ID   RAPA_SHEDO              Reviewed;         968 AA.
AC   Q12RU8;
DT   20-MAY-2008, integrated into UniProtKB/Swiss-Prot.
DT   22-AUG-2006, sequence version 1.
DT   03-AUG-2022, entry version 95.
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}; OrderedLocusNames=Sden_0536;
OS   Shewanella denitrificans (strain OS217 / ATCC BAA-1090 / DSM 15013).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales;
OC   Shewanellaceae; Shewanella.
OX   NCBI_TaxID=318161;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=OS217 / ATCC BAA-1090 / DSM 15013;
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   Brettin T., Bruce D., Han C., Tapia R., Gilna P., Kiss H., Schmutz J.,
RA   Larimer F., Land M., Hauser L., Kyrpides N., Lykidis A., Richardson P.;
RT   "Complete sequence of Shewanella denitrificans OS217.";
RL   Submitted (MAR-2006) 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; CP000302; ABE53828.1; -; Genomic_DNA.
DR   RefSeq; WP_011494994.1; NC_007954.1.
DR   AlphaFoldDB; Q12RU8; -.
DR   SMR; Q12RU8; -.
DR   STRING; 318161.Sden_0536; -.
DR   PRIDE; Q12RU8; -.
DR   EnsemblBacteria; ABE53828; ABE53828; Sden_0536.
DR   KEGG; sdn:Sden_0536; -.
DR   eggNOG; COG0553; Bacteria.
DR   HOGENOM; CLU_011520_0_0_6; -.
DR   OMA; MSILERD; -.
DR   OrthoDB; 291634at2; -.
DR   Proteomes; UP000001982; 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; Reference proteome; Transcription;
KW   Transcription regulation.
FT   CHAIN           1..968
FT                   /note="RNA polymerase-associated protein RapA"
FT                   /id="PRO_1000088381"
FT   DOMAIN          163..332
FT                   /note="Helicase ATP-binding"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01821"
FT   DOMAIN          491..641
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;  108905 MW;  8626CB25AC6DCE7D CRC64;
     MPFALGQRWI SDTESELGLG TVVQVEGRMV TLLFPATGEN RMFSRAEAPL TRVIFNPNDT
     VESHEGWSIT VTEVVEKDQL VVYHGTHSET GETVSLRETL ISHNIRFNKP QDRLFAGQID
     RLDRFGIRYQ CQLLRHKLAS SDLLGLQGPR VGLIAHQQWI AHEVGRRYAP RVLLADEVGL
     GKTIEAGLIM HQQLLTGRAE RILVIVPDTL RHQWLVEMLR RFNLRFSVFD EDRCVEAYAD
     NDNPFYTEQL VICSLELLRK KKRLDQALDA DWDLLVVDEA HHLEWSEDAP SRAYQVVEAL
     SEVVPGVLLL TATPDQLGHQ SHFARLRLLD PDRFYDYDAF LTEEQGYQAV AEAAEALSGE
     KKLNDSAINS LTELLSEKDI APSIRLIQAN EVDPEQQQAA RDGLLQELLD RHGTGRVLYR
     NSRASVKGFP KRIFNPHPQA MPEQYVTAER VNAMMSGKKT PQAKALEALS PEKLYQAFES
     DSASWWKFDT RVDWLIAFLK SHRSKKVLII ASQAETALSL EEALRTREGI LATVFHEGMS
     IIERDKAGAY FAQEDAGAQA LICSEIGSEG RNFQFASHLV LFDLPLNPDL LEQRIGRLDR
     IGQKNDIQIH LPYLEGTAQE RLMQWYHHGL NAFELTCPSG HVLFNEFAEE LTQVLCEDDA
     DAMTQLLNHT QHKYKELKQA MERGRDKLLE INSHGGARAA ALIERLAQKD NDTHLVGSVI
     RLWDIIGVDQ EDNGENTIVL RPSEHMLFPT YPGLPEDGVT VTFDRETALS RDDIAFISEE
     HPLVQTGLDL ITGSETGTTS VAVLKNKALP AGTLFLELIY MADASAPKSS QLYRYLPPTP
     IRVLLDKNGN NLATKVDYNN FEKQLSAVNR HIASKLVNAS QPLLHPLLAK GQEQAQQGLD
     ALLVDARASM TSQLTAELER LEALKAVNPN IREEELEYVR NQMAELNGYL DASQLQLDAI
     RMVLVSHV