ID   IHF_STRCO               Reviewed;         107 AA.
AC   Q9KXR9;
DT   13-SEP-2023, integrated into UniProtKB/Swiss-Prot.
DT   01-OCT-2000, sequence version 1.
DT   27-MAR-2024, entry version 127.
DE   RecName: Full=Integration host factor {ECO:0000305};
DE   AltName: Full=Streptomyces integration host factor {ECO:0000303|PubMed:22038127};
DE            Short=sIHF {ECO:0000303|PubMed:22038127};
GN   Name=sihF {ECO:0000303|PubMed:22038127};
GN   Synonyms=SC9C5.04c {ECO:0000312|EMBL:CAB93360.1};
GN   OrderedLocusNames=SCO1480 {ECO:0000312|EMBL:CAB93360.1};
OS   Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145).
OC   Bacteria; Actinomycetota; Actinomycetes; Kitasatosporales;
OC   Streptomycetaceae; Streptomyces; Streptomyces albidoflavus group.
OX   NCBI_TaxID=100226;
RN   [1] {ECO:0000312|EMBL:CAB93360.1}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC BAA-471 / A3(2) / M145;
RX   PubMed=12000953; DOI=10.1038/417141a;
RA   Bentley S.D., Chater K.F., Cerdeno-Tarraga A.-M., Challis G.L.,
RA   Thomson N.R., James K.D., Harris D.E., Quail M.A., Kieser H., Harper D.,
RA   Bateman A., Brown S., Chandra G., Chen C.W., Collins M., Cronin A.,
RA   Fraser A., Goble A., Hidalgo J., Hornsby T., Howarth S., Huang C.-H.,
RA   Kieser T., Larke L., Murphy L.D., Oliver K., O'Neil S., Rabbinowitsch E.,
RA   Rajandream M.A., Rutherford K.M., Rutter S., Seeger K., Saunders D.,
RA   Sharp S., Squares R., Squares S., Taylor K., Warren T., Wietzorrek A.,
RA   Woodward J.R., Barrell B.G., Parkhill J., Hopwood D.A.;
RT   "Complete genome sequence of the model actinomycete Streptomyces coelicolor
RT   A3(2).";
RL   Nature 417:141-147(2002).
RN   [2]
RP   FUNCTION, DISRUPTION PHENOTYPE, AND DNA-BINDING.
RC   STRAIN=ATCC BAA-471 / A3(2) / M145;
RX   PubMed=22038127; DOI=10.1007/s10482-011-9657-z;
RA   Yang Y.H., Song E., Willemse J., Park S.H., Kim W.S., Kim E.J., Lee B.R.,
RA   Kim J.N., van Wezel G.P., Kim B.G.;
RT   "A novel function of Streptomyces integration host factor (sIHF) in the
RT   control of antibiotic production and sporulation in Streptomyces
RT   coelicolor.";
RL   Antonie Van Leeuwenhoek 101:479-492(2012).
RN   [3]
RP   IDENTIFICATION BY MASS SPECTROMETRY, AND SUBCELLULAR LOCATION.
RC   STRAIN=ATCC BAA-471 / A3(2) / M145;
RX   PubMed=23523638; DOI=10.1016/j.jprot.2013.02.033;
RA   Bradshaw E., Saalbach G., McArthur M.;
RT   "Proteomic survey of the Streptomyces coelicolor nucleoid.";
RL   J. Proteomics 83:37-46(2013).
RN   [4] {ECO:0007744|PDB:4ITQ}
RP   X-RAY CRYSTALLOGRAPHY (2.70 ANGSTROMS) IN COMPLEX WITH DNA, FUNCTION,
RP   SUBUNIT, SUBCELLULAR LOCATION, INDUCTION, DOMAIN, DISRUPTION PHENOTYPE, AND
RP   DNA-BINDING.
RC   STRAIN=A3(2) / M600;
RX   PubMed=23427309; DOI=10.1093/nar/gkt095;
RA   Swiercz J.P., Nanji T., Gloyd M., Guarne A., Elliot M.A.;
RT   "A novel nucleoid-associated protein specific to the actinobacteria.";
RL   Nucleic Acids Res. 41:4171-4184(2013).
RN   [5] {ECO:0007744|PDB:6BEK}
RP   X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) IN COMPLEX WITH DNA, FUNCTION,
RP   DOMAIN, DNA-BINDING, AND MUTAGENESIS OF 2-ALA--ALA-13; 22-ARG--LYS-33;
RP   GLY-66; 85-ARG-ARG-86 AND 93-ASN-GLN-94.
RX   PubMed=31376411; DOI=10.1016/j.bbagen.2019.07.014;
RA   Nanji T., Gehrke E.J., Shen Y., Gloyd M., Zhang X., Firby C.D., Huynh A.,
RA   Razi A., Ortega J., Elliot M.A., Guarne A.;
RT   "Streptomyces IHF uses multiple interfaces to bind DNA.";
RL   Biochim. Biophys. Acta 1863:129405-129405(2019).
