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Protein

RNA polymerase-associated protein RapA

Gene

rapA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Transcription regulator that activates transcription by stimulating RNA polymerase (RNAP) recycling in case of stress conditions such as supercoiled DNA or high salt concentrations. Probably acts by releasing the RNAP, when it is trapped or immobilized on tightly supercoiled DNA. Does not activate transcription on linear DNA. Probably not involved in DNA repair (By similarity).By similarity1 Publication

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi177 – 1848ATPBy similarity

GO - Molecular functioni

  • ATPase activity Source: EcoCyc
  • ATP binding Source: UniProtKB-HAMAP
  • DNA binding Source: UniProtKB-KW
  • helicase activity Source: UniProtKB-HAMAP
  • nucleic acid binding Source: EcoCyc
  • RNA polymerase binding Source: EcoCyc

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Activator, Helicase, Hydrolase

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

ATP-binding, DNA-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG11083-MONOMER.
ECOL316407:JW0058-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
RNA polymerase-associated protein RapA (EC:3.6.4.-)
Alternative name(s):
ATP-dependent helicase HepA
Gene namesi
Name:rapA
Synonyms:hepA, yabA
Ordered Locus Names:b0059, JW0058
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11083. rapA.

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi183 – 1831K → A: Loss of function. Still interacts with RNAP. 1 Publication
Mutagenesisi280 – 2812DE → AA: Loss of function. Still interacts with RNAP. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemoved2 Publications
Chaini2 – 968967RNA polymerase-associated protein RapAPRO_0000207172Add
BLAST

Proteomic databases

PaxDbiP60240.
PRIDEiP60240.

Expressioni

Developmental stagei

During growth phase, peaking during at the early log phase.1 Publication

Interactioni

Subunit structurei

Interacts with the RNAP. Has a higher affinity for the core RNAP than for the holoenzyme. Its ATPase activity is stimulated by binding to RNAP (By similarity).By similarity

Binary interactionsi

WithEntry#Exp.IntActNotes
rpoBP0A8V23EBI-551542,EBI-544996

GO - Molecular functioni

  • RNA polymerase binding Source: EcoCyc

Protein-protein interaction databases

BioGridi4262039. 359 interactions.
DIPiDIP-35881N.
IntActiP60240. 20 interactions.
STRINGi511145.b0059.

