ID RAPA_ECOLI Reviewed; 968 AA.
AC P60240; P23852; P75633;
DT 16-JAN-2004, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 2.
DT 27-MAR-2024, entry version 160.
DE RecName: Full=RNA polymerase-associated protein RapA;
DE EC=3.6.4.-;
DE AltName: Full=ATP-dependent helicase HepA;
GN Name=rapA; Synonyms=hepA, yabA; OrderedLocusNames=b0059, JW0058;
OS Escherichia coli (strain K12).
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=1630901; DOI=10.1093/nar/20.13.3305;
RA Yura T., Mori H., Nagai H., Nagata T., Ishihama A., Fujita N., Isono K.,
RA Mizobuchi K., Nakata A.;
RT "Systematic sequencing of the Escherichia coli genome: analysis of the 0-
RT 2.4 min region.";
RL Nucleic Acids Res. 20:3305-3308(1992).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-538.
RC STRAIN=K12;
RX PubMed=1577702; DOI=10.1128/jb.174.10.3377-3385.1992;
RA Lewis L.K., Jenkins M.E., Mount D.W.;
RT "Isolation of DNA damage-inducible promoters in Escherichia coli:
RT regulation of polB (dinA), dinG, and dinH by LexA repressor.";
RL J. Bacteriol. 174:3377-3385(1992).
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-422.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=2034216; DOI=10.1007/bf00273583;
RA Iwasaki H., Ishino Y., Toh H., Nakata A., Shinagawa H.;
RT "Escherichia coli DNA polymerase II is homologous to alpha-like DNA
RT polymerases.";
RL Mol. Gen. Genet. 226:24-33(1991).
RN [6]
RP IDENTIFICATION OF FRAMESHIFT.
RX PubMed=8382805; DOI=10.1093/nar/21.3.751;
RA Bork P., Koonin E.V.;
RT "An expanding family of helicases within the 'DEAD/H' superfamily.";
RL Nucleic Acids Res. 21:751-752(1993).
RN [7]
RP PROTEIN SEQUENCE OF 2-11, AND INTERACTION WITH RNAP.
RC STRAIN=K12;
RX PubMed=9507009; DOI=10.1074/jbc.273.12.7018;
RA Sukhodolets M.V., Jin D.J.;
RT "RapA, a novel RNA polymerase-associated protein, is a bacterial homolog of
RT SWI2/SNF2.";
RL J. Biol. Chem. 273:7018-7023(1998).
RN [8]
RP PROTEIN SEQUENCE OF 2-19, AND INTERACTION WITH RNAP.
RX PubMed=9614128; DOI=10.1074/jbc.273.24.15157;
RA Muzzin O., Campbell E.A., Xia L., Severinova E., Darst S.A., Severinov K.;
RT "Disruption of Escherichia coli hepA, an RNA polymerase-associated protein,
RT causes UV sensitivity.";
RL J. Biol. Chem. 273:15157-15161(1998).
RN [9]
RP INTERACTION WITH RNAP.
RX PubMed=10801781; DOI=10.1074/jbc.m000056200;
RA Sukhodolets M.V., Jin D.J.;
RT "Interaction between RNA polymerase and RapA, a bacterial homolog of the
RT SWI/SNF protein family.";
RL J. Biol. Chem. 275:22090-22097(2000).
RN [10]
RP DEVELOPMENTAL STAGE.
RX PubMed=11567013; DOI=10.1128/jb.183.20.6126-6134.2001;
RA Cabrera J.E., Jin D.J.;
RT "Growth phase and growth rate regulation of the rapA gene, encoding the RNA
RT polymerase-associated protein RapA in Escherichia coli.";
RL J. Bacteriol. 183:6126-6134(2001).
RN [11]
RP FUNCTION, DNA-BINDING, AND MUTAGENESIS OF LYS-183 AND 280-ASP-GLU-281.
RX PubMed=11751638; DOI=10.1101/gad.936701;
RA Sukhodolets M.V., Cabrera J.E., Zhi H., Jin D.J.;
RT "RapA, a bacterial homolog of SWI2/SNF2, stimulates RNA polymerase
RT recycling in transcription.";
RL Genes Dev. 15:3330-3341(2001).
