STPA_ECOLI
ID STPA_ECOLI Reviewed; 134 AA.
AC P0ACG1; P30017;
DT 22-NOV-2005, integrated into UniProtKB/Swiss-Prot.
DT 22-NOV-2005, sequence version 1.
DT 03-AUG-2022, entry version 122.
DE RecName: Full=DNA-binding protein StpA;
DE AltName: Full=H-NS homolog StpA;
GN Name=stpA {ECO:0000303|PubMed:1480493}; Synonyms=hnsB;
GN OrderedLocusNames=b2669, JW2644;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND FUNCTION.
RC STRAIN=K12;
RX PubMed=1480493; DOI=10.1093/nar/20.24.6735;
RA Zhang A., Belfort M.;
RT "Nucleotide sequence of a newly-identified Escherichia coli gene, stpA,
RT encoding an H-NS-like protein.";
RL Nucleic Acids Res. 20:6735-6735(1992).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=7961433; DOI=10.1128/jb.176.21.6769-6775.1994;
RA Shi X., Bennett G.N.;
RT "Plasmids bearing hfq and the hns-like gene stpA complement hns mutants in
RT modulating arginine decarboxylase gene expression in Escherichia coli.";
RL J. Bacteriol. 176:6769-6775(1994).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9205837; DOI=10.1093/dnares/4.2.91;
RA Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T.,
RA Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K.,
RA Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T., Oyama S.,
RA Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H.,
RA Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T.;
RT "Construction of a contiguous 874-kb sequence of the Escherichia coli-K12
RT genome corresponding to 50.0-68.8 min on the linkage map and analysis of
RT its sequence features.";
RL DNA Res. 4:91-113(1997).
RN [4]
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 [5]
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 [6]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-21, FUNCTION, INDUCTION, AND
RP DISRUPTION PHENOTYPE.
RC STRAIN=K12, K12 / MC1029, and K12 / MC4100 / ATCC 35695 / DSM 6574;
RX PubMed=8890170; DOI=10.1002/j.1460-2075.1996.tb00877.x;
RA Sonden B., Uhlin B.E.;
RT "Coordinated and differential expression of histone-like proteins in
RT Escherichia coli: regulation and function of the H-NS analog StpA.";
RL EMBO J. 15:4970-4980(1996).
RN [7]
RP FUNCTION, SUBUNIT, AND MUTAGENESIS OF LEU-26; 65-MET--ILE-134; TYR-97 AND
RP PRO-116.
RX PubMed=8755860; DOI=10.1128/jb.178.15.4335-4343.1996;
RA Williams R.M., Rimsky S., Buc H.;
RT "Probing the structure, function, and interactions of the Escherichia coli
RT H-NS and StpA proteins by using dominant negative derivatives.";
RL J. Bacteriol. 178:4335-4343(1996).
RN [8]
RP FUNCTION (MICROBIAL INFECTION), DOMAIN, RNA-BINDING, AND MUTAGENESIS OF
RP GLY-126.
RX PubMed=17267410; DOI=10.1093/nar/gkl1143;
RA Mayer O., Rajkowitsch L., Lorenz C., Konrat R., Schroeder R.;
RT "RNA chaperone activity and RNA-binding properties of the E. coli protein
RT StpA.";
RL Nucleic Acids Res. 35:1257-1269(2007).
RN [9]
RP SUBCELLULAR LOCATION.
RC STRAIN=K12 / BW25993;
RX PubMed=21903814; DOI=10.1126/science.1204697;
RA Wang W., Li G.W., Chen C., Xie X.S., Zhuang X.;
RT "Chromosome organization by a nucleoid-associated protein in live
RT bacteria.";
RL Science 333:1445-1449(2011).
RN [10]
RP FUNCTION, REGULON, AND DISRUPTION PHENOTYPE.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=23543115; DOI=10.1093/dnares/dst008;
RA Ueda T., Takahashi H., Uyar E., Ishikawa S., Ogasawara N., Oshima T.;
RT "Functions of the Hha and YdgT proteins in transcriptional silencing by the
RT nucleoid proteins, H-NS and StpA, in Escherichia coli.";
RL DNA Res. 20:263-271(2013).
RN [11]
RP STRUCTURE BY NMR OF 90-134.
