DKSA_ECOLI
ID DKSA_ECOLI Reviewed; 151 AA.
AC P0ABS1; P18274;
DT 25-OCT-2005, integrated into UniProtKB/Swiss-Prot.
DT 25-OCT-2005, sequence version 1.
DT 03-AUG-2022, entry version 130.
DE RecName: Full=RNA polymerase-binding transcription factor DksA {ECO:0000255|HAMAP-Rule:MF_00926};
DE AltName: Full=DnaK suppressor protein;
GN Name=dksA {ECO:0000255|HAMAP-Rule:MF_00926};
GN OrderedLocusNames=b0145, JW0141;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=2180916; DOI=10.1128/jb.172.4.2055-2064.1990;
RA Kang P.J., Craig E.A.;
RT "Identification and characterization of a new Escherichia coli gene that is
RT a dosage-dependent suppressor of a dnaK deletion mutation.";
RL J. Bacteriol. 172:2055-2064(1990).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=8202364; DOI=10.1093/nar/22.9.1637;
RA Fujita N., Mori H., Yura T., Ishihama A.;
RT "Systematic sequencing of the Escherichia coli genome: analysis of the 2.4-
RT 4.1 min (110,917-193,643 bp) region.";
RL Nucleic Acids Res. 22:1637-1639(1994).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-36.
RX PubMed=2013578; DOI=10.1128/jb.173.8.2644-2648.1991;
RA Kawamukai M., Utsumi R., Takeda K., Higashi A., Matsuda H., Choi Y.-L.,
RA Komano T.;
RT "Nucleotide sequence and characterization of the sfs1 gene: sfs1 is
RT involved in CRP*-dependent mal gene expression in Escherichia coli.";
RL J. Bacteriol. 173:2644-2648(1991).
RN [6]
RP PROTEIN SEQUENCE OF 1-8.
RC STRAIN=K12 / EMG2;
RX PubMed=9298646; DOI=10.1002/elps.1150180807;
RA Link A.J., Robison K., Church G.M.;
RT "Comparing the predicted and observed properties of proteins encoded in the
RT genome of Escherichia coli K-12.";
RL Electrophoresis 18:1259-1313(1997).
RN [7]
RP PROTEIN SEQUENCE OF 1-4.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9600841; DOI=10.1006/jmbi.1998.1726;
RA Wilkins M.R., Gasteiger E., Tonella L., Ou K., Tyler M., Sanchez J.-C.,
RA Gooley A.A., Walsh B.J., Bairoch A., Appel R.D., Williams K.L.,
RA Hochstrasser D.F.;
RT "Protein identification with N and C-terminal sequence tags in proteome
RT projects.";
RL J. Mol. Biol. 278:599-608(1998).
RN [8]
RP DISRUPTION PHENOTYPE.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=12142416; DOI=10.1128/jb.184.16.4455-4465.2002;
RA Brown L., Gentry D., Elliott T., Cashel M.;
RT "DksA affects ppGpp induction of RpoS at a translational level.";
RL J. Bacteriol. 184:4455-4465(2002).
RN [9]
RP FUNCTION, AND INTERACTION WITH RNAP.
RX PubMed=15294157; DOI=10.1016/j.cell.2004.07.009;
RA Paul B.J., Barker M.M., Ross W., Schneider D.A., Webb C., Foster J.W.,
RA Gourse R.L.;
RT "DksA: a critical component of the transcription initiation machinery that
RT potentiates the regulation of rRNA promoters by ppGpp and the initiating
RT NTP.";
RL Cell 118:311-322(2004).
RN [10]
RP FUNCTION IN DNA REPAIR.
RX PubMed=15948952; DOI=10.1111/j.1365-2958.2005.04677.x;
RA Meddows T.R., Savory A.P., Grove J.I., Moore T., Lloyd R.G.;
RT "RecN protein and transcription factor DksA combine to promote faithful
RT recombinational repair of DNA double-strand breaks.";
RL Mol. Microbiol. 57:97-110(2005).