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 (By similarity). {ECO:0000250,
CC ECO:0000269|PubMed:11751638}.
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 (By similarity). {ECO:0000250}.
CC -!- INTERACTION:
CC P60240; P0A8V2: rpoB; NbExp=5; IntAct=EBI-551542, EBI-544996;
CC -!- DEVELOPMENTAL STAGE: During growth phase, peaking during at the early
CC log phase. {ECO:0000269|PubMed:11567013}.
CC -!- SIMILARITY: Belongs to the SNF2/RAD54 helicase family. RapA subfamily.
CC {ECO:0000305}.
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DR EMBL; X54847; CAA38617.1; -; Genomic_DNA.
DR EMBL; U00096; AAC73170.1; -; Genomic_DNA.
DR EMBL; AP009048; BAB96627.1; -; Genomic_DNA.
DR PIR; C64727; C64727.
DR RefSeq; NP_414601.1; NC_000913.3.
DR RefSeq; WP_001117011.1; NZ_STEB01000010.1.
DR PDB; 4S20; X-ray; 4.70 A; K/L=1-968.
DR PDB; 6BOG; X-ray; 3.20 A; A/B=1-968.
DR PDB; 7M8E; EM; 3.40 A; F=1-968.
DR PDB; 7MKN; EM; 3.30 A; L=1-968.
DR PDB; 7MKQ; EM; 4.80 A; L=1-968.
DR PDBsum; 4S20; -.
DR PDBsum; 6BOG; -.
DR PDBsum; 7M8E; -.
DR PDBsum; 7MKN; -.
DR PDBsum; 7MKQ; -.
DR AlphaFoldDB; P60240; -.
DR EMDB; EMD-23716; -.
DR EMDB; EMD-23900; -.
DR EMDB; EMD-23903; -.
DR SMR; P60240; -.
DR BioGRID; 4262039; 363.
DR BioGRID; 852817; 5.
DR DIP; DIP-35881N; -.
DR IntAct; P60240; 20.
DR STRING; 511145.b0059; -.
DR jPOST; P60240; -.
DR PaxDb; 511145-b0059; -.
DR EnsemblBacteria; AAC73170; AAC73170; b0059.
DR GeneID; 75202125; -.
DR GeneID; 948523; -.
DR KEGG; ecj:JW0058; -.
DR KEGG; eco:b0059; -.
DR PATRIC; fig|1411691.4.peg.2224; -.
DR EchoBASE; EB1075; -.
DR eggNOG; COG0553; Bacteria.
DR HOGENOM; CLU_011520_0_0_6; -.
DR InParanoid; P60240; -.
DR OMA; MSILERD; -.
DR OrthoDB; 9814088at2; -.
DR PhylomeDB; P60240; -.
DR BioCyc; EcoCyc:EG11083-MONOMER; -.
DR EvolutionaryTrace; P60240; -.
DR PRO; PR:P60240; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IDA:EcoCyc.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0016887; F:ATP hydrolysis activity; IDA:EcoCyc.
DR GO; GO:0140658; F:ATP-dependent chromatin remodeler activity; IEA:InterPro.
DR GO; GO:0001000; F:bacterial-type RNA polymerase core enzyme binding; IDA:EcoCyc.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0004386; F:helicase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0003676; F:nucleic acid binding; IDA:EcoCyc.
DR GO; GO:0045893; P:positive regulation of DNA-templated transcription; IDA:EcoCyc.
DR CDD; cd18011; DEXDc_RapA; 1.
DR CDD; cd18793; SF2_C_SNF; 1.
DR Gene3D; 2.30.30.140; -; 1.
DR Gene3D; 2.30.30.930; -; 1.
DR Gene3D; 3.30.360.80; -; 1.
DR Gene3D; 6.10.140.1500; -; 1.
DR Gene3D; 6.10.140.2230; -; 1.
DR Gene3D; 3.40.50.300; P-loop containing nucleotide triphosphate hydrolases; 1.
DR Gene3D; 3.40.50.10810; Tandem AAA-ATPase domain; 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; IPR049730; SNF2/RAD54-like_C.
DR InterPro; IPR000330; SNF2_N.
