ID   DBHA_ECOLI              Reviewed;          90 AA.
AC   P0ACF0; P02342; Q2M8T7;
DT   21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT   21-JUL-1986, sequence version 1.
DT   02-SEP-2026, entry version 153.
DE   RecName: Full=DNA-binding protein HU-alpha;
DE   AltName: Full=HU-2;
DE   AltName: Full=NS2;
GN   Name=hupA; OrderedLocusNames=b4000, JW3964;
OS   Escherichia coli (strain K12).
OC   Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria;
OC   Enterobacterales; Enterobacteriaceae; Escherichia.
OX   NCBI_TaxID=83333;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=K12;
RX   PubMed=3312963; DOI=10.1007/bf00329674;
RA   Kano Y., Osato K., Wada M., Imamoto F.;
RT   "Cloning and sequencing of the HU-2 gene of Escherichia coli.";
RL   Mol. Gen. Genet. 209:408-410(1987).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / MG1655 / ATCC 47076;
RX   PubMed=8265357; DOI=10.1093/nar/21.23.5408;
RA   Blattner F.R., Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L.;
RT   "Analysis of the Escherichia coli genome. IV. DNA sequence of the region
RT   from 89.2 to 92.8 minutes.";
RL   Nucleic Acids Res. 21:5408-5417(1993).
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   PROTEIN SEQUENCE.
RX   PubMed=215461; DOI=10.1016/0014-5793(78)80446-3;
RA   Mende L., Timm B., Subramanian A.R.;
RT   "Primary structures of two homologous ribosome-associated DNA-binding
RT   proteins of Escherichia coli.";
RL   FEBS Lett. 96:395-398(1978).
RN   [6]
RP   PROTEIN SEQUENCE.
RX   PubMed=6987059; DOI=10.1111/j.1432-1033.1980.tb05968.x;
RA   Laine B., Kmiecik D., Sautiere P., Biserte G., Cohen-Solal M.;
RT   "Complete amino-acid sequences of DNA-binding proteins HU-1 and HU-2 from
RT   Escherichia coli.";
RL   Eur. J. Biochem. 103:447-461(1980).
RN   [7]
RP   PROTEIN SEQUENCE OF 1-37.
RX   PubMed=350619; DOI=10.1016/0014-5793(78)80535-3;
RA   Laine B., Sautiere P., Biserte G., Cohen-Solal M., Gros F.,
RA   Rouviere-Yaniv J.;
RT   "The amino- and carboxy-terminal amino acid sequences of protein HU from
RT   Escherichia coli.";
RL   FEBS Lett. 89:116-120(1978).
RN   [8]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-28.
RC   STRAIN=K12;
RX   PubMed=2187099; DOI=10.1016/s0022-2836(05)80119-6;
RA   Kohno K., Wada M., Kano Y., Imamoto F.;
RT   "Promoters and autogenous control of the Escherichia coli hupA and hupB
RT   genes.";
RL   J. Mol. Biol. 213:27-36(1990).
RN   [9]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-35.
RA   Nishimura K., Inokuchi H.;
RL   Submitted (JUL-1992) to the EMBL/GenBank/DDBJ databases.
RN   [10]
RP   PROTEIN SEQUENCE OF 1-12.
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   [11]
RP   PROTEIN SEQUENCE OF 1-10.
RC   STRAIN=K12;
RX   PubMed=9868784; DOI=10.1111/j.1574-6968.1998.tb13343.x;
RA   Wasinger V.C., Humphery-Smith I.;
RT   "Small genes/gene-products in Escherichia coli K-12.";
RL   FEMS Microbiol. Lett. 169:375-382(1998).
RN   [12]
RP   SUBUNIT.
RC   STRAIN=K12 / W3350 / ATCC 27020;
RX   PubMed=227733; DOI=10.1016/0014-5793(79)80518-9;
RA   Rouviere-Yaniv J., Kjeldgaard N.O.;
RT   "Native Escherichia coli HU protein is a heterotypic dimer.";
RL   FEBS Lett. 106:297-300(1979).
RN   [13]
RP   IDENTIFICATION BY 2D-GEL.
RX   PubMed=9298644; DOI=10.1002/elps.1150180805;
RA   VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.;
RT   "Escherichia coli proteome analysis using the gene-protein database.";
RL   Electrophoresis 18:1243-1251(1997).
RN   [14]
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   [15]
RP   FUNCTION, ACTIVITY REGULATION, AND DNA-BINDING.
