ID   RAPA_SHEPC              Reviewed;         968 AA.
AC   A4YAN1;
DT   20-MAY-2008, integrated into UniProtKB/Swiss-Prot.
DT   29-MAY-2007, sequence version 1.
DT   03-AUG-2022, entry version 86.
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};
GN   OrderedLocusNames=Sputcn32_3302;
OS   Shewanella putrefaciens (strain CN-32 / ATCC BAA-453).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales;
OC   Shewanellaceae; Shewanella.
OX   NCBI_TaxID=319224;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=CN-32 / ATCC BAA-453;
RG   US DOE Joint Genome Institute;
RA   Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C.,
RA   Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S.,
RA   Chain P., Malfatti S., Shin M., Vergez L., Schmutz J., Larimer F., Land M.,
RA   Hauser L., Kyrpides N., Mikhailova N., Romine M.F., Fredrickson J.,
RA   Tiedje J., Richardson P.;
RT   "Complete sequence of Shewanella putrefaciens CN-32.";
RL   Submitted (APR-2007) to the EMBL/GenBank/DDBJ databases.
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; CP000681; ABP77014.1; -; Genomic_DNA.
DR   RefSeq; WP_011919994.1; NC_009438.1.
DR   AlphaFoldDB; A4YAN1; -.
DR   SMR; A4YAN1; -.
DR   STRING; 319224.Sputcn32_3302; -.
DR   GeneID; 45043797; -.
DR   KEGG; spc:Sputcn32_3302; -.
DR   eggNOG; COG0553; Bacteria.
DR   HOGENOM; CLU_011520_0_0_6; -.
DR   OMA; MSILERD; -.
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   CHAIN           1..968
FT                   /note="RNA polymerase-associated protein RapA"
FT                   /id="PRO_1000088386"
FT   DOMAIN          163..332
FT                   /note="Helicase ATP-binding"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01821"
FT   DOMAIN          491..643
FT                   /note="Helicase C-terminal"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01821"
FT   MOTIF           278..281
FT                   /note="DEAH box"
FT   BINDING         176..183
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01821"
SQ   SEQUENCE   968 AA;  109087 MW;  15319BD10D560CD0 CRC64;
     MPFALGQRWI SDTESELGLG TVVQVEGRMV TVLFPATGEN RMFSRAEAPL TRVTYNSGDT
     VESHEGWSLT IEELTEKDGL VIYHGIHSET GEQVTLRETL LNHNIRFNKP QDRLFAGQID
     RLDRFGVRYQ CQMLRHKLAT SDLLGLQGPR VGLIPHQMWI AHEVGRRYAP RVLLADEVGL
     GKTIEAGLII HQQLLTGRAE RVLVIVPDTL RHQWLVEMLR RFNLRFSVFD EDRCVEAYAD
     HDNPFYTEQL VICSLELLRK KKRLDQALDA DWDLLVVDEA HHLEWTEEAP SRAYQVVEAL
     SEVVPGVLLL TATPDQLGHE SHFARLRLLD PDRFYDYDAF LAEEDSYKDV AMAAEALAGN
     AKLPDAAINS LTELLSEKDI APSIRLIQAD GIDSELQQAA RSELLQELLD RHGTGRVLYR
     NSRASVKGFP KRFFNPHPQT MPEQYLTAAR VSSMMGGHKT LEAKAAQALS PEKLYQEFED
     NSASWWKFDP RVDWLIAFLK SHRSKKVLII ASQAETALSL EEALRTREGI QATVFHEGMS
     IIERDKAGAY FAQEEGGAQA LICSEIGSEG RNFQFASHLV LFDLPLNPDL LEQRIGRLDR
     IGQKNDIQIH LPYLEDTAQE RLMQWYHQGL NAFELTCPSG HVLYAEFAED LLNVLVGDDA
     DELTNLLNHT QTRYKELKHA MEQGRDKLLE INSHGGDRAK AIVERLAQND ENTQLIGSVI
     RLWDIIGVDQ EDKGENSIIL RPSEHMMFPT YPGLPEDGVT VTFDRDTALS RDDIALITQE
     HPLVQTGLDL ITGSETGTTS VAVLKNKALP AGTLFLELIY MADASAPKSS QLYRYLPPTP
     IRILLDKNGN DLSAKVDYAS FDKQLSAVNR HIGGKLVTAS QPILHPLFAK GEEYAQAAVD
     ELVIQAREKM TTQLTGELDR LESLKAVNPN IREEELEYLR NQMQELNTYL DASQLQLDAI
     RMVLVSHV