RA Fuertig B., Doetsch M., Stampfl S., Kontaxis G., Schroeder R.;
RT "Chaperones modulate RNA structural dynamics through anti-folding.";
RL Submitted (APR-2012) to the PDB data bank.
CC -!- FUNCTION: A DNA-binding protein that acts in a fashion similar to H-NS
CC protein upon overexpression, represses a number of genes including the
CC cryptic blg operon, hns, papB and the proU locus (PubMed:8890170). A
CC subset of H-NS/StpA-regulated genes also require Hha for repression;
CC Hha and Cnu (YdgT) increases the number of genes DNA bound by H-NS/StpA
CC and may also modulate the oligomerization of the H-NS/StpA-complex
CC (PubMed:23543115). Repression can be inhibited by dominant-negative
CC mutants of StpA or H-NS (PubMed:8755860). {ECO:0000269|PubMed:23543115,
CC ECO:0000269|PubMed:8755860, ECO:0000269|PubMed:8890170}.
CC -!- FUNCTION: (Microbial infection) Originally isolated as a suppressor of
CC a splicing defect of the thymidylate synthase (td) gene from
CC bacteriophage T4 (PubMed:1480493). Acts as an RNA chaperone,
CC accelerating splicing of viral pre-mRNA. Binds preferentially to
CC unstructured over structured RNA; does not have a detectable high-
CC affinity RNA-binding site in the pre-mRNA. There do not seem to be any
CC specific RNA targets in transcribed E.coli DNA (PubMed:17267410).
CC {ECO:0000269|PubMed:1480493, ECO:0000269|PubMed:17267410}.
CC -!- SUBUNIT: When overexpressed forms homodimers, can interact with the N-
CC terminus (residues 1-64) of H-NS (PubMed:8755860). May interact with
CC Hha and/or Cnu. {ECO:0000269|PubMed:8755860, ECO:0000305}.
CC -!- INTERACTION:
CC P0ACG1; P0ACF8: hns; NbExp=4; IntAct=EBI-551928, EBI-544934;
CC -!- SUBCELLULAR LOCATION: Cytoplasm, nucleoid
CC {ECO:0000269|PubMed:21903814}. Note=Scattered throughout the nucleoid
CC (PubMed:21903814). {ECO:0000269|PubMed:21903814}.
CC -!- INDUCTION: Expressed at low levels at 37 degrees Celsius, barely
CC detectable at 26 degrees Celsius; expression is repressed by hns and
CC partially activated by lrp (PubMed:8890170).
CC {ECO:0000269|PubMed:8890170}.
CC -!- DOMAIN: Both the N-terminus (residues 1-76) and the C-terminus
CC (residues 90-134) have RNA chaperone activity for splicing of td, a
CC bacteriophage T4 pre-mRNA (PubMed:17267410).
CC {ECO:0000269|PubMed:17267410}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype in rich medium; double hns-
CC stpA mutants grow slower and have reduced viable cell counts compared
CC to single hns mutants in MC1029 and MC4100 backgrounds
CC (PubMed:8890170). In 0.3M NaCl a double hns-stpA deletion up-regulates
CC 583 and down-regulates 86 genes, 363 of which are thought to have been
CC horizontally acquired; 131 are also up-regulated in a double cnu-hha
CC deletion (PubMed:23543115). {ECO:0000269|PubMed:23543115,
CC ECO:0000269|PubMed:8890170}.
CC -!- SIMILARITY: Belongs to the histone-like protein H-NS family.
CC {ECO:0000305}.
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DR EMBL; X69210; CAA49146.1; -; Genomic_DNA.
DR EMBL; U07823; AAA64940.1; -; Genomic_DNA.
DR EMBL; U00096; AAC75716.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA16535.1; -; Genomic_DNA.
DR PIR; JH0774; JH0774.
DR RefSeq; NP_417155.1; NC_000913.3.
DR RefSeq; WP_000115383.1; NZ_STEB01000042.1.
DR PDB; 2LRX; NMR; -; A=90-134.
DR PDBsum; 2LRX; -.
DR AlphaFoldDB; P0ACG1; -.
DR BMRB; P0ACG1; -.
DR SMR; P0ACG1; -.
DR BioGRID; 4262261; 8.
DR BioGRID; 851464; 2.
