ID   RAPA_PSEPW              Reviewed;         948 AA.
AC   B1J1F5;
DT   28-JUL-2009, integrated into UniProtKB/Swiss-Prot.
DT   29-APR-2008, sequence version 1.
DT   03-AUG-2022, entry version 81.
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=PputW619_1162;
OS   Pseudomonas putida (strain W619).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
OC   Pseudomonadaceae; Pseudomonas.
OX   NCBI_TaxID=390235;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=W619;
RA   Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C.,
RA   Glavina del Rio T., Dalin E., Tice H., Pitluck S., Chain P., Malfatti S.,
RA   Shin M., Vergez L., Schmutz J., Larimer F., Land M., Hauser L.,
RA   Kyrpides N., Kim E., Taghavi S., Vangronsveld D., van der Lelie D.,
RA   Richardson P.;
RT   "Complete sequence of Pseudomonas putida W619.";
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; CP000949; ACA71667.1; -; Genomic_DNA.
DR   RefSeq; WP_012313078.1; NC_010501.1.
DR   AlphaFoldDB; B1J1F5; -.
DR   SMR; B1J1F5; -.
DR   STRING; 390235.PputW619_1162; -.
DR   PRIDE; B1J1F5; -.
DR   EnsemblBacteria; ACA71667; ACA71667; PputW619_1162.
DR   KEGG; ppw:PputW619_1162; -.
DR   eggNOG; COG0553; Bacteria.
DR   HOGENOM; CLU_011520_0_0_6; -.
DR   OMA; MSILERD; -.
DR   OrthoDB; 291634at2; -.
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..948
FT                   /note="RNA polymerase-associated protein RapA"
FT                   /id="PRO_1000188182"
FT   DOMAIN          164..332
FT                   /note="Helicase ATP-binding"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01821"
FT   DOMAIN          473..627
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   948 AA;  106024 MW;  000F8A77B02148D4 CRC64;
     MAQQYQPGQR WISDSEAELG LGTILAQDGR LLTVLYPATG DTRQYSLRNA PLTRVRFSPG
     DQITHFEGWK LTVREVEDID GLMVYHGLDG QNQPRTLPET QLSNFIQFRL ASDRLFAGQI
     DPLSWFSLRY NTLQHTSKQV QSSLWGLGGC RAQPIAHQLH IAREVADRSA PRVLLADEVG
     LGKTIEAGLV IHRQLLTGRA NRVLILVPEN LQHQWLVEMR RRFNLQVALF DAERFIESDA
     SNPFEDAQLA LVALEWLVED EKAQDALFAA GWDLMVVDEA HHLVWHEDKA STEYSLVEQL
     AQVIPGVLLL TATPEQLGQD SHFARLRLLD PNRFHDLAAF RAESEHYRPV AEAVQELLDE
     GRLSPKAHAT IQGFLGAEGE ALLAAVSDGD SQASARLIRE LLDRHGTGRV LFRNTRAAIQ
     GFPERELHPY PLPMPEQYRD LPAGEHAELY PEVAFQAQGE VSDDERWWRF DPRVDWLIDT
     LKMLKRTKVL VICAHAETAM DLEDALRVRS GIPASVFHEG MSILERDRAA AYFADEEFGA
     QVLICSEIGS EGRNFQFAHH LVMFDLPAHP DLLEQRIGRL DRIGQKHVIQ LHIPYLQEGP
     QERLFQWYHE ALNAFLNTCP TGNALQHQFG PRLLPMLEGG DSKAWDALVA EAKGERERLE
     AELHSGRDRL LELNSGGAGE GQALVEDILE QDDQFALPIY METLFDAFGI DSEDHSENAL
     ILKPSEKMLD ASFPLGDDEG VTITYDRGQA LSREDMQFLT WEHPMVQGGM DLVLSGSMGN
     TAVALIKNKA LKPGTVLLEL LFVSEVVAPR SLQLGRYLPP AALRCLLDAN GNDLASRVAF
     ETLNEQLESV PRASANKFVQ AQRDVLAKRI SGGEAKIMPT HVERVAEAQR RLAAEADEEL
     ARLTALKAVN PSVRDSEIDA LRKQREDGLA MLEKAALRLE AIRVLVAG