P0A809 (RUVA_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Holliday junction ATP-dependent DNA helicase RuvA
EC=3.6.4.12

Gene names

Name:	ruvA
Ordered Locus Names:	b1861, JW1850

Organism

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

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	203 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	The RuvA-RuvB complex in the presence of ATP renatures cruciform structure in supercoiled DNA with palindromic sequence, indicating that it may promote strand exchange reactions in homologous recombination. RuvAB is a helicase that mediates the Holliday junction migration by localized denaturation and reannealing. RuvA stimulates, in the presence of DNA, the weak ATPase activity of RuvB. Binds both single- and double-stranded DNA (dsDNA). Binds preferentially to supercoiled rather than to relaxed dsDNA. Ref.7
Catalytic activity	ATP + H2O = ADP + phosphate. Ref.7
Subunit structure	Homotetramer; forms a complex with RuvB. Ref.9 Ref.11
Subcellular location	Cytoplasm. Note: In 15% of cell localizes to discrete nucleoid foci (probable DNA damage sites) upon treatment with mitomycin C (MMC) for 2 hours. Ref.8
Induction	Expression of the ruv region is induced by damage to DNA and is regulated by LexA as part of the SOS response. RuvA and RuvB are also involved in mutagenesis induced by UV and X irradiation and by some chemicals. Ref.1
Sequence similarities	Belongs to the RuvA family.

Ontologies

Keywords
Biological process	DNA damage DNA recombination DNA repair SOS response
Cellular component	Cytoplasm
Ligand	ATP-binding DNA-binding Nucleotide-binding
Molecular function	Helicase Hydrolase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	SOS response Inferred from expression pattern Ref.2. Source: EcoCyc recombinational repair Inferred from mutant phenotype PubMed 6374379. Source: EcoCyc
Cellular_component	Holliday junction helicase complex Inferred from direct assay PubMed 1617728. Source: EcoCyc cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW DNA binding Inferred from electronic annotation. Source: UniProtKB-KW four-way junction helicase activity Inferred from direct assay PubMed 1617728. Source: EcoCyc
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 203

203

Holliday junction ATP-dependent DNA helicase RuvA HAMAP-Rule MF_00031

PRO_0000094629

Experimental info

Sequence conflict

166

1

A → R in CAA30119. Ref.1

Secondary structure

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203

Helix Strand Turn

Details...

