ID   RAPA_SHESM              Reviewed;         968 AA.
AC   Q0HMR2;
DT   20-MAY-2008, integrated into UniProtKB/Swiss-Prot.
DT   03-OCT-2006, sequence version 1.
DT   03-AUG-2022, entry version 92.
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=Shewmr4_0575;
OS   Shewanella sp. (strain MR-4).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales;
OC   Shewanellaceae; Shewanella.
OX   NCBI_TaxID=60480;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=MR-4;
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   Kiss H., Brettin T., Bruce D., Han C., Tapia R., Gilna P., Schmutz J.,
RA   Larimer F., Land M., Hauser L., Kyrpides N., Mikhailova N., Nealson K.,
RA   Konstantinidis K., Klappenbach J., Tiedje J., Richardson P.;
RT   "Complete sequence of Shewanella sp. MR-4.";
RL   Submitted (AUG-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}.
CC   ---------------------------------------------------------------------------
CC   Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC   Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC   ---------------------------------------------------------------------------
DR   EMBL; CP000446; ABI37655.1; -; Genomic_DNA.
DR   RefSeq; WP_011621377.1; NC_008321.1.
DR   AlphaFoldDB; Q0HMR2; -.
DR   SMR; Q0HMR2; -.
DR   KEGG; she:Shewmr4_0575; -.
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_1000088389"
FT   DOMAIN          163..332
FT                   /note="Helicase ATP-binding"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01821"
FT   DOMAIN          491..655
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;  109012 MW;  3E128ABBC497F469 CRC64;
     MPFALGQRWI SDTESELGLG TVVQVEGRMV TVLFPATGEN RMFSRNEAPL TRVIYNPGDT
     VESHEGWSLA IEELTEKDGL VVYHGIHSET GEKASLRETL LNHNIRFNKP QDRLFAGQID
     RLDRFGIRYQ CQLLRHQLAT SDLLGLQGPR VGLIPHQMWI AHEVGRRYAP RVLLADEVGL
     GKTIEAGLII HQQLLTGRAE RVLIIVPDTL RHQWLVEMLR RFNLRFSVFD EDRCVEAFAD
     HDNPFYTEQL VICSLELLRK KKRLDQALDA DWDLLVVDEA HHLEWTEEAP SRAYQVVEAL
     SEVVPGVLLL TATPDQLGHE SHFARLRLLD PDRFYDYDAF LAEENSYKDV AVAAEALAGD
     AKLSDAAINS LTELLSEKDI APSIRLIQAE DIDSELQQAA RSELLQELLD RHGTGRVLYR
     NSRASVKGFP KRIFNAYPHA MPEQYLTAAR VNEMMGGRKT LEAKAAQALS PEKLYQEFED
     NSASWWKFDP RVDWLIEFLK SHRSKKVLII ASGADTALSL EEALRTREGI QATVFHEGMS
     IIERDKAGAY FAQEEGGAQA LICSEIGSEG RNFQFASHLV LFDLPLNPDL LEQRIGRLDR
     IGQKNDIQIH LPYLQDTAQE RLLNWYHQGL NAFELTCPSG HVLYSEFAED LLNVLVGGDE
     DELTNLLNHT QSRYKELKHA MEQGRDKLLE INSHGGDKAK AIVERLAQSD QDTKLIGSVI
     RLWDIIGVDQ EDKGENSIIL RPSEHMMFPT YPGLHEDGVT VTFDRDTALS RDDIALITQE
     HPLVQTGLDL ITGSDTGTTS VAILKNKALP AGTLFLELIY MADASAPKSS QLYRYLPPTP
     IRVLLDKNGN DLSAKVDYTS FDKQLSAVNR HIGSKLVTAS QPILHPLFAK GEEYAQAAVD
     ELVAQAREKM TSQLTGELDR LESLKAVNPN IREEELEYLR NQMQELSTYL NASQLQLDAI
     RMVLVSHV