CC   -!- FUNCTION: A nucleoid-associated protein (NAP) that probably plays a
CC       role in chromosome compactation. Contributes to development and
CC       secondary metabolism, but is dispensable for growth and viability
CC       (PubMed:22038127, PubMed:23427309). Binds to the promoter region of a
CC       number of genes (including itself); multiple molecules of the protein
CC       bind to the DNA simultaneously, deletion alters the expression of about
CC       30 genes (both up- and down-regulation occurs). Plays a role in
CC       controlling viability (PubMed:22038127). Binds dsDNA without any
CC       obvious sequence specificity, in a concentration and length-dependent
CC       manner. Promotes supercoiling in a topoisomerase-dependent manner
CC       (counteracts TopA plasmid relaxation). Binds DNA as a monomer,
CC       contacting 8 base pairs via the phosphate backbone; each monomer can
CC       bind 2 DNA duplexes, allowing a bridging function (PubMed:23427309).
CC       Alters DNA topology, constraining negative supercoils, possibly by DNA
CC       twist. Longer dsDNA binds more than one sIHF subunit (PubMed:31376411).
CC       {ECO:0000269|PubMed:22038127, ECO:0000269|PubMed:23427309,
CC       ECO:0000269|PubMed:31376411}.
CC   -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:23427309}.
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:23427309}. Spore
CC       {ECO:0000269|PubMed:23427309}. Cytoplasm, nucleoid
CC       {ECO:0000269|PubMed:23427309, ECO:0000269|PubMed:23523638}.
CC       Note=Cytoplasmic, associates with the nucleoid in liquid culture and in
CC       spores. {ECO:0000269|PubMed:23427309}.
CC   -!- INDUCTION: Constitutively expressed on MS (minimal) or R2YE (rich)
CC       medium; more highly expressed on R2YE medium, levels decrease after 3
CC       days on MS (at protein level). {ECO:0000269|PubMed:23427309}.
CC   -!- DOMAIN: The N-terminus (up to residue 33) is important in DNA binding
CC       in solution but not in the crystal structures (PubMed:31376411). The
CC       lid region binds the phosphate backbone of one DNA duplex, while the
CC       H2TH motif contacts another duplex (PubMed:23427309, PubMed:31376411).
CC       {ECO:0000269|PubMed:23427309, ECO:0000269|PubMed:31376411}.
CC   -!- DISRUPTION PHENOTYPE: Not essential for growth. Has altered antibiotic
CC       production (actinorhodin and undecylprodigiosin) in minimal and complex
CC       (R5- or R2YE) media; antibiotic production may be differentially
CC       responsive to carbon source and growth conditions. Decreased
CC       sporulation; on some media no spores are formed. Spores are larger, 8-
CC       10% are empty and their DNA content varies widely (PubMed:22038127,
CC       PubMed:23427309). More sensitive to heat shock. Altered expression of
CC       some transcriptional regulators (PubMed:22038127). DNA is less
CC       compacted in spores (PubMed:23427309). {ECO:0000269|PubMed:22038127,
CC       ECO:0000269|PubMed:23427309}.
CC   -!- MISCELLANEOUS: In S.coelicolor chromosome condensation only takes place
CC       during sporulation in aerial cells. {ECO:0000305|PubMed:23427309,
CC       ECO:0000305|PubMed:31376411}.
CC   -!- SIMILARITY: Belongs to the actinobacterial IHF (aIHF) family.
CC       {ECO:0000305|PubMed:22038127}.
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DR   EMBL; AL939109; CAB93360.1; -; Genomic_DNA.
DR   RefSeq; NP_625760.1; NC_003888.3.
DR   RefSeq; WP_003977346.1; NZ_VNID01000021.1.
DR   PDB; 4ITQ; X-ray; 2.70 A; A=1-107.
DR   PDB; 6BEK; X-ray; 1.70 A; A/D=1-107.
DR   PDBsum; 4ITQ; -.
DR   PDBsum; 6BEK; -.
DR   AlphaFoldDB; Q9KXR9; -.
DR   SMR; Q9KXR9; -.
DR   STRING; 100226.gene:17759066; -.
DR   PaxDb; 100226-SCO1480; -.
DR   GeneID; 85836198; -.
DR   PATRIC; fig|100226.15.peg.1489; -.
DR   eggNOG; COG0099; Bacteria.
DR   HOGENOM; CLU_151796_1_0_11; -.
DR   InParanoid; Q9KXR9; -.
DR   OrthoDB; 3197442at2; -.
DR   PhylomeDB; Q9KXR9; -.
DR   Proteomes; UP000001973; Chromosome.
DR   GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR   GO; GO:0009295; C:nucleoid; IEA:UniProtKB-SubCell.
DR   GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR   GO; GO:0030261; P:chromosome condensation; IEA:UniProtKB-KW.