Structurei

Secondary structure

1
968
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi8 – 136Combined sources
Helixi15 – 173Combined sources
Beta strandi19 – 257Combined sources
Beta strandi27 – 337Combined sources
Turni35 – 373Combined sources
Beta strandi40 – 445Combined sources
Turni45 – 473Combined sources
Beta strandi50 – 523Combined sources
Beta strandi60 – 634Combined sources
Beta strandi68 – 758Combined sources
Beta strandi77 – 793Combined sources
Beta strandi82 – 876Combined sources
Turni88 – 903Combined sources
Beta strandi94 – 985Combined sources
Helixi99 – 1013Combined sources
Helixi111 – 1144Combined sources
Helixi123 – 1264Combined sources
Helixi129 – 14012Combined sources
Beta strandi146 – 1483Combined sources
Helixi156 – 16712Combined sources
Beta strandi168 – 1703Combined sources
Beta strandi172 – 1754Combined sources
Helixi183 – 19614Combined sources
Beta strandi203 – 2064Combined sources
Turni209 – 2113Combined sources
Helixi212 – 22211Combined sources
Helixi232 – 2409Combined sources
Beta strandi244 – 2463Combined sources
Beta strandi250 – 2545Combined sources
Helixi256 – 2605Combined sources
Turni263 – 2664Combined sources
Helixi267 – 2704Combined sources
Beta strandi276 – 2794Combined sources
Helixi294 – 30310Combined sources
Beta strandi307 – 3126Combined sources
Beta strandi317 – 3193Combined sources
Helixi325 – 3317Combined sources
Turni333 – 3353Combined sources
Helixi340 – 35718Combined sources
Turni358 – 3603Combined sources
Helixi367 – 3693Combined sources
Turni374 – 3774Combined sources
Helixi386 – 3883Combined sources
Turni397 – 3993Combined sources
Helixi400 – 4078Combined sources
Helixi408 – 4103Combined sources
Turni412 – 4165Combined sources
Turni422 – 4243Combined sources
Beta strandi435 – 4384Combined sources
Helixi442 – 45312Combined sources
Helixi460 – 4634Combined sources
Helixi465 – 4684Combined sources
Helixi471 – 4733Combined sources
Turni474 – 4785Combined sources
Beta strandi479 – 4813Combined sources
Turni484 – 4874Combined sources
Helixi489 – 50012Combined sources
Beta strandi502 – 5043Combined sources
Helixi514 – 52411Combined sources
Turni525 – 5273Combined sources
Beta strandi531 – 5344Combined sources
Helixi542 – 55110Combined sources
Beta strandi558 – 5614Combined sources
Beta strandi577 – 5793Combined sources
Helixi587 – 5959Combined sources
Beta strandi600 – 6023Combined sources
Beta strandi607 – 6137Combined sources
Helixi617 – 62711Combined sources
Beta strandi632 – 6343Combined sources
Helixi639 – 65517Combined sources
Helixi663 – 68220Combined sources
Helixi689 – 6924Combined sources
Helixi697 – 70610Combined sources
Turni707 – 7104Combined sources
Helixi713 – 72513Combined sources
Beta strandi734 – 7407Combined sources
Beta strandi747 – 7493Combined sources
Helixi763 – 7675Combined sources
Beta strandi775 – 7773Combined sources
Helixi780 – 7856Combined sources
Helixi787 – 7904Combined sources
Beta strandi796 – 7983Combined sources
Beta strandi820 – 8234Combined sources
Helixi828 – 8303Combined sources
Turni832 – 8354Combined sources
Beta strandi844 – 8496Combined sources
Helixi857 – 8604Combined sources
Beta strandi870 – 8734Combined sources
Helixi874 – 8763Combined sources
Turni877 – 8804Combined sources
Helixi881 – 89313Combined sources
Helixi896 – 92530Combined sources
Helixi934 – 95017Combined sources
Beta strandi954 – 9574Combined sources
Beta strandi960 – 9623Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3DMQX-ray3.20A/B1-968[»]
4S20X-ray4.70K/L1-968[»]
ProteinModelPortaliP60240.
SMRiP60240. Positions 2-962.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP60240.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini164 – 334171Helicase ATP-bindingAdd
BLAST
Domaini490 – 662173Helicase C-terminalAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi280 – 2834DEAH box

Sequence similaritiesi

Contains 1 helicase ATP-binding domain.Curated
Contains 1 helicase C-terminal domain.Curated