RN [11]
RP SUBCELLULAR LOCATION.
RX PubMed=16858726; DOI=10.1002/elps.200500912;
RA Lasserre J.P., Beyne E., Pyndiah S., Lapaillerie D., Claverol S.,
RA Bonneu M.;
RT "A complexomic study of Escherichia coli using two-dimensional blue
RT native/SDS polyacrylamide gel electrophoresis.";
RL Electrophoresis 27:3306-3321(2006).
RN [12]
RP FUNCTION IN FIS REGULATION.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=16885445; DOI=10.1128/jb.00276-06;
RA Mallik P., Paul B.J., Rutherford S.T., Gourse R.L., Osuna R.;
RT "DksA is required for growth phase-dependent regulation, growth rate-
RT dependent control, and stringent control of fis expression in Escherichia
RT coli.";
RL J. Bacteriol. 188:5775-5782(2006).
RN [13]
RP FUNCTION, INDUCTION, DISRUPTION PHENOTYPE, AND MUTAGENESIS OF ASP-71 AND
RP ASP-74.
RC STRAIN=K12 / CF7789;
RX PubMed=21488981; DOI=10.1111/j.1365-2958.2011.07663.x;
RA Edwards A.N., Patterson-Fortin L.M., Vakulskas C.A., Mercante J.W.,
RA Potrykus K., Vinella D., Camacho M.I., Fields J.A., Thompson S.A.,
RA Georgellis D., Cashel M., Babitzke P., Romeo T.;
RT "Circuitry linking the Csr and stringent response global regulatory
RT systems.";
RL Mol. Microbiol. 80:1561-1580(2011).
RN [14]
RP FUNCTION.
RX PubMed=22210857; DOI=10.1093/nar/gkr1273;
RA Furman R., Sevostyanova A., Artsimovitch I.;
RT "Transcription initiation factor DksA has diverse effects on RNA chain
RT elongation.";
RL Nucleic Acids Res. 40:3392-3402(2012).
RN [15]
RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEX WITH ZINC, FUNCTION,
RP INTERACTION WITH RNAP, AND MUTAGENESIS OF ASP-71 AND ASP-74.
RX PubMed=15294156; DOI=10.1016/j.cell.2004.06.030;
RA Perederina A., Svetlov V., Vassylyeva M.N., Tahirov T.H., Yokoyama S.,
RA Artsimovitch I., Vassylyev D.G.;
RT "Regulation through the secondary channel--structural framework for ppGpp-
RT DksA synergism during transcription.";
RL Cell 118:297-309(2004).
CC -!- FUNCTION: Transcription factor that acts by binding directly to the RNA
CC polymerase (RNAP). Required for negative regulation of rRNA expression
CC and positive regulation of several amino acid biosynthesis promoters.
CC Also required for regulation of fis expression. Binding to RNAP
CC disrupts interaction of RNAP with DNA, inhibits formation of initiation
CC complexes, and amplifies effects of ppGpp and the initiating NTP on
CC rRNA transcription. Inhibits transcript elongation, exonucleolytic RNA
CC cleavage and pyrophosphorolysis, and increases intrinsic termination.
CC Also involved, with RecN, in repair of DNA double-strand breaks.
CC Required, probably upstream of the two-component system BarA-UvrY, for
CC expression of CsrA-antagonistic small RNAs CsrB and CsrC
CC (PubMed:21488981). {ECO:0000255|HAMAP-Rule:MF_00926,
CC ECO:0000269|PubMed:15294156, ECO:0000269|PubMed:15294157,
CC ECO:0000269|PubMed:15948952, ECO:0000269|PubMed:16885445,
CC ECO:0000269|PubMed:21488981, ECO:0000269|PubMed:22210857}.
CC -!- SUBUNIT: Interacts directly with the RNA polymerase.
CC {ECO:0000255|HAMAP-Rule:MF_00926, ECO:0000269|PubMed:15294156,
CC ECO:0000269|PubMed:15294157}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00926,
CC ECO:0000269|PubMed:16858726}.
