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Protein

RNA polymerase-binding transcription factor DksA

Gene

dksA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: -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. Required, probably upstream of the two-component system BarA-UvrY, for expression of CsrA-antagonistic small RNAs CsrB and CsrC (PubMed:21488981).UniRule annotation6 Publications

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

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

Keywordsi

LigandMetal-binding, Zinc

Enzyme and pathway databases

BioCyciEcoCyc:EG10230-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

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 (PubMed:12142416). Increased expression of ectopic dksA, 2-fold decreased expression of CsrA, 10-fold decreased expression of sRNAs CsrB and CsrC (PubMed:21488981).2 Publications

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. Increased transcription of its own RNA; when associated with N-74. 2 Publications1
Mutagenesisi74D → N: Does not increase ppGpp-dependent inhibition of transcription, but retains its ability to bind to RNAP; when associated with N-71. Increased transcription of its own RNA; when associated with N-71. 2 Publications1

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-2DPAGEiP0ABS1

Expressioni

Inductioni

Expression levels are constant during exponential and stationary phase (at protein level) (PubMed:21488981). Negatively regulates its own transcription, translationally activated by CsrA (PubMed:21488981).1 Publication

Interactioni

Subunit structurei

Interacts directly with the RNA polymerase.UniRule annotation2 Publications

Protein-protein interaction databases

BioGridi425974248 interactors.
DIPiDIP-31875N
IntActiP0ABS1 12 interactors.
MINTiP0ABS1
STRINGi316385.ECDH10B_0125

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[»]
5VSWX-ray4.29M1-151[»]
5W1TX-ray4.50M/N1-151[»]
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

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
InterProiView protein in InterPro
IPR012784 DksA_RNA_pol-bd
IPR037187 DnaK_N
IPR020460 Znf_C4-type_bac
IPR000962 Znf_DskA_TraR
IPR020458 Znf_DskA_TraR_CS
PfamiView protein in Pfam
PF01258 zf-dskA_traR, 1 hit
PRINTSiPR00618 DKSAZNFINGER
SUPFAMiSSF109635 SSF109635, 1 hit
TIGRFAMsiTIGR02420 dksA, 1 hit
PROSITEiView protein in PROSITE
PS01102 ZF_DKSA_1, 1 hit
PS51128 ZF_DKSA_2, 1 hit

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
GeneIDi32370326
944850
KEGGiecj:JW0141
eco:b0145
PATRICifig|1411691.4.peg.2136

Similar proteinsi

Entry informationi

Entry nameiDKSA_ECOLI
AccessioniPrimary (citable) accession number: P0ABS1
Secondary accession number(s): P18274
Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 25, 2005
Last sequence update: October 25, 2005
Last modified: March 28, 2018
This is version 106 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

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