Phylogenomic databases

eggNOGiENOG4105BZK. Bacteria.
COG0553. LUCA.
HOGENOMiHOG000218482.
InParanoidiP60240.
KOiK03580.
OMAiHHLVLFD.
OrthoDBiEOG6D2KQT.
PhylomeDBiP60240.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
HAMAPiMF_01821. Helicase_RapA.
InterProiIPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR023949. Helicase_RapA.
IPR027417. P-loop_NTPase.
IPR022737. RapA_C.
IPR000330. SNF2_N.
[Graphical view]
PfamiPF00271. Helicase_C. 1 hit.
PF12137. RapA_C. 1 hit.
PF00176. SNF2_N. 1 hit.
[Graphical view]
SMARTiSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 3 hits.
PROSITEiPS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P60240-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MPFTLGQRWI SDTESELGLG TVVAVDARTV TLLFPSTGEN RLYARSDSPV
60 70 80 90 100
TRVMFNPGDT ITSHDGWQMQ VEEVKEENGL LTYIGTRLDT EESGVALREV
110 120 130 140 150
FLDSKLVFSK PQDRLFAGQI DRMDRFALRY RARKYSSEQF RMPYSGLRGQ
160 170 180 190 200
RTSLIPHQLN IAHDVGRRHA PRVLLADEVG LGKTIEAGMI LHQQLLSGAA
210 220 230 240 250
ERVLIIVPET LQHQWLVEML RRFNLRFALF DDERYAEAQH DAYNPFDTEQ
260 270 280 290 300
LVICSLDFAR RSKQRLEHLC EAEWDLLVVD EAHHLVWSED APSREYQAIE
310 320 330 340 350
QLAEHVPGVL LLTATPEQLG MESHFARLRL LDPNRFHDFA QFVEEQKNYR
360 370 380 390 400
PVADAVAMLL AGNKLSNDEL NMLGEMIGEQ DIEPLLQAAN SDSEDAQSAR
410 420 430 440 450
QELVSMLMDR HGTSRVLFRN TRNGVKGFPK RELHTIKLPL PTQYQTAIKV
460 470 480 490 500
SGIMGARKSA EDRARDMLYP ERIYQEFEGD NATWWNFDPR VEWLMGYLTS
510 520 530 540 550
HRSQKVLVIC AKAATALQLE QVLREREGIR AAVFHEGMSI IERDRAAAWF
560 570 580 590 600
AEEDTGAQVL LCSEIGSEGR NFQFASHMVM FDLPFNPDLL EQRIGRLDRI
610 620 630 640 650
GQAHDIQIHV PYLEKTAQSV LVRWYHEGLD AFEHTCPTGR TIYDSVYNDL
660 670 680 690 700
INYLASPDQT EGFDDLIKNC REQHEALKAQ LEQGRDRLLE IHSNGGEKAQ
710 720 730 740 750
ALAESIEEQD DDTNLIAFAM NLFDIIGINQ DDRGDNMIVL TPSDHMLVPD
760 770 780 790 800
FPGLSEDGIT ITFDREVALA REDAQFITWE HPLIRNGLDL ILSGDTGSST
810 820 830 840 850
ISLLKNKALP VGTLLVELIY VVEAQAPKQL QLNRFLPPTP VRMLLDKNGN
860 870 880 890 900
NLAAQVEFET FNRQLNAVNR HTGSKLVNAV QQDVHAILQL GEAQIEKSAR
910 920 930 940 950
ALIDAARNEA DEKLSAELSR LEALRAVNPN IRDDELTAIE SNRQQVMESL
960
DQAGWRLDAL RLIVVTHQ
Length:968
Mass (Da):109,769
Last modified:January 23, 2007 - v2
Checksum:i2943B818AB67A67E
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti11 – 111S → V AA sequence (PubMed:9507009).Curated
Sequence conflicti510 – 53829CAKAA…FHEGM → RGIRNHGHSCFLCEIVIRSQ FHTTYEPEA (PubMed:1577702).CuratedAdd
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X54847 Genomic DNA. Translation: CAA38617.1.
U00096 Genomic DNA. Translation: AAC73170.1.
AP009048 Genomic DNA. Translation: BAB96627.1.
PIRiC64727.
RefSeqiNP_414601.1. NC_000913.3.
WP_001117011.1. NZ_CP011342.2.

Genome annotation databases

EnsemblBacteriaiAAC73170; AAC73170; b0059.
BAB96627; BAB96627; BAB96627.
GeneIDi948523.
KEGGiecj:JW0058.
eco:b0059.
PATRICi32115217. VBIEscCol129921_0060.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X54847 Genomic DNA. Translation: CAA38617.1.
U00096 Genomic DNA. Translation: AAC73170.1.
AP009048 Genomic DNA. Translation: BAB96627.1.
PIRiC64727.
RefSeqiNP_414601.1. NC_000913.3.
WP_001117011.1. NZ_CP011342.2.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3DMQX-ray3.20A/B1-968[»]
4S20X-ray4.70K/L1-968[»]
ProteinModelPortaliP60240.
SMRiP60240. Positions 2-962.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4262039. 359 interactions.
DIPiDIP-35881N.
IntActiP60240. 20 interactions.
STRINGi511145.b0059.

