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Protein

RNA polymerase-binding transcription factor DksA

Gene

dksA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Transcription factor that acts by binding directly to the RNA polymerase (RNAP). Required for negative regulation of rRNA expression and positive regulation of several amino acid biosynthesis promoters. Also required for regulation of fis expression. Binding to RNAP disrupts interaction of RNAP with DNA, inhibits formation of initiation complexes, and amplifies effects of ppGpp and the initiating NTP on rRNA transcription. Inhibits transcript elongation, exonucleolytic RNA cleavage and pyrophosphorolysis, and increases intrinsic termination. Also involved, with RecN, in repair of DNA double-strand breaks.UniRule annotation5 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi114ZincUniRule annotation1 Publication1
Metal bindingi117ZincUniRule annotation1 Publication1
Metal bindingi135ZincUniRule annotation1 Publication1
Metal bindingi138ZincUniRule annotation1 Publication1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri114 – 138dksA C4-typeUniRule annotationAdd BLAST25

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

BioCyciEcoCyc:EG10230-MONOMER.
ECOL316407:JW0141-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
RNA polymerase-binding transcription factor DksAUniRule annotation
Alternative name(s):
DnaK suppressor protein
Gene namesi
Name:dksAUniRule annotation
Ordered Locus Names:b0145, JW0141
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10230. dksA.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: UniProtKB
  • cytosol Source: EcoCyc
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Disruption phenotypei

Deletion blocks induction of rpoS by ppGpp, but does not alter relA expression, ppGpp regulation or RNA control during the stringent response.1 Publication

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi71D → N: Does not increase ppGpp-dependent inhibition of transcription, but retains its ability to bind to RNAP; when associated with N-74. 1 Publication1
Mutagenesisi74D → N: Does not increase ppGpp-dependent inhibition of transcription, but retains its ability to bind to RNAP; when associated with N-71. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001875361 – 151RNA polymerase-binding transcription factor DksAAdd BLAST151

Proteomic databases

EPDiP0ABS1.
PaxDbiP0ABS1.
PRIDEiP0ABS1.

2D gel databases

SWISS-2DPAGEP0ABS1.

Interactioni

Subunit structurei

Interacts directly with the RNA polymerase.UniRule annotation2 Publications

Protein-protein interaction databases

BioGridi4259742. 22 interactors.
DIPiDIP-31875N.
IntActiP0ABS1. 11 interactors.
MINTiMINT-8413451.
STRINGi511145.b0145.

Structurei

Secondary structure

1151
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi13 – 17Combined sources5
Helixi34 – 67Combined sources34
Helixi72 – 74Combined sources3
Helixi75 – 107Combined sources33
Beta strandi115 – 118Combined sources4
Helixi123 – 128Combined sources6
Helixi136 – 150Combined sources15

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1TJLX-ray2.00A/B/C/D/E/F/G/H/I/J1-151[»]
DisProtiDP00414.
ProteinModelPortaliP0ABS1.
SMRiP0ABS1.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0ABS1.

Family & Domainsi

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili33 – 54UniRule annotationAdd BLAST22

Sequence similaritiesi

Belongs to the DksA family.UniRule annotation
Contains 1 dksA C4-type zinc finger.UniRule annotation

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri114 – 138dksA C4-typeUniRule annotationAdd BLAST25

Keywords - Domaini

Coiled coil, Zinc-finger

Phylogenomic databases

eggNOGiCOG1734. LUCA.
HOGENOMiHOG000178407.
InParanoidiP0ABS1.
KOiK06204.
OMAiAQERHEK.
PhylomeDBiP0ABS1.