DR InterPro; IPR040765; Tudor_1_RapA.
DR InterPro; IPR040766; Tudor_2_RapA.
DR PANTHER; PTHR45766; DNA ANNEALING HELICASE AND ENDONUCLEASE ZRANB3 FAMILY MEMBER; 1.
DR PANTHER; PTHR45766:SF3; SWI_SNF-RELATED MATRIX-ASSOCIATED ACTIN-DEPENDENT REGULATOR OF CHROMATIN SUBFAMILY A-LIKE PROTEIN 1; 1.
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; P-loop containing nucleoside triphosphate hydrolases; 2.
DR PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
DR PROSITE; PS51194; HELICASE_CTER; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Activator; ATP-binding; Direct protein sequencing;
KW DNA-binding; Helicase; Hydrolase; Nucleotide-binding; Reference proteome;
KW Transcription; Transcription regulation.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:9507009,
FT ECO:0000269|PubMed:9614128"
FT CHAIN 2..968
FT /note="RNA polymerase-associated protein RapA"
FT /id="PRO_0000207172"
FT DOMAIN 164..334
FT /note="Helicase ATP-binding"
FT DOMAIN 490..662
FT /note="Helicase C-terminal"
FT MOTIF 280..283
FT /note="DEAH box"
FT BINDING 177..184
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT MUTAGEN 183
FT /note="K->A: Loss of function. Still interacts with RNAP."
FT /evidence="ECO:0000269|PubMed:11751638"
FT MUTAGEN 280..281
FT /note="DE->AA: Loss of function. Still interacts with
FT RNAP."
FT /evidence="ECO:0000269|PubMed:11751638"
FT CONFLICT 11
FT /note="S -> V (in Ref. 7; AA sequence)"
FT /evidence="ECO:0000305"
FT CONFLICT 510..538
FT /note="CAKAATALQLEQVLREREGIRAAVFHEGM -> RGIRNHGHSCFLCEIVIRS
FT QFHTTYEPEA (in Ref. 4)"
FT /evidence="ECO:0000305"
FT STRAND 8..10
FT /evidence="ECO:0007829|PDB:7MKN"
FT HELIX 15..17
FT /evidence="ECO:0007829|PDB:7MKN"
FT STRAND 20..25
FT /evidence="ECO:0007829|PDB:7MKN"
FT STRAND 27..33
FT /evidence="ECO:0007829|PDB:7MKN"
FT TURN 35..37
FT /evidence="ECO:0007829|PDB:7MKN"
FT STRAND 40..45
FT /evidence="ECO:0007829|PDB:7MKN"
FT STRAND 50..52
FT /evidence="ECO:0007829|PDB:7M8E"
FT STRAND 60..63
FT /evidence="ECO:0007829|PDB:7MKN"
FT STRAND 68..77
FT /evidence="ECO:0007829|PDB:7MKN"
FT STRAND 80..87
FT /evidence="ECO:0007829|PDB:7MKN"
FT TURN 88..91
FT /evidence="ECO:0007829|PDB:7MKN"
FT STRAND 92..98
FT /evidence="ECO:0007829|PDB:7MKN"
FT HELIX 99..101
FT /evidence="ECO:0007829|PDB:7MKN"
FT HELIX 111..116
FT /evidence="ECO:0007829|PDB:7MKN"
FT STRAND 117..119
FT /evidence="ECO:0007829|PDB:7MKN"
FT HELIX 123..140
FT /evidence="ECO:0007829|PDB:7MKN"
FT TURN 143..146
FT /evidence="ECO:0007829|PDB:7MKN"
