ID   RAPA_PSEU5              Reviewed;         949 AA.
AC   A4VNR4;
DT   20-MAY-2008, integrated into UniProtKB/Swiss-Prot.
DT   29-MAY-2007, sequence version 1.
DT   03-AUG-2022, entry version 94.
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=PST_2969;
OS   Pseudomonas stutzeri (strain A1501).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
OC   Pseudomonadaceae; Pseudomonas.
OX   NCBI_TaxID=379731;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=A1501;
RX   PubMed=18495935; DOI=10.1073/pnas.0801093105;
RA   Yan Y., Yang J., Dou Y., Chen M., Ping S., Peng J., Lu W., Zhang W.,
RA   Yao Z., Li H., Liu W., He S., Geng L., Zhang X., Yang F., Yu H., Zhan Y.,
RA   Li D., Lin Z., Wang Y., Elmerich C., Lin M., Jin Q.;
RT   "Nitrogen fixation island and rhizosphere competence traits in the genome
RT   of root-associated Pseudomonas stutzeri A1501.";
RL   Proc. Natl. Acad. Sci. U.S.A. 105:7564-7569(2008).
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; CP000304; ABP80615.1; -; Genomic_DNA.
DR   RefSeq; WP_011914070.1; NC_009434.1.
DR   AlphaFoldDB; A4VNR4; -.
DR   SMR; A4VNR4; -.
DR   STRING; 379731.PST_2969; -.
DR   EnsemblBacteria; ABP80615; ABP80615; PST_2969.
DR   KEGG; psa:PST_2969; -.
DR   eggNOG; COG0553; Bacteria.
DR   HOGENOM; CLU_011520_0_0_6; -.
DR   OMA; MSILERD; -.
DR   Proteomes; UP000000233; 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..949
FT                   /note="RNA polymerase-associated protein RapA"
FT                   /id="PRO_1000088371"
FT   DOMAIN          164..332
FT                   /note="Helicase ATP-binding"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01821"
FT   DOMAIN          474..628
FT                   /note="Helicase C-terminal"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01821"
FT   MOTIF           278..281
FT                   /note="DEAH box"
FT   BINDING         177..184
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01821"
SQ   SEQUENCE   949 AA;  106297 MW;  CEE5F800A47E87C1 CRC64;
     MAQQYLPGQR WISDSEAELG LGTILTQDGR MLTVLYPATG ETRQYATRSA PLTRVRFVPG
     DEITHFEGWK MTVREVDDVD GLLVYHGLTA QNEARTLPET QLSNFIQFRL ASDRLFAGQI
     DPLAWFSLRY HTLQHQSAQL QSSLWGLGGV RAQPIAHQLH IAKEVADRIA PRVLLADEVG
     LGKTIEAGLI IHRQLLSGRA SRVLILVPEN LQHQWLVEMR RRFNLEVALF DAERFIESDA
     SNPFEDTQLA LVSLEWLKED ERAQDAAFAA GWDLLVVDEA HHLVWHPESA SAEYRLVEQL
     AEVIPGVLLL TATPEQLGLD SHFARLRLLD PNRFHDLDAF RAESSSYQPV AEAVQELLDE
     GRLSQQAHQT IHDFLGAEGE ALLAAATDGD IEASSRLIRE LLDRHGTGRL LFRNTRAAVQ
     GFPERQLHPY PLPCPAEYME LPLGEHAELY PEVAFQSQQE PADEQNRWWQ FDPRVEWLID
     TLKMLKKYKV LVICAHAETA LDLEDALRVR SGIPATVFHE GMSILERDRA AAYFADEEFG
     AQVLICSEIG SEGRNFQFSH HLVLFDLPAH PDLLEQRIGR LDRIGQQHTI QLHVPYLETS
     PQERLFKWYH EALNAFLATC PTGNALQHQF GPRLLPLLED GDDDTFQGLI DEARAERERL
     EAELHAGRDR LLELNSGGGE QGTALVDAIE EQDDQFALPI YMEQLFDAFG IDSEDHSENA
     LVLRPSEKML DASFPLGDDE AVTITYDREQ ALAREDMQFL TWEHPMVQGG MDLVLSGSMG
     NTAVALIKNK ALKPGTVLLE LLFVSEVVAP RALQLSRFLP PLALRCLLDG NGNDLAAKVA
     FDTLNDQLES VPRASANKFV QAQRDVLATQ IAAAEAKIKP RHVERVAEAQ RKLKAGLDEE
     LARLVALQAV NPSVRDSEIE ALRQQREDGL AALEKAALRL EAIRVLVAG