ID   RAPA_PSEP1              Reviewed;         948 AA.
AC   A5VZN0;
DT   20-MAY-2008, integrated into UniProtKB/Swiss-Prot.
DT   10-JUL-2007, 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}; OrderedLocusNames=Pput_1179;
OS   Pseudomonas putida (strain ATCC 700007 / DSM 6899 / BCRC 17059 / F1).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
OC   Pseudomonadaceae; Pseudomonas.
OX   NCBI_TaxID=351746;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 700007 / DSM 6899 / BCRC 17059 / F1;
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., Lykidis A., Parales R., Richardson P.;
RT   "Complete sequence of Pseudomonas putida F1.";
RL   Submitted (MAY-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}.
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DR   EMBL; CP000712; ABQ77340.1; -; Genomic_DNA.
DR   RefSeq; WP_003254868.1; NC_009512.1.
DR   AlphaFoldDB; A5VZN0; -.
DR   SMR; A5VZN0; -.
DR   STRING; 351746.Pput_1179; -.
DR   EnsemblBacteria; ABQ77340; ABQ77340; Pput_1179.
DR   KEGG; ppf:Pput_1179; -.
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_1000088367"
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;  106025 MW;  0C7648B5CEE76D57 CRC64;
     MAQQYQPGQR WISDSEAELG LGTILAQDGR LLTVLYPATG DTRQYSLRNA PLTRVRFSPG
     DQITHFEGWK LTVREVEDID GLMVYHGLDG QNQPRTLPET QLSNFIQFRL ASDRLFAGQI
     DPLSWFSLRY NTLQHTSKQM QSALWGLGGC RAQPIAHQLH IAREVADRSA PRVLLADEVG
     LGKTIEAGLV IHRQLLSGRA SRVLILVPEN LQHQWLVEMR RRFNLQVALF DAERFIESDA
     SNPFEDAQLA LVALEWLVDD EKAQDALFAA GWDLMVVDEA HHLVWHEDQV SAEYGLVEQL
     AQVIPGVLLL TATPEQLGQD SHFARLRLLD PNRFHDLAAF RAESEHYRPV AEAVQELLDE
     GRLSPKAHAT ILGFLGAEGE ALLAAVSDGD TQASARLIRE LLDRHGTGRV LFRNTRAAIQ
     GFPERQLHPY PLATPEQYRN LPAGEHAELY PEVAFQAQGE VADDERWWRF DPRVDWLIDT
     LKMLKRTKVL VICAHAETAM DLEDALRVRS GIPASVFHEG MSILERDRAA AYFADEEFGA
     QVLICSEIGS EGRNFQFAHH LVMFDLPAHP DLLEQRIGRL DRIGQKHTIQ LHIPYLQDSP
     QERLFQWYHE GLNAFLNTCP TGNALQHQFG PRLLPLLEGG DHKAWDTLVA DARSERERLE
     AELHTGRDRL LELNSGGAGE GQALVEAILE QDDQFALPIY METLFDAFGI DSEDHSENAL
     ILKPSEKMLD ASFPLGDDEG VTITYDRGQA LSREDMQFLT WEHPMVQGGM DLVLSGSMGN
     TAVALIKNKA LKPGTVLLEL LFVSEVVAPR SLQLGRYLPP AALRCLLDAN GNDLASRVAF
     ETLNDQLESV PRASANKFVQ AQRDVLAKRI SGGEEKILPA HNERVAEAQR RLTAEADEEL
     ARLVALQAVN PSVRDSEIDA LRKRREDGLA MLEKAALRLE AIRVLVAG