Beta strand

4 – 13

10

Beta strand

16 – 21

6

Beta strand

24 – 29

6

Helix

32 – 35

4

Beta strand

43 – 54

12

Beta strand

57 – 65

9

Helix

66 – 77

12

Beta strand

78 – 80

3

Helix

83 – 92

10

Helix

95 – 103

9

Helix

107 – 111

5

Helix

118 – 131

14

Helix

132 – 134

3

Turn

138 – 140

3

Helix

144 – 149

6

Helix

158 – 170

13

Helix

174 – 183

10

Helix

191 – 200

10

Sequences

	Sequence		Length	Mass (Da)
	P0A809 [UniParc]. Last modified June 7, 2005. Version 1. Checksum: 805DDB79DC5A8385	FASTA	203	22,086
	10 20 30 40 50 60 MIGRLRGIII EKQPPLVLIE VGGVGYEVHM PMTCFYELPE AGQEAIVFTH FVVREDAQLL 70 80 90 100 110 120 YGFNNKQERT LFKELIKTNG VGPKLALAIL SGMSAQQFVN AVEREEVGAL VKLPGIGKKT 130 140 150 160 170 180 AERLIVEMKD RFKGLHGDLF TPAADLVLTS PASPATDDAE QEAVAALVAL GYKPQEASRM 190 200 VSKIARPDAS SETLIREALR AAL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Nucleotide sequencing of the ruv region of Escherichia coli K-12 reveals a LexA regulated operon encoding two genes." Benson F.E., Illing G.T., Sharples G.J., Lloyd R.G. Nucleic Acids Res. 16:1541-1549(1988) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], INDUCTION. Strain: K12.
[2]	"Structure and regulation of the Escherichia coli ruv operon involved in DNA repair and recombination." Shinagawa H., Makino K., Amemura M., Kimura S., Iwasaki H., Nakata A. J. Bacteriol. 170:4322-4329(1988) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]	"A 460-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 40.1-50.0 min region on the linkage map." Itoh T., Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K., Kasai H., Kimura S., Kitakawa M., Kitagawa M., Makino K., Miki T., Mizobuchi K., Mori H., Mori T., Motomura K., Nakade S. , Nakamura Y., Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G., Seki Y., Sivasundaram S., Tagami H., Takeda J., Takemoto K., Wada C., Yamamoto Y., Horiuchi T. DNA Res. 3:379-392(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[4]	"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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[5]	"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.
[6]	"Molecular analysis of the Escherichia coli ruvC gene, which encodes a Holliday junction-specific endonuclease." Takahagi M., Iwasaki H., Nakata A., Shinagawa H. J. Bacteriol. 173:5747-5753(1991) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-29.
[7]	"RuvA and RuvB proteins of Escherichia coli exhibit DNA helicase activity in vitro." Tsaneva I.R., Mueller B., West S.C. Proc. Natl. Acad. Sci. U.S.A. 90:1315-1319(1993) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, CATALYTIC ACTIVITY.
[8]	"A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair." Babu M., Beloglazova N., Flick R., Graham C., Skarina T., Nocek B., Gagarinova A., Pogoutse O., Brown G., Binkowski A., Phanse S., Joachimiak A., Koonin E.V., Savchenko A., Emili A., Greenblatt J., Edwards A.M., Yakunin A.F. Mol. Microbiol. 79:484-502(2011) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION. Strain: K12.
[9]	"Crystal structure of DNA recombination protein RuvA and a model for its binding to the Holliday junction." Rafferty J.B., Sedelnikova S.E., Hargreaves D., Artymiuk P.J., Baker P.J., Sharples G.J., Mahdi A.A., Lloyd R.G., Rice D.W. Science 274:415-421(1996) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS), SUBUNIT.
[10]	"Crystal structure of E.coli RuvA with bound DNA Holliday junction at 6-A resolution." Hargreaves D., Rice D.W., Sedelnikova S.E., Artymiuk P.J., Lloyd R.G., Rafferty J.B. Nat. Struct. Biol. 5:441-446(1998) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (6.0 ANGSTROMS).
[11]	"Functional analyses of the domain structure in the Holliday junction binding protein RuvA." Nishino T., Ariyoshi M., Iwasaki H., Shinagawa H., Morikawa K. Structure 6:11-21(1998) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS), SUBUNIT.
[12]	"Modulation of RuvB function by the mobile domain III of the Holliday junction recognition protein RuvA." Nishino T., Iwasaki H., Kataoka M., Ariyoshi M., Fujita T., Shinagawa H., Morikawa K. J. Mol. Biol. 298:407-416(2000) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 1-149.
[13]	"Processing of recombination intermediates by the RuvABC proteins." West S.C. Annu. Rev. Genet. 31:213-244(1997) [PubMed] [Europe PMC] [Abstract] Cited for: REVIEW.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X07091 Genomic DNA. Translation: CAA30119.1.
M21298 Genomic DNA. Translation: AAA24612.1.
U00096 Genomic DNA. Translation: AAC74931.1.
AP009048 Genomic DNA. Translation: BAA15672.1.
D10165 Genomic DNA. Translation: BAA01034.1.

PIR

BVECRV. E64948.

RefSeq

NP_416375.1. NC_000913.2.
YP_490123.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1BDX	X-ray	6.00	A/B/C/D	1-203	[»]
1C7Y	X-ray	3.10	A	1-203	[»]
1CUK	X-ray	1.90	A	1-203	[»]
1D8L	X-ray	2.50	A/B	1-149	[»]
1HJP	X-ray	2.50	A	1-203	[»]

ProteinModelPortal

P0A809.

SMR

P0A809. Positions 1-203.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-48064N.

IntAct

P0A809. 7 interactions.

MINT

MINT-1321234.

STRING

511145.b1861.

Proteomic databases

PaxDb

P0A809.

PRIDE

P0A809.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC74931; AAC74931; b1861.
BAA15672; BAA15672; BAA15672.

GeneID

12930344.
946369.

KEGG

ecj:Y75_p1837.
eco:b1861.

PATRIC

32119045. VBIEscCol129921_1940.

Organism-specific databases

EchoBASE

EB0916.

EcoGene

EG10923. ruvA.

Phylogenomic databases

eggNOG

COG0632.

HOGENOM

HOG000057116.

KO

K03550.

OMA

ALEREWF.

ProtClustDB

PRK00116.

Enzyme and pathway databases

BioCyc

EcoCyc:EG10923-MONOMER.
ECOL316407:JW1850-MONOMER.
MetaCyc:EG10923-MONOMER.

Gene expression databases

Genevestigator

P0A809.

Family and domain databases

Gene3D

2.40.50.140. 1 hit.

HAMAP

MF_00031. DNA_helic_RuvA.

InterPro

IPR011114. DNA_helicas_Holl-junc_RuvA_C.
IPR013849. DNA_helicase_Holl-junc_RuvA_I.
IPR003583. Hlx-hairpin-Hlx_DNA-bd_motif.
IPR012340. NA-bd_OB-fold.
IPR000085. RuvA.
IPR010994. RuvA_2-like.
[Graphical view]

Pfam

PF07499. RuvA_C. 1 hit.
PF01330. RuvA_N. 1 hit.
[Graphical view]

SMART

SM00278. HhH1. 2 hits.
[Graphical view]

SUPFAM

SSF50249. Nucleic_acid_OB. 1 hit.
SSF47781. RuvA_2_like. 1 hit.
SSF46929. RuvA_C-like. 1 hit.

TIGRFAMs

TIGR00084. ruvA. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

P0A809.

Entry information

Entry name

RUVA_ECOLI

Accession

Primary (citable) accession number: P0A809
Secondary accession number(s): P08576

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 1, 1988
Last sequence update:	June 7, 2005
Last modified:	May 1, 2013
This is version 80 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program