RX   PubMed=24916461; DOI=10.1038/ncomms5124;
RA   Bhowmick T., Ghosh S., Dixit K., Ganesan V., Ramagopal U.A., Dey D.,
RA   Sarma S.P., Ramakumar S., Nagaraja V.;
RT   "Targeting Mycobacterium tuberculosis nucleoid-associated protein HU with
RT   structure-based inhibitors.";
RL   Nat. Commun. 5:4124-4124(2014).
CC   -!- FUNCTION: Histone-like DNA-binding protein which is capable of wrapping
CC       DNA to stabilize it, and thus to prevent its denaturation under extreme
CC       environmental conditions. {ECO:0000305|PubMed:24916461}.
CC   -!- ACTIVITY REGULATION: Trans-stilbene derivative 4,4'-[(E)-ethene-1,2
CC       diylbis({5[(phenylcarbonyl)amino]benzene-2,1-diyl}sulfonylimino)]
CC       dibenzoic acid (SD1) inhibits DNA binding at 50 uM. However SD1 did not
CC       inhibit growth in a range of 3-1600 uM. {ECO:0000269|PubMed:24916461}.
CC   -!- SUBUNIT: Heterodimer of an alpha and a beta chain.
CC       {ECO:0000269|PubMed:227733}.
CC   -!- INTERACTION:
CC       P0ACF0; P03004: dnaA; NbExp=5; IntAct=EBI-547648, EBI-548951;
CC       P0ACF0; P0ACF0: hupA; NbExp=2; IntAct=EBI-547648, EBI-547648;
CC       P0ACF0; P0ACF4: hupB; NbExp=9; IntAct=EBI-547648, EBI-370411;
CC   -!- SUBCELLULAR LOCATION: Cytoplasm, nucleoid
CC       {ECO:0000269|PubMed:21903814}. Note=Scattered throughout the nucleoid
CC       (PubMed:21903814). {ECO:0000269|PubMed:21903814}.
CC   -!- SIMILARITY: Belongs to the bacterial histone-like protein family.
CC       {ECO:0000305}.
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DR   EMBL; X05994; CAA29412.1; -; Genomic_DNA.
DR   EMBL; U00006; AAC43098.1; -; Genomic_DNA.
DR   EMBL; U00096; AAC76974.1; -; Genomic_DNA.
DR   EMBL; AP009048; BAE77319.1; -; Genomic_DNA.
DR   EMBL; X54555; CAA38426.1; -; Genomic_DNA.
DR   EMBL; D12624; BAA02149.1; -; Genomic_DNA.
DR   PIR; S06269; DNECS2.
DR   RefSeq; NP_418428.1; NC_000913.3.
DR   RefSeq; WP_001044513.1; NZ_CP009789.1.
DR   PDB; 1MUL; X-ray; 2.30 A; A=1-90.
DR   PDB; 2O97; X-ray; 2.45 A; A=1-90.
DR   PDB; 4YEW; X-ray; 2.68 A; C=1-90.
DR   PDB; 4YEX; X-ray; 3.20 A; A/C=1-90.
DR   PDB; 4YEY; X-ray; 3.35 A; A/C=1-90.
DR   PDB; 4YF0; X-ray; 2.79 A; A/B=1-90.
DR   PDB; 4YFH; X-ray; 3.49 A; A/B=1-90.
DR   PDB; 4YFT; X-ray; 2.91 A; C=1-90.
DR   PDB; 6O6K; X-ray; 3.60 A; A/B=1-90.
DR   PDB; 6O8Q; X-ray; 3.22 A; A/B/C/D/E/F/G/H/I/J=1-90.
DR   PDB; 6OAJ; X-ray; 4.09 A; A/B/C/D=1-90.
DR   AlphaFoldDB; P0ACF0; -.
DR   SASBDB; P0ACF0; -.
DR   SMR; P0ACF0; -.
DR   BioGRID; 4263459; 248.
DR   BioGRID; 852793; 4.
DR   ComplexPortal; CPX-1958; HU complex, variant hupAB.
DR   ComplexPortal; CPX-1959; HU complex, variant hupA.
DR   ComplexPortal; CPX-1961; DnaA-HU complex, variant hupAB.
DR   ComplexPortal; CPX-1962; DnaA-HU complex, variant hupA.
DR   DIP; DIP-35892N; -.
DR   FunCoup; P0ACF0; 680.
DR   IntAct; P0ACF0; 77.
DR   STRING; 511145.b4000; -.
DR   jPOST; P0ACF0; -.
DR   PaxDb; 511145-b4000; -.
DR   EnsemblBacteria; AAC76974; AAC76974; b4000.
DR   GeneID; 67175032; -.
DR   GeneID; 93777894; -.
DR   GeneID; 948499; -.
DR   KEGG; ecj:JW3964; -.
DR   KEGG; eco:b4000; -.
