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Standard Name	dksA
Gene Synonym(s)	ECK0144, b0145, JW0141, msmA^[1], msmA
Product Desc.	RNAP-binding transcriptional regulator of rRNA transcription^[2]^[3] RNAP-binding protein modulating ppGpp and iNTP regulation; reduces open complex half-life on rRNA promoters^[4]
Product Synonyms(s)	RNAP-binding transcriptional regulator of rRNA transcription, DnaK suppressor protein^[1], B0145^[2]^[1], MsmA^[2]^[1], DksA^[2]^[1] , ECK0144, JW0141, msmA, b0145
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s):
Regulation/Activity
Quick Links
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Notes

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High copy dksA suppresses mukB and TS growth and filamentation of a dnaK mutant. dksA is also a multicopy suppressor of dnaJ, grpE and prc. dksA transcription is alkali-inducible. Mutations affect chromosomal supercoiling. Binds TrxA (Kumar, 2004). HT_Cmplx24_Cyt: DksA+GreA. dksA and ybiI are paralogs.^[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	dksA
Mnemonic	dnaK suppressor
Synonyms	ECK0144, b0145, JW0141, msmA^[1], msmA
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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	3.45 minutes	MG1655: 160604..160149 <gbrowseImage> name=NC_000913:160149..160604 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 163455..163000 <gbrowseImage> name=NC_012967:163000..163455 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 160148..160603 <gbrowseImage> name=NC_012759:160148..160603 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 160604..160149 <gbrowseImage> name=NC_007779:160149..160604 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 134708..134253 <gbrowseImage> name=NC_010473:134253..134708 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	160149	Edman degradation	PMID:9298646 PMID:9600841 PMID:9740056
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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
dksA(del) (Keio:JW0141)	deletion	deletion			PMID:16738554	Shigen CGSC8412^[5]
dksA(del)::kan	deletion		Biolog:respiration	unable to respire Acetate	PMID:16095938
dksA(del)::kan	deletion		Biolog:respiration	unable to respire a-Hydroxybutyrate	PMID:16095938
dksA(del)::kan	deletion		Biolog:respiration	unable to respire a-Ketobutyrate	PMID:16095938
dksA(del)::kan	deletion		Biolog:respiration	unable to respire L-Alanine	PMID:16095938
dksA(del)::kan	deletion		Biolog:respiration	unable to respire L-Alanyl-glycine	PMID:16095938
dksA761(del)::kan					PMID:16738554	CGSC:100618
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Notes

Suppressors of ΔdksA map to rpoBand rpoC. The mutations map to the area of the RNA polymerase structure that binds the template strand around the switch regions.

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
JW0141	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCCAAGAAGGGCAAAACCGTAA Primer 2:CCGCCAGCCATCTGTTTTTCGCG
11C5	Kohara Phage	Genobase	PMID:3038334
15A7	Kohara Phage	Genobase	PMID:3038334
zad-220::Tn10	Linked marker	CAG12025 = CGSC7326^[5]	est. P1 cotransduction: 67% ^[6]
yafC502::Tn10	Linked marker	CAG18436 = CGSC7328^[5]	est. P1 cotransduction: 1% ^[6] Synonyms:zae-502::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:EG10230	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10230	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000224	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:944850	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0226	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000499	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	DksA
Synonyms	RNAP-binding transcriptional regulator of rRNA transcription, DnaK suppressor protein^[1], B0145^[2]^[1], MsmA^[2]^[1], DksA^[2]^[1] , ECK0144, JW0141, msmA, b0145
Product description	RNAP-binding transcriptional regulator of rRNA transcription^[2]^[3] RNAP-binding protein modulating ppGpp and iNTP regulation; reduces open complex half-life on rRNA promoters^[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:0008270	zinc ion binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000962	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008270	zinc ion binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012784	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008270	zinc ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0862	F	Seeded from EcoCyc (v14.0)	complete
	GO:0046872	metal ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0479	F	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	References	Evidence
Protein	ykgF	PMID:16606699	Experiment(s):EBI-1135704
Protein	yedD	PMID:16606699	Experiment(s):EBI-1135704
Protein	uspG	PMID:16606699	Experiment(s):EBI-1135704
Protein	yneG	PMID:16606699	Experiment(s):EBI-1135704
Protein	bcsZ	PMID:16606699	Experiment(s):EBI-1135704
Protein	glpK	PMID:16606699	Experiment(s):EBI-1135704
Protein	pepD	PMID:16606699	Experiment(s):EBI-1135704
Protein	ydiH	PMID:19402753	LCMS(ID Probability):99.6
Protein	mrcB	PMID:19402753	LCMS(ID Probability):99.6
Protein	eno	PMID:19402753	LCMS(ID Probability):99.6
Protein	dnaN	PMID:19402753	LCMS(ID Probability):91.6 MALDI(Z-score):21.608492
Protein	rpsJ	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
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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 MQEGQNRKTS SLSILAIAGV EPYQEKPGEE YMNEAQLAHF RRILEAWRNQ LRDEVDRTVT HMQDEAANFP DPVDRAAQEE EFSLELRNRD RERKLIKKIE KTLKKVEDED FGYCESCGVE IGIRRLEARP TADLCIDCKT LAEIREKQMA G
Length	151
Mol. Wt	17.527 kDa
pI	4.9 (calculated)
Extinction coefficient	9,970 - 10,470 (calc based on 3 Y, 1 W, and 4 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
Domain	109..147	PF01258 Prokaryotic dksA/traR C4-type zinc finger		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=dksA taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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Notes

DksA is a small protein with a long coiled-coil that resembles the coiled coil in Gre factors. DksA binds in the same position in the RNA polymerase secondary channel.

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:16128138	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:944850	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000499	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0ABS1	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10230	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10230	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:944850	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000224	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0226	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	3.19E+03	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	E. coli K-12 EMG2	260	molecules/cell	Medium: MOPS glucose minimal Temperature (°C): 37 Doubling time (min): Growth phase: Exponential OD: OD600 = 0.2 to 0.25 other: aerated	Quantitative protein sequencing	Spot ID: Ml37	PMID: 9298646
Protein	E. coli K-12 MG1655	21225	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	5438	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	17469	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)
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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_000913:160584..160624 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:b0145 (EcoliWiki Page)	NCBI GEO profiles for dksA
microarray	GenExpDB:b0145 (EcoliWiki Page)	Summary of data for dksA 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 (160512..160833) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ10; Well:B4^[7]
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Notes

Accessions Related to dksA Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10230	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0226	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0145
EcoGene	EcoGene:EG10230	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000224	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000499	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	DKSA	From SHIGELLACYC
E. coli O157	DKSA	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:57716
Superfamily (EcoliWiki Page)	SUPERFAMILY:109635
Pfam (EcoliWiki Page)	PF01258 Prokaryotic dksA/traR C4-type zinc finger
EcoCyc	EcoCyc:EG10230	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10230	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000224	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0226	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000499	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 ^1.8 ^1.9 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 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

dksA:On One Page

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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 dksA Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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