ID   RAPA_SHEAM              Reviewed;         967 AA.
AC   A1SAC7;
DT   20-MAY-2008, integrated into UniProtKB/Swiss-Prot.
DT   06-FEB-2007, sequence version 1.
DT   03-AUG-2022, entry version 88.
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=Sama_3131;
OS   Shewanella amazonensis (strain ATCC BAA-1098 / SB2B).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales;
OC   Shewanellaceae; Shewanella.
OX   NCBI_TaxID=326297;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC BAA-1098 / SB2B;
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   Munk A.C., Brettin T., Bruce D., Han C., Tapia R., Gilna P., Schmutz J.,
RA   Larimer F., Land M., Hauser L., Kyrpides N., Mikhailova N., Fredrickson J.,
RA   Richardson P.;
RT   "Complete sequence of Shewanella amazonensis SB2B.";
RL   Submitted (DEC-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; CP000507; ABM01334.1; -; Genomic_DNA.
DR   RefSeq; WP_011761238.1; NC_008700.1.
DR   AlphaFoldDB; A1SAC7; -.
DR   SMR; A1SAC7; -.
DR   STRING; 326297.Sama_3131; -.
DR   EnsemblBacteria; ABM01334; ABM01334; Sama_3131.
DR   KEGG; saz:Sama_3131; -.
DR   eggNOG; COG0553; Bacteria.
DR   HOGENOM; CLU_011520_0_0_6; -.
DR   OMA; MSILERD; -.
DR   OrthoDB; 291634at2; -.
DR   Proteomes; UP000009175; 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..967
FT                   /note="RNA polymerase-associated protein RapA"
FT                   /id="PRO_1000088377"
FT   DOMAIN          163..332
FT                   /note="Helicase ATP-binding"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01821"
FT   DOMAIN          491..639
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   967 AA;  108828 MW;  BB8E3CBF820F5EAC CRC64;
     MSFAVGQRWI SDTESELGLG TVVQIEGRMV TLLFPATGEN RMFAMAEAPL TRVIYNPGDT
     IDSAEGWGMT VDKVEELNGL VFYLGKRTDT GEDTMLRETL LEHNIRFNKP QDRLYAGQID
     RIERFGVRYK AQLLRHKQAT SPLLGLQGPR VGLIPHQLWI AHEVGRRHAP RVLLADEVGL
     GKTIEAGLII HQQLMTGRAE RVLVIVPDTL RHQWLVEMLR RFNLRFSVFD EDRCVEAFAD
     HDNPFYTEQL VICSLELLRK KRRLEQALDA DWDLMVVDEA HHLEWSEDEP SRAYQVVEAL
     AEVVPGVLLL TATPDQLGHQ SHFARLRLLD PDRFYDYQAF LDEEKGYQAV AEAADALASG
     IKLSDEAING LTELLSEKDI APAIRQIQAE NLDEELRQAA RDELLQELLD RHGTGRVLFR
     NSRASVKGFP KREFHSHGFE LPEQYVTAMR VNAMMGGART QEARVAQALS PERIYQEFDD
     NNASWWKFDP RVDWLIDFLK SHRSKKVLVI ASRAETALAL EEALRTREGI QATVFHEGMS
     IIERDKAGAY FAQEEGGAQA LICSEIGSEG RNFQFASQLV LFDLPLNPDL LEQRIGRLDR
     IGQRHDVQIH LPFLKHTAQE QLMHWYHEGL CAFELTCPGG HVLFGEFKER LLSVLTGESD
     ELDELMADTK ARYKALKAAM EQGRDKLLEL NSHGGAKAEA ITASLSDADE DTDLIASVIR
     LWDVIGIDQD DKGENSIVLR TTEHMMYPTY PGLNEDGVTV TFDRNTALSR DDIALITLEH
     PLVQTGLDLI TGSDTGTTCV ALLKNKALPA GTIFLELIYL AETTAPKASQ LYRYLPPTPV
     RVLLDKNGNN LSDKVDYDSF DKQLSGVNRH IASKLVNASQ TMLHPLFAKG EEFAGEALET
     LTQDARARME SQLGAELSRL EALKAVNPSI REEELEHLRN MMQELSGYLG NTQLKLDAIR
     LVLVSHN