DR   KEGG; ecoc:C3026_21605; -.
DR   PATRIC; fig|1411691.4.peg.2711; -.
DR   EchoBASE; EB0461; -.
DR   eggNOG; COG0776; Bacteria.
DR   HOGENOM; CLU_105066_3_1_6; -.
DR   InParanoid; P0ACF0; -.
DR   OMA; ISQEKQC; -.
DR   OrthoDB; 9799835at2; -.
DR   PhylomeDB; P0ACF0; -.
DR   BioCyc; EcoCyc:EG10466-MONOMER; -.
DR   EvolutionaryTrace; P0ACF0; -.
DR   PRO; PR:P0ACF0; -.
DR   Proteomes; UP000000625; Chromosome.
DR   AbasyAtlas; P0ACF0; -.
DR   GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR   GO; GO:1990103; C:DnaA-HU complex; IPI:ComplexPortal.
DR   GO; GO:1990178; C:HU-DNA complex; IDA:CACAO.
DR   GO; GO:0016020; C:membrane; HDA:UniProtKB.
DR   GO; GO:0003677; F:DNA binding; IDA:EcoliWiki.
DR   GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR   GO; GO:0030527; F:structural constituent of chromatin; IEA:InterPro.
DR   GO; GO:0036386; P:bacterial nucleoid DNA packaging; NAS:ComplexPortal.
DR   GO; GO:0006974; P:DNA damage response; IEP:EcoliWiki.
DR   GO; GO:0006281; P:DNA repair; NAS:ComplexPortal.
DR   GO; GO:0006270; P:DNA replication initiation; IDA:ComplexPortal.
DR   GO; GO:0006351; P:DNA-templated transcription; IDA:EcoCyc.
DR   CDD; cd13831; HU; 1.
DR   FunFam; 4.10.520.10:FF:000001; DNA-binding protein HU; 1.
DR   Gene3D; 4.10.520.10; IHF-like DNA-binding proteins; 1.
DR   InterPro; IPR000119; Hist_DNA-bd.
DR   InterPro; IPR020816; Histone-like_DNA-bd_CS.
DR   InterPro; IPR010992; IHF-like_DNA-bd_dom_sf.
DR   NCBIfam; NF008023; PRK10753.1; 1.
DR   PANTHER; PTHR33175; DNA-BINDING PROTEIN HU; 1.
DR   PANTHER; PTHR33175:SF12; DNA-BINDING PROTEIN HU-ALPHA; 1.
DR   Pfam; PF00216; Bac_DNA_binding; 1.
DR   PRINTS; PR01727; DNABINDINGHU.
DR   SMART; SM00411; BHL; 1.
DR   SUPFAM; SSF47729; IHF-like DNA-binding proteins; 1.
DR   PROSITE; PS00045; HISTONE_LIKE; 1.
PE   1: Evidence at protein level;
KW   3D-structure; Cytoplasm; Direct protein sequencing; DNA condensation;
KW   DNA-binding; Reference proteome.
FT   CHAIN           1..90
FT                   /note="DNA-binding protein HU-alpha"
FT                   /id="PRO_0000104935"
FT   CONFLICT        19..32
FT                   /note="TQAKAALESTLAAI -> AAAGRALDAIIASV (in Ref. 7; AA
FT                   sequence)"
FT                   /evidence="ECO:0000305"
FT   HELIX           3..13
FT                   /evidence="ECO:0007829|PDB:1MUL"
FT   HELIX           18..37
FT                   /evidence="ECO:0007829|PDB:1MUL"
FT   STRAND          42..44
FT                   /evidence="ECO:0007829|PDB:1MUL"
FT   TURN            45..47
FT                   /evidence="ECO:0007829|PDB:1MUL"
FT   STRAND          48..55
FT                   /evidence="ECO:0007829|PDB:1MUL"
FT   STRAND          59..62
FT                   /evidence="ECO:0007829|PDB:6O8Q"
FT   TURN            63..66
FT                   /evidence="ECO:0007829|PDB:6O8Q"
FT   STRAND          67..70
FT                   /evidence="ECO:0007829|PDB:6O8Q"
FT   STRAND          74..81
FT                   /evidence="ECO:0007829|PDB:1MUL"
FT   HELIX           83..89
FT                   /evidence="ECO:0007829|PDB:1MUL"
SQ   SEQUENCE   90 AA;  9535 MW;  6B5B8536FDBD13DC CRC64;
     MNKTQLIDVI AEKAELSKTQ AKAALESTLA AITESLKEGD AVQLVGFGTF KVNHRAERTG
     RNPQTGKEIK IAAANVPAFV SGKALKDAVK
//