FT STRAND 147..152
FT /evidence="ECO:0007829|PDB:7MKN"
FT HELIX 156..166
FT /evidence="ECO:0007829|PDB:7MKN"
FT STRAND 168..170
FT /evidence="ECO:0007829|PDB:7MKN"
FT STRAND 172..175
FT /evidence="ECO:0007829|PDB:7MKN"
FT HELIX 183..196
FT /evidence="ECO:0007829|PDB:7MKN"
FT STRAND 203..206
FT /evidence="ECO:0007829|PDB:7MKN"
FT HELIX 209..223
FT /evidence="ECO:0007829|PDB:7MKN"
FT HELIX 232..241
FT /evidence="ECO:0007829|PDB:7MKN"
FT HELIX 245..247
FT /evidence="ECO:0007829|PDB:7MKN"
FT STRAND 250..254
FT /evidence="ECO:0007829|PDB:7MKN"
FT HELIX 256..259
FT /evidence="ECO:0007829|PDB:7MKN"
FT HELIX 263..271
FT /evidence="ECO:0007829|PDB:7MKN"
FT STRAND 275..280
FT /evidence="ECO:0007829|PDB:7MKN"
FT HELIX 282..284
FT /evidence="ECO:0007829|PDB:7MKN"
FT HELIX 294..302
FT /evidence="ECO:0007829|PDB:7MKN"
FT TURN 303..305
FT /evidence="ECO:0007829|PDB:7M8E"
FT STRAND 307..312
FT /evidence="ECO:0007829|PDB:7MKN"
FT HELIX 316..318
FT /evidence="ECO:0007829|PDB:7M8E"
FT HELIX 321..324
FT /evidence="ECO:0007829|PDB:7MKN"
FT HELIX 325..331
FT /evidence="ECO:0007829|PDB:7MKN"
FT TURN 333..335
FT /evidence="ECO:0007829|PDB:7MKN"
FT HELIX 339..361
FT /evidence="ECO:0007829|PDB:7MKN"
FT HELIX 367..376
FT /evidence="ECO:0007829|PDB:7MKN"
FT HELIX 382..391
FT /evidence="ECO:0007829|PDB:7MKN"
FT HELIX 396..410
FT /evidence="ECO:0007829|PDB:7MKN"
FT TURN 414..416
FT /evidence="ECO:0007829|PDB:7MKN"
FT STRAND 422..424
FT /evidence="ECO:0007829|PDB:7MKN"
FT STRAND 431..438
FT /evidence="ECO:0007829|PDB:7MKN"
FT HELIX 442..454
FT /evidence="ECO:0007829|PDB:7MKN"
FT STRAND 456..458
FT /evidence="ECO:0007829|PDB:7MKN"
FT HELIX 460..467
FT /evidence="ECO:0007829|PDB:7MKN"
FT HELIX 470..472
FT /evidence="ECO:0007829|PDB:7MKN"
FT HELIX 474..477
FT /evidence="ECO:0007829|PDB:7MKN"
FT HELIX 484..486
FT /evidence="ECO:0007829|PDB:7MKN"
FT HELIX 489..500
FT /evidence="ECO:0007829|PDB:7MKN"
FT STRAND 506..509
FT /evidence="ECO:0007829|PDB:7MKN"
FT HELIX 513..527
FT /evidence="ECO:0007829|PDB:7MKN"
FT STRAND 531..534
FT /evidence="ECO:0007829|PDB:7M8E"
FT HELIX 540..551
FT /evidence="ECO:0007829|PDB:7MKN"
FT TURN 553..555
FT /evidence="ECO:0007829|PDB:7MKN"
FT STRAND 558..560
FT /evidence="ECO:0007829|PDB:7MKN"
FT STRAND 577..582
FT /evidence="ECO:0007829|PDB:7MKN"
FT HELIX 587..595
FT /evidence="ECO:0007829|PDB:7MKN"
FT STRAND 606..616
FT /evidence="ECO:0007829|PDB:7MKN"
FT HELIX 617..626
FT /evidence="ECO:0007829|PDB:7MKN"
FT TURN 627..629
FT /evidence="ECO:0007829|PDB:7MKN"