DR DIP; DIP-35951N; -.
DR IntAct; P0ACG1; 24.
DR STRING; 511145.b2669; -.
DR jPOST; P0ACG1; -.
DR PaxDb; P0ACG1; -.
DR PRIDE; P0ACG1; -.
DR EnsemblBacteria; AAC75716; AAC75716; b2669.
DR EnsemblBacteria; BAA16535; BAA16535; BAA16535.
DR GeneID; 66673461; -.
DR GeneID; 947130; -.
DR KEGG; ecj:JW2644; -.
DR KEGG; eco:b2669; -.
DR PATRIC; fig|1411691.4.peg.4072; -.
DR EchoBASE; EB1515; -.
DR eggNOG; COG2916; Bacteria.
DR HOGENOM; CLU_117503_0_0_6; -.
DR OMA; NTWLELM; -.
DR PhylomeDB; P0ACG1; -.
DR BioCyc; EcoCyc:EG11554-MON; -.
DR PRO; PR:P0ACG1; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0009295; C:nucleoid; IEA:UniProtKB-SubCell.
DR GO; GO:0032993; C:protein-DNA complex; IBA:GO_Central.
DR GO; GO:0003681; F:bent DNA binding; IBA:GO_Central.
DR GO; GO:0003677; F:DNA binding; IDA:EcoliWiki.
DR GO; GO:0001217; F:DNA-binding transcription repressor activity; IBA:GO_Central.
DR GO; GO:0003680; F:minor groove of adenine-thymine-rich DNA binding; IBA:GO_Central.
DR GO; GO:0046983; F:protein dimerization activity; IEA:InterPro.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0030527; F:structural constituent of chromatin; IEA:InterPro.
DR GO; GO:0000976; F:transcription cis-regulatory region binding; IBA:GO_Central.
DR Gene3D; 1.10.287.1050; -; 1.
DR Gene3D; 4.10.430.10; -; 1.
DR InterPro; IPR027444; H-NS_C_dom.
DR InterPro; IPR037150; H-NS_C_dom_sf.
DR InterPro; IPR001801; Histone_HNS.
DR InterPro; IPR027454; Histone_HNS_N.
DR Pfam; PF00816; Histone_HNS; 1.
DR PIRSF; PIRSF002096; HnS; 1.
DR SMART; SM00528; HNS; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Chaperone; Cytoplasm; DNA-binding; Reference proteome;
KW RNA-binding; Transcription; Transcription regulation.
FT CHAIN 1..134
FT /note="DNA-binding protein StpA"
FT /id="PRO_0000168513"
FT DNA_BIND 112..117
FT /evidence="ECO:0000250|UniProtKB:P0A1S2"
FT REGION 73..94
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MUTAGEN 26
FT /note="L->P: Partial loss of repressor function when
FT overexpressed in the absence of hns."
FT /evidence="ECO:0000269|PubMed:8755860"
FT MUTAGEN 65..134
FT /note="Missing: Partial loss of repressor function when
FT overexpressed in the absence of hns."
FT /evidence="ECO:0000269|PubMed:8755860"
FT MUTAGEN 97
FT /note="Y->C: Partial loss of repressor function when
FT overexpressed in the absence of hns."
FT /evidence="ECO:0000269|PubMed:8755860"
FT MUTAGEN 116
FT /note="P->S: Partial loss of repressor function when
FT overexpressed in the absence of hns."
FT /evidence="ECO:0000269|PubMed:8755860"
FT MUTAGEN 126
FT /note="G->V: Higher RNA chaperone activity than wild-type,
FT decreased ability to bind structured RNA."
FT /evidence="ECO:0000269|PubMed:17267410"
FT HELIX 117..124
FT /evidence="ECO:0007829|PDB:2LRX"
FT HELIX 129..131
FT /evidence="ECO:0007829|PDB:2LRX"
SQ SEQUENCE 134 AA; 15348 MW; 5870BD95F144CE6A CRC64;
MSVMLQSLNN IRTLRAMARE FSIDVLEEML EKFRVVTKER REEEEQQQRE LAERQEKIST
WLELMKADGI NPEELLGNSS AAAPRAGKKR QPRPAKYKFT DVNGETKTWT GQGRTPKPIA
QALAEGKSLD DFLI
