ID   RAPA_SHEWM              Reviewed;         968 AA.
AC   B1KJA5;
DT   28-JUL-2009, integrated into UniProtKB/Swiss-Prot.
DT   29-APR-2008, sequence version 1.
DT   03-AUG-2022, entry version 82.
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=Swoo_4324;
OS   Shewanella woodyi (strain ATCC 51908 / MS32).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales;
OC   Shewanellaceae; Shewanella.
OX   NCBI_TaxID=392500;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 51908 / MS32;
RG   US DOE Joint Genome Institute;
RA   Copeland A., Lucas S., Lapidus A., Glavina del Rio T., Dalin E., Tice H.,
RA   Bruce D., Goodwin L., Pitluck S., Sims D., Brettin T., Detter J.C., Han C.,
RA   Kuske C.R., Schmutz J., Larimer F., Land M., Hauser L., Kyrpides N.,
RA   Lykidis A., Zhao J.-S., Richardson P.;
RT   "Complete sequence of Shewanella woodyi ATCC 51908.";
RL   Submitted (FEB-2008) 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; CP000961; ACA88577.1; -; Genomic_DNA.
DR   RefSeq; WP_012326903.1; NC_010506.1.
DR   AlphaFoldDB; B1KJA5; -.
DR   SMR; B1KJA5; -.
DR   STRING; 392500.Swoo_4324; -.
DR   PRIDE; B1KJA5; -.
DR   EnsemblBacteria; ACA88577; ACA88577; Swoo_4324.
DR   KEGG; swd:Swoo_4324; -.
DR   eggNOG; COG0553; Bacteria.
DR   HOGENOM; CLU_011520_0_0_6; -.
DR   OMA; MSILERD; -.
DR   OrthoDB; 291634at2; -.
DR   Proteomes; UP000002168; 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_1000188192"
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;  108948 MW;  399BD68A087B4F62 CRC64;
     MPFSLGQRWI SDTESELGLG TVVAVEGRMV TVMFPATDEN RMFSRADAPL TRVIFNPGDK
     AESHEGWSLT VSEVEEKDNL IIYHGIHDET GEQVSLRETL LNHNIRFNKP QDRLFAGQID
     RLERFGIRYQ CQQLRHKLAT SDMLGLQGPR VGLIPHQQWI AHEVGRRFAP RVLLADEVGL
     GKTIEAGLII HQQLLTGRAE RILVIVPDTL RHQWLVEMLR RFNLKFSVFD EDRCVEAYAD
     SDNPFYTEQL VICSLELLRK KRRLDQALAA DWDLMVVDEA HHLEWTEDAP SRAYRIVEAL
     SEEIPGVLLL TATPDQLGHQ SHFARLRLLD PDRFYDYEAF LKEETNYADI ASTADALAGN
     EPLSQEIIDN LKTQLAEKDI TAATDIIQAT DADVDQQQAA RDALLQDLLD RHGTGRVLYR
     NSRASVKGFP TRIFNQYPQK MPAQYVTAAR VGAMMNGHLD TAGKVKQALS PEKIYQEFES
     SSASWWKFDP RVDWLIDFLK ENRREKVLII ASQAETALSL EEALRTREGI QATVFHEGMS
     IIERDKAGAY FAQETGGAQA LICSEIGSEG RNFQFASQLI LFDLPLNPDL LEQRIGRLDR
     IGQNNDVSIH VPYLEDTAQE SLMQWYHKGL NAFEQTCPSG HILFNEFSES LLNVLISQDK
     EVLEQVLSDT QTRYAELKSV MEQGRDKLLE INSHGGERAN KLVNALAERD EDTNLIGSVI
     RLWDIIGVEQ EDSGENAIVL RPSEHMMFPT YPGLPEDGIT VTFDREMALS RDDIALITQE
     HPLVQTGLDL ITSSETGTTS VAVLKNKSLP AGTIFLELIY MADASAPKSS QLYRYLPPTP
     VRVLLDKNGN NLADNVNYES FNKQLSAVNR HIASKLVNAS QAVLHPLFAK GEEFASSELT
     LLTESSRAKM TTQLNGELER LEALKAVNPN IRDEELAHLR EQMVELNGYL DGAVLQLDAI
     RLVLVSHA