CC -!- INDUCTION: Expression levels are constant during exponential and
CC stationary phase (at protein level) (PubMed:21488981). Negatively
CC regulates its own transcription, translationally activated by CsrA
CC (PubMed:21488981). {ECO:0000269|PubMed:21488981}.
CC -!- DISRUPTION PHENOTYPE: Deletion blocks induction of rpoS by ppGpp, but
CC does not alter relA expression, ppGpp regulation or RNA control during
CC the stringent response (PubMed:12142416). Increased expression of
CC ectopic dksA, 2-fold decreased expression of CsrA, 10-fold decreased
CC expression of sRNAs CsrB and CsrC (PubMed:21488981).
CC {ECO:0000269|PubMed:12142416, ECO:0000269|PubMed:21488981}.
CC -!- MISCELLANEOUS: Dosage-dependent suppressor of a dnaK deletion mutation.
CC It suppressed not only the temperature-sensitive growth but also the
CC filamentous phenotype of the dnaK deletion strain, while the defect of
CC lambda growth is not suppressed (PubMed:2180916).
CC {ECO:0000305|PubMed:2180916}.
CC -!- SIMILARITY: Belongs to the DksA family. {ECO:0000255|HAMAP-
CC Rule:MF_00926}.
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DR EMBL; M34945; AAA23687.1; -; Genomic_DNA.
DR EMBL; U00096; AAC73256.1; -; Genomic_DNA.
DR EMBL; AP009048; BAB96722.1; -; Genomic_DNA.
DR EMBL; M60726; AAA72978.1; -; Genomic_DNA.
DR PIR; S45214; S45214.
DR RefSeq; NP_414687.1; NC_000913.3.
DR RefSeq; WP_001155227.1; NZ_STEB01000010.1.
DR PDB; 1TJL; X-ray; 2.00 A; A/B/C/D/E/F/G/H/I/J=1-151.
DR PDB; 5VSW; X-ray; 4.29 A; M=1-151.
DR PDB; 5W1T; X-ray; 4.50 A; M/N=1-151.
DR PDB; 7KHE; EM; 3.58 A; M=1-151.
DR PDB; 7KHI; EM; 3.62 A; M=1-151.
DR PDBsum; 1TJL; -.
DR PDBsum; 5VSW; -.
DR PDBsum; 5W1T; -.
DR PDBsum; 7KHE; -.
DR PDBsum; 7KHI; -.
DR AlphaFoldDB; P0ABS1; -.
DR SMR; P0ABS1; -.
DR BioGRID; 4259742; 48.
DR BioGRID; 849250; 1.
DR DIP; DIP-31875N; -.
DR IntAct; P0ABS1; 12.
DR MINT; P0ABS1; -.
DR STRING; 511145.b0145; -.
DR SWISS-2DPAGE; P0ABS1; -.
DR jPOST; P0ABS1; -.
DR PaxDb; P0ABS1; -.
DR PRIDE; P0ABS1; -.
DR EnsemblBacteria; AAC73256; AAC73256; b0145.
DR EnsemblBacteria; BAB96722; BAB96722; BAB96722.
DR GeneID; 60371850; -.
DR GeneID; 67416218; -.
DR GeneID; 944850; -.
DR KEGG; ecj:JW0141; -.
DR KEGG; eco:b0145; -.
DR PATRIC; fig|1411691.4.peg.2136; -.
DR EchoBASE; EB0226; -.
DR eggNOG; COG1734; Bacteria.
DR HOGENOM; CLU_043144_2_0_6; -.
DR InParanoid; P0ABS1; -.
DR OMA; KKGEEYM; -.
DR PhylomeDB; P0ABS1; -.
DR BioCyc; EcoCyc:EG10230-MON; -.
DR EvolutionaryTrace; P0ABS1; -.