Family and domain databases

HAMAPiMF_00926. DksA. 1 hit.
InterProiIPR012784. DksA_RNA_pol-bd.
IPR020460. Znf_C4-type_bac.
IPR000962. Znf_DskA_TraR.
IPR020458. Znf_DskA_TraR_CS.
[Graphical view]
PfamiPF01258. zf-dskA_traR. 1 hit.
[Graphical view]
PRINTSiPR00618. DKSAZNFINGER.
TIGRFAMsiTIGR02420. dksA. 1 hit.
PROSITEiPS01102. ZF_DKSA_1. 1 hit.
PS51128. ZF_DKSA_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P0ABS1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQEGQNRKTS SLSILAIAGV EPYQEKPGEE YMNEAQLAHF RRILEAWRNQ
60 70 80 90 100
LRDEVDRTVT HMQDEAANFP DPVDRAAQEE EFSLELRNRD RERKLIKKIE
110 120 130 140 150
KTLKKVEDED FGYCESCGVE IGIRRLEARP TADLCIDCKT LAEIREKQMA

G
Length:151
Mass (Da):17,528
Last modified:October 25, 2005 - v1
Checksum:i620842DB15E066A9
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti4G → Q AA sequence (PubMed:9298646).Curated1
Sequence conflicti94 – 95KL → NV in AAA23687 (PubMed:2180916).Curated2

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M34945 Genomic DNA. Translation: AAA23687.1.
U00096 Genomic DNA. Translation: AAC73256.1.
AP009048 Genomic DNA. Translation: BAB96722.1.
M60726 Genomic DNA. Translation: AAA72978.1.
PIRiS45214.
RefSeqiNP_414687.1. NC_000913.3.
WP_001155227.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC73256; AAC73256; b0145.
BAB96722; BAB96722; BAB96722.
GeneIDi5549448.
944850.
KEGGiecj:JW0141.
eco:b0145.
PATRICi32115397. VBIEscCol129921_0150.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M34945 Genomic DNA. Translation: AAA23687.1.
U00096 Genomic DNA. Translation: AAC73256.1.
AP009048 Genomic DNA. Translation: BAB96722.1.
M60726 Genomic DNA. Translation: AAA72978.1.
PIRiS45214.
RefSeqiNP_414687.1. NC_000913.3.
WP_001155227.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1TJLX-ray2.00A/B/C/D/E/F/G/H/I/J1-151[»]
DisProtiDP00414.
ProteinModelPortaliP0ABS1.
SMRiP0ABS1.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4259742. 22 interactors.
DIPiDIP-31875N.
IntActiP0ABS1. 11 interactors.
MINTiMINT-8413451.
STRINGi511145.b0145.

2D gel databases

SWISS-2DPAGEP0ABS1.

Proteomic databases

EPDiP0ABS1.
PaxDbiP0ABS1.
PRIDEiP0ABS1.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73256; AAC73256; b0145.
BAB96722; BAB96722; BAB96722.
GeneIDi5549448.
944850.
KEGGiecj:JW0141.
eco:b0145.
PATRICi32115397. VBIEscCol129921_0150.

Organism-specific databases

EchoBASEiEB0226.
EcoGeneiEG10230. dksA.

Phylogenomic databases

eggNOGiCOG1734. LUCA.
HOGENOMiHOG000178407.
InParanoidiP0ABS1.
KOiK06204.
OMAiAQERHEK.
PhylomeDBiP0ABS1.

Enzyme and pathway databases

BioCyciEcoCyc:EG10230-MONOMER.
ECOL316407:JW0141-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP0ABS1.
PROiP0ABS1.

Family and domain databases

HAMAPiMF_00926. DksA. 1 hit.
InterProiIPR012784. DksA_RNA_pol-bd.
IPR020460. Znf_C4-type_bac.
IPR000962. Znf_DskA_TraR.
IPR020458. Znf_DskA_TraR_CS.
[Graphical view]
PfamiPF01258. zf-dskA_traR. 1 hit.
[Graphical view]
PRINTSiPR00618. DKSAZNFINGER.
TIGRFAMsiTIGR02420. dksA. 1 hit.
PROSITEiPS01102. ZF_DKSA_1. 1 hit.
PS51128. ZF_DKSA_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiDKSA_ECOLI
AccessioniPrimary (citable) accession number: P0ABS1
Secondary accession number(s): P18274
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 25, 2005
Last sequence update: October 25, 2005
Last modified: November 2, 2016
This is version 96 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

Dosage-dependent suppressor of a dnaK deletion mutation. It suppressed not only the temperature-sensitive growth but also the filamentous phenotype of the dnaK deletion strain, while the defect of lambda growth is not suppressed (PubMed:2180916).1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.