Reviewed, UniProtKB/Swiss-Prot P60240 (RAPA_ECOLI)

Names and origin

Protein names

Recommended name:
    RNA polymerase-associated protein rapA
    EC=3.6.1.-
Alternative name(s):
    ATP-dependent helicase hepA

Gene names

Name:	rapA
Synonyms:	hepA, yabA
Ordered Locus Names:	b0059, JW0058

Organism

Escherichia coli (strain K12) [Complete proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	968 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	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. Ref.11
Subunit structure	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. Ref.7 Ref.8 Ref.9
Developmental stage	During growth phase, peaking during at the early log phase. Ref.10
Sequence similarities	Belongs to the SNF2/RAD54 helicase family. RapA subfamily. Contains 1 helicase ATP-binding domain. Contains 1 helicase C-terminal domain.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Ligand	ATP-binding DNA-binding Nucleotide-binding
Molecular function	Activator Helicase Hydrolase
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: HAMAP transcription Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	ATP binding Inferred from electronic annotation. Source: HAMAP DNA binding Inferred from electronic annotation. Source: UniProtKB-KW helicase activity Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.7 Ref.8

Chain

2 – 968

967

RNA polymerase-associated protein rapA HAMAP MF_01821

PRO_0000207172

Regions

Domain

164 – 334

171

Helicase ATP-binding

Domain

490 – 662

173

Helicase C-terminal

Nucleotide binding

177 – 184

8

ATP By similarity

Motif

280 – 283

4

DEAH box HAMAP MF_01821

Experimental info

Mutagenesis

183

1

K → A: Loss of function. Still interacts with RNAP. Ref.11

Mutagenesis

280 – 281

2

DE → AA: Loss of function. Still interacts with RNAP.

Sequence conflict

11

1

S → V AA sequence Ref.7

Sequence conflict

510 – 538

29

CAKAA…FHEGM → RGIRNHGHSCFLCEIVIRSQ FHTTYEPEA Ref.4

Secondary structure

1

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968

Helix Strand Turn

Details...

