ID   RAPA_SALTI              Reviewed;         968 AA.
AC   Q8Z9J4;
DT   16-JAN-2004, integrated into UniProtKB/Swiss-Prot.
DT   23-JAN-2007, sequence version 3.
DT   03-AUG-2022, entry version 123.
DE   RecName: Full=RNA polymerase-associated protein RapA {ECO:0000255|HAMAP-Rule:MF_01821};
DE            EC=3.6.4.- {ECO:0000255|HAMAP-Rule:MF_01821};
DE   AltName: Full=ATP-dependent helicase HepA {ECO:0000255|HAMAP-Rule:MF_01821};
GN   Name=rapA {ECO:0000255|HAMAP-Rule:MF_01821}; Synonyms=hepA;
GN   OrderedLocusNames=STY0111, t0099;
OS   Salmonella typhi.
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC   Enterobacteriaceae; Salmonella.
OX   NCBI_TaxID=90370;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=CT18;
RX   PubMed=11677608; DOI=10.1038/35101607;
RA   Parkhill J., Dougan G., James K.D., Thomson N.R., Pickard D., Wain J.,
RA   Churcher C.M., Mungall K.L., Bentley S.D., Holden M.T.G., Sebaihia M.,
RA   Baker S., Basham D., Brooks K., Chillingworth T., Connerton P., Cronin A.,
RA   Davis P., Davies R.M., Dowd L., White N., Farrar J., Feltwell T.,
RA   Hamlin N., Haque A., Hien T.T., Holroyd S., Jagels K., Krogh A.,
RA   Larsen T.S., Leather S., Moule S., O'Gaora P., Parry C., Quail M.A.,
RA   Rutherford K.M., Simmonds M., Skelton J., Stevens K., Whitehead S.,
RA   Barrell B.G.;
RT   "Complete genome sequence of a multiple drug resistant Salmonella enterica
RT   serovar Typhi CT18.";
RL   Nature 413:848-852(2001).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 700931 / Ty2;
RX   PubMed=12644504; DOI=10.1128/jb.185.7.2330-2337.2003;
RA   Deng W., Liou S.-R., Plunkett G. III, Mayhew G.F., Rose D.J., Burland V.,
RA   Kodoyianni V., Schwartz D.C., Blattner F.R.;
RT   "Comparative genomics of Salmonella enterica serovar Typhi strains Ty2 and
RT   CT18.";
RL   J. Bacteriol. 185:2330-2337(2003).
CC   -!- FUNCTION: Transcription regulator that activates transcription by
CC       stimulating RNA polymerase (RNAP) recycling in case of stress
CC       conditions such as supercoiled DNA or high salt concentrations.
CC       Probably acts by releasing the RNAP, when it is trapped or immobilized
CC       on tightly supercoiled DNA. Does not activate transcription on linear
CC       DNA. Probably not involved in DNA repair. {ECO:0000255|HAMAP-
CC       Rule:MF_01821}.
CC   -!- SUBUNIT: Interacts with the RNAP. Has a higher affinity for the core
CC       RNAP than for the holoenzyme. Its ATPase activity is stimulated by
CC       binding to RNAP. {ECO:0000255|HAMAP-Rule:MF_01821}.
CC   -!- SIMILARITY: Belongs to the SNF2/RAD54 helicase family. RapA subfamily.
CC       {ECO:0000255|HAMAP-Rule:MF_01821}.
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DR   EMBL; AL513382; CAD01252.1; -; Genomic_DNA.
DR   EMBL; AE014613; AAO67832.1; -; Genomic_DNA.
DR   RefSeq; NP_454708.1; NC_003198.1.
DR   RefSeq; WP_001116972.1; NZ_WSUR01000028.1.
DR   AlphaFoldDB; Q8Z9J4; -.
DR   SMR; Q8Z9J4; -.
DR   STRING; 220341.16501381; -.
DR   EnsemblBacteria; AAO67832; AAO67832; t0099.
DR   KEGG; stt:t0099; -.
DR   KEGG; sty:STY0111; -.
DR   PATRIC; fig|220341.7.peg.111; -.
DR   eggNOG; COG0553; Bacteria.
DR   HOGENOM; CLU_011520_0_0_6; -.
DR   OMA; MSILERD; -.
DR   Proteomes; UP000000541; Chromosome.
DR   Proteomes; UP000002670; Chromosome.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0140658; F:ATP-dependent chromatin remodeler activity; IEA:InterPro.
DR   GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR   GO; GO:0004386; F:helicase activity; IEA:UniProtKB-UniRule.
DR   GO; GO:0016817; F:hydrolase activity, acting on acid anhydrides; IEA:InterPro.