DR PRO; PR:P0ABS1; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005737; C:cytoplasm; HDA:UniProtKB.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0097216; F:guanosine tetraphosphate binding; IDA:EcoCyc.
DR GO; GO:0008270; F:zinc ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0006302; P:double-strand break repair; IMP:EcoCyc.
DR GO; GO:0010468; P:regulation of gene expression; IEA:UniProtKB-UniRule.
DR DisProt; DP00414; -.
DR HAMAP; MF_00926; DksA; 1.
DR InterPro; IPR012784; DksA_RNA_pol-bd.
DR InterPro; IPR037187; DnaK_N.
DR InterPro; IPR020460; Znf_C4-type_bac.
DR InterPro; IPR000962; Znf_DskA_TraR.
DR InterPro; IPR020458; Znf_DskA_TraR_CS.
DR Pfam; PF01258; zf-dskA_traR; 1.
DR PRINTS; PR00618; DKSAZNFINGER.
DR SUPFAM; SSF109635; SSF109635; 1.
DR TIGRFAMs; TIGR02420; dksA; 1.
DR PROSITE; PS01102; ZF_DKSA_1; 1.
DR PROSITE; PS51128; ZF_DKSA_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Coiled coil; Cytoplasm; Direct protein sequencing;
KW Metal-binding; Reference proteome; Zinc; Zinc-finger.
FT CHAIN 1..151
FT /note="RNA polymerase-binding transcription factor DksA"
FT /id="PRO_0000187536"
FT ZN_FING 114..138
FT /note="dksA C4-type"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00926"
FT COILED 33..54
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00926"
FT BINDING 114
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00926,
FT ECO:0000269|PubMed:15294156"
FT BINDING 117
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00926,
FT ECO:0000269|PubMed:15294156"
FT BINDING 135
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00926,
FT ECO:0000269|PubMed:15294156"
FT BINDING 138
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00926,
FT ECO:0000269|PubMed:15294156"
FT MUTAGEN 71
FT /note="D->N: Does not increase ppGpp-dependent inhibition
FT of transcription, but retains its ability to bind to RNAP;
FT when associated with N-74. Increased transcription of its
FT own RNA; when associated with N-74."
FT /evidence="ECO:0000269|PubMed:15294156,
FT ECO:0000269|PubMed:21488981"
FT MUTAGEN 74
FT /note="D->N: Does not increase ppGpp-dependent inhibition
FT of transcription, but retains its ability to bind to RNAP;
FT when associated with N-71. Increased transcription of its
FT own RNA; when associated with N-71."
FT /evidence="ECO:0000269|PubMed:15294156,
FT ECO:0000269|PubMed:21488981"
FT CONFLICT 4
FT /note="G -> Q (in Ref. 6; AA sequence)"
FT /evidence="ECO:0000305"
FT CONFLICT 94..95
FT /note="KL -> NV (in Ref. 1; AAA23687)"
FT /evidence="ECO:0000305"
FT HELIX 13..17
FT /evidence="ECO:0007829|PDB:1TJL"
FT HELIX 34..67
FT /evidence="ECO:0007829|PDB:1TJL"
FT HELIX 72..74
FT /evidence="ECO:0007829|PDB:1TJL"
FT HELIX 75..107
FT /evidence="ECO:0007829|PDB:1TJL"
FT STRAND 115..118
FT /evidence="ECO:0007829|PDB:1TJL"
FT HELIX 123..128
FT /evidence="ECO:0007829|PDB:1TJL"
FT HELIX 136..150
FT /evidence="ECO:0007829|PDB:1TJL"
SQ SEQUENCE 151 AA; 17528 MW; 620842DB15E066A9 CRC64;
MQEGQNRKTS SLSILAIAGV EPYQEKPGEE YMNEAQLAHF RRILEAWRNQ LRDEVDRTVT
HMQDEAANFP DPVDRAAQEE EFSLELRNRD RERKLIKKIE KTLKKVEDED FGYCESCGVE
IGIRRLEARP TADLCIDCKT LAEIREKQMA G
