ID   RAPA_SHELP              Reviewed;         968 AA.
AC   A3QA31;
DT   20-MAY-2008, integrated into UniProtKB/Swiss-Prot.
DT   17-APR-2007, sequence version 1.
DT   03-AUG-2022, entry version 103.
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=Shew_0457;
OS   Shewanella loihica (strain ATCC BAA-1088 / PV-4).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales;
OC   Shewanellaceae; Shewanella.
OX   NCBI_TaxID=323850;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC BAA-1088 / PV-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   Chain P., Malfatti S., Shin M., Vergez L., Schmutz J., Larimer F., Land M.,
RA   Hauser L., Kyrpides N., Mikhailova N., Romine M.F., Serres G.,
RA   Fredrickson J., Tiedje J., Richardson P.;
RT   "Complete sequence of Shewanella loihica PV-4.";
RL   Submitted (MAR-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}.
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; CP000606; ABO22329.1; -; Genomic_DNA.
DR   RefSeq; WP_011864263.1; NC_009092.1.
DR   AlphaFoldDB; A3QA31; -.
DR   SMR; A3QA31; -.
DR   STRING; 323850.Shew_0457; -.
DR   PRIDE; A3QA31; -.
DR   EnsemblBacteria; ABO22329; ABO22329; Shew_0457.
DR   KEGG; slo:Shew_0457; -.
DR   eggNOG; COG0553; Bacteria.
DR   HOGENOM; CLU_011520_0_0_6; -.
DR   OMA; MSILERD; -.
DR   OrthoDB; 291634at2; -.
DR   Proteomes; UP000001558; 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_1000088384"
FT   DOMAIN          163..332
FT                   /note="Helicase ATP-binding"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01821"
FT   DOMAIN          491..645
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;  109620 MW;  B17A4E66667A9EA9 CRC64;
     MPFSLGQRWI SDTESELGLG TVIGLEGRMV TLMFPATDEN RMFARDDAPL TRVIYNPGDI
     IESHEGWSLK VSEIEEKNQL VIYHGIHTET GEEVSLRETL LNHNIRFNKP QDRLFAGQID
     RLDRFGVRYQ SQLLRHKLAT SDLLGLQGPR VGLIPHQQWI AHEVGQRFAP RVLLADEVGL
     GKTIEAGLII HQQLLTGRAE RILIIVPDTL RHQWLVEMLR RFNLRFSVFD EDRCVEAYAD
     HDNPFYTEQL VICSLELLRK KKRLDQALDA DWDLMVVDEA HHLEWTEEEP SRAYRVVEAL
     SEVVPGVLLL TATPDQLGHQ SHFARLRLLD PDRFYDYQAF LKEEESYKEV ASAADALASG
     KRLPDEAVAS LTELLNEKDI TPALRLIEDE SVDNEQRDQA RSELLQELLD RHGTGRVLYR
     NSRASVKGFP TRIFNAHPQT MPAQYKTAAR VSDMMGGQTD LTAKVKQALS PEKLYQAFES
     DSASWWKFDP RVDWLIDFLK NHRSKKVLII ASQAETALSL EEALRTREGI QATVFHEGMS
     IIERDKAGAY FAQESGGAQA LICSEIGSEG RNFQFASHLV LFDLPLNPDL LEQRIGRLDR
     IGQANDVEIH LPYLANTAQE NLMNWYHKGL NAFEQTCPTG HILFNEFSEE LLTQLVYRDE
     DKFTQLLNHT QSRYKALKKA MEQGRDKLLE INSHGGDKAQ KLVENLAARD QDTQLIGSVI
     RLWDIIGVEQ EDSGENAIVL HPSEHMMFPT YPGLPEDGIT VTFDREMALS RDDIALITQE
     HPLVQTGLDL ITSSETGTTS VAVLKNKALP AGTIFLELIY MADASAPRSS QLYRYMPPTP
     VRVLLDKNGN NLSQNVSYES FDKQLSAVNR HIASKLVNAS QTLLHPLFAK GEEFAQAAMK
     QLTEEASNKM TQQLTAELER LEALKAVNPN IRDEELEHLR NQMVELGNYL DACQLQLDAV
     RLVLVSHA