DR   Gene3D; 1.10.8.50; -; 1.
DR   InterPro; IPR047806; IHF_actinobact.
DR   InterPro; IPR010979; Ribosomal_uS13-like_H2TH.
DR   NCBIfam; NF041260; actino_IHF; 1.
DR   SUPFAM; SSF46946; S13-like H2TH domain; 1.
DR   PROSITE; PS50159; RIBOSOMAL_S13_2; 1.
PE   1: Evidence at protein level;
KW   3D-structure; Activator; Cytoplasm; DNA condensation; DNA-binding;
KW   Reference proteome; Repressor; Transcription; Transcription regulation.
FT   CHAIN           1..107
FT                   /note="Integration host factor"
FT                   /id="PRO_0000458544"
FT   REGION          1..20
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          82..94
FT                   /note="Lid, binds DNA"
FT                   /evidence="ECO:0000269|PubMed:23427309,
FT                   ECO:0000269|PubMed:31376411"
FT   MOTIF           64..71
FT                   /note="H2TH motif, binds DNA"
FT                   /evidence="ECO:0000269|PubMed:23427309,
FT                   ECO:0000269|PubMed:31376411"
FT   BINDING         54
FT                   /ligand="DNA"
FT                   /ligand_id="ChEBI:CHEBI:16991"
FT                   /evidence="ECO:0000269|PubMed:31376411,
FT                   ECO:0000312|PDB:6BEK"
FT   BINDING         82
FT                   /ligand="DNA"
FT                   /ligand_id="ChEBI:CHEBI:16991"
FT                   /evidence="ECO:0000269|PubMed:23427309,
FT                   ECO:0000312|PDB:4ITQ"
FT   BINDING         85
FT                   /ligand="DNA"
FT                   /ligand_id="ChEBI:CHEBI:16991"
FT                   /evidence="ECO:0000269|PubMed:23427309,
FT                   ECO:0000269|PubMed:31376411, ECO:0000312|PDB:4ITQ,
FT                   ECO:0000312|PDB:6BEK"
FT   BINDING         88
FT                   /ligand="DNA"
FT                   /ligand_id="ChEBI:CHEBI:16991"
FT                   /evidence="ECO:0000269|PubMed:31376411,
FT                   ECO:0000312|PDB:6BEK"
FT   BINDING         92
FT                   /ligand="DNA"
FT                   /ligand_id="ChEBI:CHEBI:16991"
FT                   /evidence="ECO:0000269|PubMed:31376411,
FT                   ECO:0000312|PDB:6BEK"
FT   BINDING         93
FT                   /ligand="DNA"
FT                   /ligand_id="ChEBI:CHEBI:16991"
FT                   /evidence="ECO:0000269|PubMed:23427309,
FT                   ECO:0000269|PubMed:31376411, ECO:0000312|PDB:4ITQ,
FT                   ECO:0000312|PDB:6BEK"
FT   BINDING         94
FT                   /ligand="DNA"
FT                   /ligand_id="ChEBI:CHEBI:16991"
FT                   /evidence="ECO:0000269|PubMed:23427309,
FT                   ECO:0000269|PubMed:31376411, ECO:0000312|PDB:4ITQ,
FT                   ECO:0000312|PDB:6BEK"
FT   MUTAGEN         2..13
FT                   /note="Missing: Protein does not stably accumulate in vivo,
FT                   in vitro decreased DNA binding, decreased constraint of
FT                   negative supercoils."
FT                   /evidence="ECO:0000269|PubMed:31376411"
FT   MUTAGEN         22..33
FT                   /note="RRERAEVKNRLK->SRESAEVSNRLS: Protein does not stably
FT                   accumulate in vivo, in vitro strongly decreased DNA
FT                   binding, decreased constraint of negative supercoils."
FT                   /evidence="ECO:0000269|PubMed:31376411"
FT   MUTAGEN         66
FT                   /note="G->GG: Moderately decreased DNA binding, decreased
FT                   constraint of negative supercoils, partially complements
FT                   deletion mutant."
FT                   /evidence="ECO:0000269|PubMed:31376411"
FT   MUTAGEN         85..86
FT                   /note="RR->AS: Moderately decreased DNA binding, decreased
FT                   constraint of negative supercoils."
FT                   /evidence="ECO:0000269|PubMed:31376411"
FT   MUTAGEN         93..94
FT                   /note="NQ->AS: Moderately decreased DNA binding, decreased
FT                   constraint of negative supercoils, partially complements
FT                   deletion mutant."
FT                   /evidence="ECO:0000269|PubMed:31376411"
SQ   SEQUENCE   107 AA;  11555 MW;  3AC884F8E455FE2C CRC64;
     MALPPLTPEQ RAAALEKAAA ARRERAEVKN RLKHSGASLH EVIKQGQEND VIGKMKVSAL
     LESLPGVGKV RAKQIMERLG ISESRRVRGL GSNQIASLER EFGSTGS
//