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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)DescriptionActionsGraphical viewLength
Nucleotide bindingi177 – 184ATPBy similarity8

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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11083. rapA.

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi183K → A: Loss of function. Still interacts with RNAP. 1 Publication1
Mutagenesisi280 – 281DE → AA: Loss of function. Still interacts with RNAP. 1 Publication2

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved2 Publications
ChainiPRO_00002071722 – 968RNA polymerase-associated protein RapAAdd BLAST967

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 interactors.
DIPiDIP-35881N.
IntActiP60240. 20 interactors.
STRINGi511145.b0059.

Structurei

Secondary structure

1968
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi8 – 13Combined sources6
Helixi15 – 17Combined sources3
Beta strandi19 – 25Combined sources7
Beta strandi27 – 33Combined sources7
Turni35 – 37Combined sources3
Beta strandi40 – 44Combined sources5
Turni45 – 47Combined sources3
Beta strandi50 – 52Combined sources3
Beta strandi60 – 63Combined sources4
Beta strandi68 – 75Combined sources8
Beta strandi77 – 79Combined sources3
Beta strandi82 – 87Combined sources6
Turni88 – 90Combined sources3
Beta strandi94 – 98Combined sources5
Helixi99 – 101Combined sources3
Helixi111 – 114Combined sources4
Helixi123 – 126Combined sources4
Helixi129 – 140Combined sources12
Beta strandi146 – 148Combined sources3
Helixi156 – 167Combined sources12
Beta strandi168 – 170Combined sources3
Beta strandi172 – 175Combined sources4
Helixi183 – 196Combined sources14
Beta strandi203 – 206Combined sources4
Turni209 – 211Combined sources3
Helixi212 – 222Combined sources11
Helixi232 – 240Combined sources9
Beta strandi244 – 246Combined sources3
Beta strandi250 – 254Combined sources5
Helixi256 – 260Combined sources5
Turni263 – 266Combined sources4
Helixi267 – 270Combined sources4
Beta strandi276 – 279Combined sources4
Helixi294 – 303Combined sources10
Beta strandi307 – 312Combined sources6
Beta strandi317 – 319Combined sources3
Helixi325 – 331Combined sources7
Turni333 – 335Combined sources3
Helixi340 – 357Combined sources18
Turni358 – 360Combined sources3
Helixi367 – 369Combined sources3
Turni374 – 377Combined sources4
Helixi386 – 388Combined sources3
Turni397 – 399Combined sources3
Helixi400 – 407Combined sources8
Helixi408 – 410Combined sources3
Turni412 – 416Combined sources5
Turni422 – 424Combined sources3
Beta strandi435 – 438Combined sources4
Helixi442 – 453Combined sources12
Helixi460 – 463Combined sources4
Helixi465 – 468Combined sources4
Helixi471 – 473Combined sources3
Turni474 – 478Combined sources5
Beta strandi479 – 481Combined sources3
Turni484 – 487Combined sources4
Helixi489 – 500Combined sources12
Beta strandi502 – 504Combined sources3
Helixi514 – 524Combined sources11
Turni525 – 527Combined sources3
Beta strandi531 – 534Combined sources4
Helixi542 – 551Combined sources10
Beta strandi558 – 561Combined sources4
Beta strandi577 – 579Combined sources3
Helixi587 – 595Combined sources9
Beta strandi600 – 602Combined sources3
Beta strandi607 – 613Combined sources7
Helixi617 – 627Combined sources11
Beta strandi632 – 634Combined sources3
Helixi639 – 655Combined sources17
Helixi663 – 682Combined sources20
Helixi689 – 692Combined sources4
Helixi697 – 706Combined sources10
Turni707 – 710Combined sources4
Helixi713 – 725Combined sources13
Beta strandi734 – 740Combined sources7
Beta strandi747 – 749Combined sources3
Helixi763 – 767Combined sources5
Beta strandi775 – 777Combined sources3
Helixi780 – 785Combined sources6
Helixi787 – 790Combined sources4
Beta strandi796 – 798Combined sources3
Beta strandi820 – 823Combined sources4
Helixi828 – 830Combined sources3
Turni832 – 835Combined sources4
Beta strandi844 – 849Combined sources6
Helixi857 – 860Combined sources4
Beta strandi870 – 873Combined sources4
Helixi874 – 876Combined sources3
Turni877 – 880Combined sources4
Helixi881 – 893Combined sources13
Helixi896 – 925Combined sources30
Helixi934 – 950Combined sources17
Beta strandi954 – 957Combined sources4
Beta strandi960 – 962Combined sources3

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiP60240.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini164 – 334Helicase ATP-bindingAdd BLAST171
Domaini490 – 662Helicase C-terminalAdd BLAST173

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi280 – 283DEAH box4

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.
PhylomeDBiP60240.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
HAMAPiMF_01821. Helicase_RapA. 1 hit.
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)DescriptionActionsGraphical viewLength
Sequence conflicti11S → V AA sequence (PubMed:9507009).Curated1
Sequence conflicti510 – 538CAKAA…FHEGM → RGIRNHGHSCFLCEIVIRSQ FHTTYEPEA (PubMed:1577702).CuratedAdd BLAST29

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_CP011343.2.

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_CP011343.2.

3D structure databases

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

Protein-protein interaction databases

BioGridi4262039. 359 interactors.
DIPiDIP-35881N.
IntActiP60240. 20 interactors.
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.
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. 1 hit.
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...

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: November 2, 2016
This is version 117 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.