Proteomic databases

PaxDbiP60240.
PRIDEiP60240.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73170; AAC73170; b0059.
BAB96627; BAB96627; BAB96627.
GeneIDi948523.
KEGGiecj:JW0058.
eco:b0059.
PATRICi32115217. VBIEscCol129921_0060.

Organism-specific databases

EchoBASEiEB1075.
EcoGeneiEG11083. rapA.

Phylogenomic databases

eggNOGiENOG4105BZK. Bacteria.
COG0553. LUCA.
HOGENOMiHOG000218482.
InParanoidiP60240.
KOiK03580.
OMAiHHLVLFD.
OrthoDBiEOG6D2KQT.
PhylomeDBiP60240.

Enzyme and pathway databases

BioCyciEcoCyc:EG11083-MONOMER.
ECOL316407:JW0058-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP60240.
PROiP60240.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
HAMAPiMF_01821. Helicase_RapA.
InterProiIPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR023949. Helicase_RapA.
IPR027417. P-loop_NTPase.
IPR022737. RapA_C.
IPR000330. SNF2_N.
[Graphical view]
PfamiPF00271. Helicase_C. 1 hit.
PF12137. RapA_C. 1 hit.
PF00176. SNF2_N. 1 hit.
[Graphical view]
SMARTiSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 3 hits.
PROSITEiPS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Systematic sequencing of the Escherichia coli genome: analysis of the 0-2.4 min region."
    Yura T., Mori H., Nagai H., Nagata T., Ishihama A., Fujita N., Isono K., Mizobuchi K., Nakata A.
    Nucleic Acids Res. 20:3305-3308(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  3. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  4. "Isolation of DNA damage-inducible promoters in Escherichia coli: regulation of polB (dinA), dinG, and dinH by LexA repressor."
    Lewis L.K., Jenkins M.E., Mount D.W.
    J. Bacteriol. 174:3377-3385(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-538.
    Strain: K12.
  5. "Escherichia coli DNA polymerase II is homologous to alpha-like DNA polymerases."
    Iwasaki H., Ishino Y., Toh H., Nakata A., Shinagawa H.
    Mol. Gen. Genet. 226:24-33(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-422.
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  6. "An expanding family of helicases within the 'DEAD/H' superfamily."
    Bork P., Koonin E.V.
    Nucleic Acids Res. 21:751-752(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION OF FRAMESHIFT.
  7. "RapA, a novel RNA polymerase-associated protein, is a bacterial homolog of SWI2/SNF2."
    Sukhodolets M.V., Jin D.J.
    J. Biol. Chem. 273:7018-7023(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 2-11, INTERACTION WITH RNAP.
    Strain: K12.
  8. "Disruption of Escherichia coli hepA, an RNA polymerase-associated protein, causes UV sensitivity."
    Muzzin O., Campbell E.A., Xia L., Severinova E., Darst S.A., Severinov K.
    J. Biol. Chem. 273:15157-15161(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 2-19, INTERACTION WITH RNAP.
  9. "Interaction between RNA polymerase and RapA, a bacterial homolog of the SWI/SNF protein family."
    Sukhodolets M.V., Jin D.J.
    J. Biol. Chem. 275:22090-22097(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH RNAP.
  10. "Growth phase and growth rate regulation of the rapA gene, encoding the RNA polymerase-associated protein RapA in Escherichia coli."
    Cabrera J.E., Jin D.J.
    J. Bacteriol. 183:6126-6134(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: DEVELOPMENTAL STAGE.
  11. "RapA, a bacterial homolog of SWI2/SNF2, stimulates RNA polymerase recycling in transcription."
    Sukhodolets M.V., Cabrera J.E., Zhi H., Jin D.J.
    Genes Dev. 15:3330-3341(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DNA-BINDING, MUTAGENESIS OF LYS-183 AND 280-ASP-GLU-281.

Entry informationi

Entry nameiRAPA_ECOLI
AccessioniPrimary (citable) accession number: P60240
Secondary accession number(s): P23852, P75633
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 16, 2004
Last sequence update: January 23, 2007
Last modified: May 11, 2016
This is version 114 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.