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2358	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013509	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.

↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 ^1.5 ^1.6 ^1.7 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.0 ^2.1 ^2.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^3.0 ^3.1 ^3.2 ^3.3 ^3.4 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 ^4.2 CGSC: The Coli Genetics Stock Center
↑ ^5.0 ^5.1 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).
↑ Daley, DO et al. (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 308 1321-3 PubMed
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

dcuS: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 dcuS Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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