FT TURN 631..633
FT /evidence="ECO:0007829|PDB:7MKN"
FT HELIX 639..655
FT /evidence="ECO:0007829|PDB:7MKN"
FT HELIX 663..683
FT /evidence="ECO:0007829|PDB:7MKN"
FT HELIX 687..694
FT /evidence="ECO:0007829|PDB:7MKN"
FT HELIX 696..709
FT /evidence="ECO:0007829|PDB:7MKN"
FT HELIX 713..726
FT /evidence="ECO:0007829|PDB:7MKN"
FT STRAND 729..732
FT /evidence="ECO:0007829|PDB:7MKN"
FT STRAND 734..736
FT /evidence="ECO:0007829|PDB:7MKN"
FT STRAND 738..741
FT /evidence="ECO:0007829|PDB:7MKN"
FT STRAND 747..749
FT /evidence="ECO:0007829|PDB:7MKN"
FT STRAND 759..763
FT /evidence="ECO:0007829|PDB:7MKN"
FT HELIX 765..770
FT /evidence="ECO:0007829|PDB:7MKN"
FT STRAND 774..776
FT /evidence="ECO:0007829|PDB:7MKN"
FT HELIX 782..793
FT /evidence="ECO:0007829|PDB:7MKN"
FT STRAND 798..804
FT /evidence="ECO:0007829|PDB:7MKN"
FT STRAND 814..823
FT /evidence="ECO:0007829|PDB:7MKN"
FT HELIX 828..830
FT /evidence="ECO:0007829|PDB:7MKN"
FT HELIX 832..834
FT /evidence="ECO:0007829|PDB:7MKN"
FT STRAND 839..845
FT /evidence="ECO:0007829|PDB:7MKN"
FT TURN 853..855
FT /evidence="ECO:0007829|PDB:7MKN"
FT HELIX 858..863
FT /evidence="ECO:0007829|PDB:7MKN"
FT HELIX 870..878
FT /evidence="ECO:0007829|PDB:7MKN"
FT HELIX 881..925
FT /evidence="ECO:0007829|PDB:7MKN"
FT HELIX 933..951
FT /evidence="ECO:0007829|PDB:7MKN"
FT STRAND 954..965
FT /evidence="ECO:0007829|PDB:7MKN"
SQ SEQUENCE 968 AA; 109769 MW; 2943B818AB67A67E CRC64;
MPFTLGQRWI SDTESELGLG TVVAVDARTV TLLFPSTGEN RLYARSDSPV TRVMFNPGDT
ITSHDGWQMQ VEEVKEENGL LTYIGTRLDT EESGVALREV FLDSKLVFSK PQDRLFAGQI
DRMDRFALRY RARKYSSEQF RMPYSGLRGQ RTSLIPHQLN IAHDVGRRHA PRVLLADEVG
LGKTIEAGMI LHQQLLSGAA ERVLIIVPET LQHQWLVEML RRFNLRFALF DDERYAEAQH
DAYNPFDTEQ LVICSLDFAR RSKQRLEHLC EAEWDLLVVD EAHHLVWSED APSREYQAIE
QLAEHVPGVL LLTATPEQLG MESHFARLRL LDPNRFHDFA QFVEEQKNYR PVADAVAMLL
AGNKLSNDEL NMLGEMIGEQ DIEPLLQAAN SDSEDAQSAR QELVSMLMDR HGTSRVLFRN
TRNGVKGFPK RELHTIKLPL PTQYQTAIKV SGIMGARKSA EDRARDMLYP ERIYQEFEGD
NATWWNFDPR VEWLMGYLTS HRSQKVLVIC AKAATALQLE QVLREREGIR AAVFHEGMSI
IERDRAAAWF AEEDTGAQVL LCSEIGSEGR NFQFASHMVM FDLPFNPDLL EQRIGRLDRI
GQAHDIQIHV PYLEKTAQSV LVRWYHEGLD AFEHTCPTGR TIYDSVYNDL INYLASPDQT
EGFDDLIKNC REQHEALKAQ LEQGRDRLLE IHSNGGEKAQ ALAESIEEQD DDTNLIAFAM
NLFDIIGINQ DDRGDNMIVL TPSDHMLVPD FPGLSEDGIT ITFDREVALA REDAQFITWE
HPLIRNGLDL ILSGDTGSST ISLLKNKALP VGTLLVELIY VVEAQAPKQL QLNRFLPPTP
VRMLLDKNGN NLAAQVEFET FNRQLNAVNR HTGSKLVNAV QQDVHAILQL GEAQIEKSAR
ALIDAARNEA DEKLSAELSR LEALRAVNPN IRDDELTAIE SNRQQVMESL DQAGWRLDAL
RLIVVTHQ
//
