ID   RAPA_SHESH              Reviewed;         968 AA.
AC   A8FQW4;
DT   20-MAY-2008, integrated into UniProtKB/Swiss-Prot.
DT   13-NOV-2007, sequence version 1.
DT   03-AUG-2022, entry version 85.
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=Ssed_0625;
OS   Shewanella sediminis (strain HAW-EB3).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales;
OC   Shewanellaceae; Shewanella.
OX   NCBI_TaxID=425104;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=HAW-EB3;
RG   US DOE Joint Genome Institute;
RA   Copeland A., Lucas S., Lapidus A., Barry K., Glavina del Rio T., Dalin E.,
RA   Tice H., Pitluck S., Chertkov O., Brettin T., Bruce D., Detter J.C.,
RA   Han C., Schmutz J., Larimer F., Land M., Hauser L., Kyrpides N., Kim E.,
RA   Zhao J.-S., Richardson P.;
RT   "Complete sequence of Shewanella sediminis HAW-EB3.";
RL   Submitted (AUG-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; CP000821; ABV35237.1; -; Genomic_DNA.
DR   RefSeq; WP_012140974.1; NC_009831.1.
DR   AlphaFoldDB; A8FQW4; -.
DR   SMR; A8FQW4; -.
DR   STRING; 425104.Ssed_0625; -.
DR   EnsemblBacteria; ABV35237; ABV35237; Ssed_0625.
DR   KEGG; sse:Ssed_0625; -.
DR   eggNOG; COG0553; Bacteria.
DR   HOGENOM; CLU_011520_0_0_6; -.
DR   OMA; MSILERD; -.
DR   OrthoDB; 291634at2; -.
DR   Proteomes; UP000002015; 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   CHAIN           1..968
FT                   /note="RNA polymerase-associated protein RapA"
FT                   /id="PRO_1000088388"
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;  109249 MW;  75F566D1F0B2F805 CRC64;
     MPFSLGQRWI SDTESELGLG TVVALEGRMV TLMFPATDEN RLFSRTDAPL TRVIFNPGDK
     AESHEGWSLT VSEVEEKDNL IIYHGIHSET GEQASLRETL LNHNIRFNKP QDRLFAGQID
     RLERFGVRYQ CQLLRHKLAT SDLLGLQGPR VGLIPHQQWI AHEVGRRFAP RVLLADEVGL
     GKTIEAGLII HQQLLTGRAE RILVIVPDTL RHQWLVEMLR RFNLKFSVFD EDRCIEAYAD
     NDNPFYTEQL VICSLELLRK KKRLEQALDA DWDLMVVDEA HHLEWTEDAP SRAYRVVEAL
     SEVVPGVLLL TATPDQLGHQ SHFARLRLLD PDRFYDYEAF LKEESSYKDV ASAADALASG
     NKLPDDAINS LTELLSEKDI TPSINVIQAT DIDPDQQQDA RDELLQELLD RHGTGRVLYR
     NSRASVKGFP TRIFNAYPQA MPSQYVTAAR VGAMMNGHLD TQGKVKQALS PEKIYQDFDS
     NSASWWKFDP RVDWLINFLK ENRRKKVLII ASQAETALSL EEALRTREGI QTTVFHEGMS
     IIERDKAGAY FAQETGGAQA LICSEIGSEG RNFQFASQLI LFDLPLNPDL LEQRIGRLDR
     IGQNNDVEIH VPYLEKTAQE CLMQWYHKGL NAFEQTCPSG HILFSEFAEP LLDVLINQND
     DSLTELLNHT QTRYKELKTV MEQGRDKLLE INSHGGERAN KLVQSLAARD EDTQLIGSVI
     RLWDVIGVEQ EDCGENAIVL NPSEHMMFPT YPGLPEDGIT VTFDREMALS RDDIALITQE
     HPIVQTGLDL ITSSETGTTS VAVLKNKALP AGTIFLELIY MADASAPKSS QLYRYLPPTP
     VRILLDKNGN NLSDNVTYES FNKQLSAVNR HIASKLVNAS QTILHPLFAK GEEFAEVELK
     LLADSARAKM TSQLTLELER LEALKAVNPN IRDEELEHIR EQMNELNGYL DGCLLQLDAI
     RLVLVSHA