DR   GO; GO:0006355; P:regulation of transcription, DNA-templated; IEA:UniProtKB-UniRule.
DR   Gene3D; 3.40.50.10810; -; 1.
DR   Gene3D; 3.40.50.300; -; 1.
DR   HAMAP; MF_01821; Helicase_RapA; 1.
DR   InterPro; IPR014001; Helicase_ATP-bd.
DR   InterPro; IPR001650; Helicase_C.
DR   InterPro; IPR023949; Helicase_RapA.
DR   InterPro; IPR027417; P-loop_NTPase.
DR   InterPro; IPR022737; RapA_C.
DR   InterPro; IPR038718; SNF2-like_sf.
DR   InterPro; IPR000330; SNF2_N.
DR   InterPro; IPR040765; Tudor_1_RapA.
DR   InterPro; IPR040766; Tudor_2_RapA.
DR   Pfam; PF00271; Helicase_C; 1.
DR   Pfam; PF12137; RapA_C; 1.
DR   Pfam; PF00176; SNF2-rel_dom; 1.
DR   Pfam; PF18339; Tudor_1_RapA; 1.
DR   Pfam; PF18337; Tudor_RapA; 1.
DR   SMART; SM00487; DEXDc; 1.
DR   SMART; SM00490; HELICc; 1.
DR   SUPFAM; SSF52540; SSF52540; 2.
DR   PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
DR   PROSITE; PS51194; HELICASE_CTER; 1.
PE   3: Inferred from homology;
KW   Activator; ATP-binding; DNA-binding; Helicase; Hydrolase;
KW   Nucleotide-binding; Transcription; Transcription regulation.
FT   INIT_MET        1
FT                   /note="Removed"
FT                   /evidence="ECO:0000250"
FT   CHAIN           2..968
FT                   /note="RNA polymerase-associated protein RapA"
FT                   /id="PRO_0000207184"
FT   DOMAIN          164..334
FT                   /note="Helicase ATP-binding"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01821"
FT   DOMAIN          490..685
FT                   /note="Helicase C-terminal"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01821"
FT   MOTIF           280..283
FT                   /note="DEAH box"
FT   BINDING         177..184
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01821"
SQ   SEQUENCE   968 AA;  109816 MW;  4F0ECD07547B7BDC CRC64;
     MPFTLGQRWI SDTESELGLG TVVAMDARTV TLLFPSTGEN RLYARSDSPV TRVMFNPGDT
     ITSHEGWQLH IDEVKEENGL LVYVGTRLDT EETNVTLREV LLDSKLVFSK PQDRLFAGQI
     DRMDRFALRY RARKFQSEQY RMPYSGLRGQ RTNLIPHQLN IAHDVGRRHA PRVLLADEVG
     LGKTIEAGMI LHQQLLSGAA ERVLIIVPET LQHQWLVEML RRFNLRFALF DDERYTEAQH
     DAYNPFETEQ LVICSLDFAR RNKQRLEHLC DAEWDLLVVD EAHHLVWSTD APSREYMAIE
     QLAERVPGVL LLTATPEQLG MESHFARLRL LDPNRFHDFE QFVEEQKNYR PVADAVAMLL
     AGNKLSNDEL NRLGDLIGEQ DIEPLLQAAN SDRDDAQAAR DELVSMLMDR HGTSRVLFRN
     TRNGVKGFPK RELHTVKLPL PTQYQTAIKV SGIMGARKSA EDRARDMLYP EQIYQEFEGD
     TGTWWNFDPR VEWLMGYLTS HRSQKVLVIC AKATTALQLE QVLREREGIR AAVFHEGMSI
     IERDRAAAWF AEEDTGAQVL LCSEIGSEGR NFQFASNLVM FDLPFNPDLL EQRIGRLDRI
     GQAHDIQIHV PYLEKTAQSV LVRWYHEGLD AFEHTCPTGR AIYDSAYASL INYLAAPEET
     DGFDDLIKSC REQHEALKAQ LEQGRDRLLE INSNGGEKAQ QLAQSIEEQD DDTNLIAFAM
     NLFDIVGINQ DDRGDNLIVL TPSDHMLVPD FPGLPEDGCT ITFERDVALS REDAQFITWE
     HPLIRNGLDL ILSGDTGSST ISLLKNKALP VGTLLVELVY VVEAQAPKQL QLNRFLPPTP
     VRMLLDKNGN NLAAQVEFET FNRQLSAVNR HTGSKLVNAV QQDVHAILQL GETQIEQSAR
     ALIDNARREA DEKLSGELSR LEALRAVNPN IRDDELAAID SNRQQVLESL NQAGWRLDAL
     RLIVVTHQ