Beta strand

9 – 13

5

Beta strand

22 – 25

4

Beta strand

27 – 33

7

Beta strand

40 – 44

5

Turn

45 – 47

3

Beta strand

50 – 52

3

Beta strand

60 – 63

4

Beta strand

68 – 75

8

Beta strand

82 – 84

3

Turn

88 – 90

3

Helix

99 – 101

3

Helix

111 – 114

4

Helix

123 – 126

4

Helix

129 – 140

12

Helix

156 – 164

9

Beta strand

173 – 175

3

Turn

184 – 186

3

Helix

190 – 196

7

Beta strand

203 – 206

4

Turn

209 – 211

3

Helix

212 – 222

11

Helix

232 – 240

9

Beta strand

244 – 246

3

Beta strand

250 – 254

5

Helix

256 – 260

5

Turn

263 – 266

4

Helix

267 – 270

4

Beta strand

276 – 279

4

Helix

294 – 303

10

Beta strand

310 – 312

3

Helix

325 – 331

7

Turn

333 – 335

3

Helix

340 – 357

18

Turn

358 – 360

3

Helix

367 – 369

3

Helix

386 – 388

3

Turn

397 – 399

3

Helix

400 – 407

8

Helix

408 – 410

3

Turn

414 – 416

3

Beta strand

435 – 438

4

Helix

442 – 450

9

Helix

460 – 463

4

Helix

465 – 468

4

Helix

471 – 473

3

Turn

474 – 477

4

Turn

484 – 487

4

Helix

489 – 494

6

Helix

499 – 501

3

Beta strand

502 – 504

3

Helix

514 – 524

11

Beta strand

531 – 534

4

Helix

542 – 551

10

Beta strand

558 – 561

4

Beta strand

577 – 579

3

Beta strand

581 – 583

3

Helix

587 – 593

7

Beta strand

607 – 613

7

Helix

617 – 626

10

Beta strand

632 – 634

3

Helix

641 – 655

15

Helix

664 – 682

19

Helix

689 – 692

4

Helix

698 – 706

9

Turn

707 – 710

4

Helix

713 – 725

13

Beta strand

747 – 749

3

Helix

763 – 767

5

Beta strand

775 – 777

3

Helix

780 – 785

6

Helix

828 – 830

3

Turn

832 – 835

4

Beta strand

844 – 846

3

Helix

857 – 860

4

Turn

875 – 880

6

Helix

881 – 889

9

Helix

896 – 925

30

Helix

934 – 950

17

Sequences

	Sequence		Length	Mass (Da)
	P60240-1 [UniParc]. Last modified January 23, 2007. Version 2. Checksum: 2943B818AB67A67E	FASTA	968	109,769
	10 20 30 40 50 60 MPFTLGQRWI SDTESELGLG TVVAVDARTV TLLFPSTGEN RLYARSDSPV TRVMFNPGDT 70 80 90 100 110 120 ITSHDGWQMQ VEEVKEENGL LTYIGTRLDT EESGVALREV FLDSKLVFSK PQDRLFAGQI 130 140 150 160 170 180 DRMDRFALRY RARKYSSEQF RMPYSGLRGQ RTSLIPHQLN IAHDVGRRHA PRVLLADEVG 190 200 210 220 230 240 LGKTIEAGMI LHQQLLSGAA ERVLIIVPET LQHQWLVEML RRFNLRFALF DDERYAEAQH 250 260 270 280 290 300 DAYNPFDTEQ LVICSLDFAR RSKQRLEHLC EAEWDLLVVD EAHHLVWSED APSREYQAIE 310 320 330 340 350 360 QLAEHVPGVL LLTATPEQLG MESHFARLRL LDPNRFHDFA QFVEEQKNYR PVADAVAMLL 370 380 390 400 410 420 AGNKLSNDEL NMLGEMIGEQ DIEPLLQAAN SDSEDAQSAR QELVSMLMDR HGTSRVLFRN 430 440 450 460 470 480 TRNGVKGFPK RELHTIKLPL PTQYQTAIKV SGIMGARKSA EDRARDMLYP ERIYQEFEGD 490 500 510 520 530 540 NATWWNFDPR VEWLMGYLTS HRSQKVLVIC AKAATALQLE QVLREREGIR AAVFHEGMSI 550 560 570 580 590 600 IERDRAAAWF AEEDTGAQVL LCSEIGSEGR NFQFASHMVM FDLPFNPDLL EQRIGRLDRI 610 620 630 640 650 660 GQAHDIQIHV PYLEKTAQSV LVRWYHEGLD AFEHTCPTGR TIYDSVYNDL INYLASPDQT 670 680 690 700 710 720 EGFDDLIKNC REQHEALKAQ LEQGRDRLLE IHSNGGEKAQ ALAESIEEQD DDTNLIAFAM 730 740 750 760 770 780 NLFDIIGINQ DDRGDNMIVL TPSDHMLVPD FPGLSEDGIT ITFDREVALA REDAQFITWE 790 800 810 820 830 840 HPLIRNGLDL ILSGDTGSST ISLLKNKALP VGTLLVELIY VVEAQAPKQL QLNRFLPPTP 850 860 870 880 890 900 VRMLLDKNGN NLAAQVEFET FNRQLNAVNR HTGSKLVNAV QQDVHAILQL GEAQIEKSAR 910 920 930 940 950 960 ALIDAARNEA DEKLSAELSR LEALRAVNPN IRDDELTAIE SNRQQVMESL DQAGWRLDAL RLIVVTHQ

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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: 1630901] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12.
[2]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed: 9278503] [Abstract] 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: 16738553] [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: 1577702] [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: 2034216] [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: 8382805] [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: 9507009] [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: 9614128] [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: 10801781] [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: 11567013] [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: 11751638] [Abstract] Cited for: FUNCTION, DNA-BINDING, MUTAGENESIS OF LYS-183 AND 280-ASP-GLU-281.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X54847 Genomic DNA. Translation: CAA38617.1.
U00096 Genomic DNA. Translation: AAC73170.1.
AP009048 Genomic DNA. Translation: BAB96627.1.

PIR

C64727.

RefSeq

AP_000723.1.
NP_414601.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3DMQ	X-ray	3.20	A/B	1-968	[»]

ModBase

Search...

Protein-protein interaction databases

STRING

P60240.

Genome annotation databases

GeneID

948523.

GenomeReviews

Gene locus JW0058 in contig AP009048_GR.
Gene locus b0059 in contig U00096_GR.

KEGG

ecj:JW0058.
eco:b0059.

Organism-specific databases

EchoBASE

EB1075.

EcoGene

EG11083. rapA.

CMR

Search...

Phylogenomic databases

eggNOG

COG0553.

HOGENOM

HBG290025.

OMA

AGLVIHR.

Enzyme and pathway databases

BioCyc

EcoCyc:EG11083-MONOMER.
ECOL168927:B0059-MONOMER.

Gene expression databases

Genevestigator

P60240.

Family and domain databases

HAMAP

MF_01821. Helicase_RapA.
[Tree]

InterPro

IPR014001. DEAD-like_N.
IPR001650. DNA/RNA_helicase_C.
IPR014021. Helicase_SF1/SF2_ATP-bd.
IPR000330. SNF2_N.
[Graphical view]

Pfam

PF00271. Helicase_C. 1 hit.
PF00176. SNF2_N. 1 hit.
[Graphical view]

SMART

SM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]

PROSITE

PS00690. DEAH_ATP_HELICASE. False negative.
PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

RAPA_ECOLI

Accession

Primary (citable) accession number: P60240
Secondary accession number(s): P23852, P75633

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 16, 2004
Last sequence update:	January 23, 2007
Last modified:	January 19, 2010
This is version 63 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)