P0AG74 (RUSA_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Crossover junction endodeoxyribonuclease RusA
EC=3.1.22.4

Alternative name(s):
Holliday junction nuclease RusA
Holliday junction resolvase

Gene names

Name:	rusA
Synonyms:	rus, ybcP
Ordered Locus Names:	b0550, JW0538

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	120 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Endonuclease that resolves Holliday junction intermediates made during homologous genetic recombination and DNA repair. Exhibits sequence and structure-selective cleavage of four-way DNA junctions, where it introduces symmetrical nicks in two strands of the same polarity at the 5' side of CC dinucleotides. Corrects the defects in genetic recombination and DNA repair associated with inactivation of ruvAB or ruvC.
Catalytic activity	Endonucleolytic cleavage at a junction such as a reciprocal single-stranded crossover between two homologous DNA duplexes (Holliday junction).
Cofactor	Binds 1 magnesium ion per subunit Probable.
Subunit structure	Homodimer. Ref.6 Ref.10 Ref.11
Miscellaneous	Encoded by the cryptic lambdoid prophage DLP12. Normally not expressed. Complete suppression of ruv mutations by RusA is dependent on the activity of RecG.
Sequence similarities	Belongs to the RusA family.

Ontologies

Keywords
Biological process	DNA damage DNA recombination DNA repair
Ligand	Magnesium Metal-binding
Molecular function	Endonuclease Hydrolase Nuclease
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	DNA recombination Inferred from electronic annotation. Source: UniProtKB-KW DNA repair Inferred from direct assay Ref.5. Source: EcoCyc
Cellular_component	Holliday junction resolvase complex Inferred from direct assay Ref.5. Source: EcoCyc
Molecular_function	crossover junction endodeoxyribonuclease activity Inferred from direct assay Ref.5. Source: EcoCyc magnesium ion binding Inferred from electronic annotation. Source: InterPro recombination hotspot binding Inferred from direct assay Ref.5. Source: EcoCyc
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 120

120

Crossover junction endodeoxyribonuclease RusA

PRO_0000192004

Regions

Region

13 – 16

4

DNA binding

Region

66 – 73

8

DNA binding

Sites

Metal binding

70

1

Magnesium Probable

Metal binding

72

1

Magnesium Probable

Metal binding

91

1

Magnesium Probable

Experimental info

Mutagenesis

16

1

R → Q: No effect on ability to promote DNA repair. Ref.9

Mutagenesis

17

1

Y → L: No effect on ability to promote DNA repair. Ref.9

Mutagenesis

19

1

R → Q: No effect on ability to promote DNA repair. Ref.9

Mutagenesis

58

1

R → Q: No effect on ability to promote DNA repair. Ref.9

Mutagenesis

68

1

R → Q: No effect on ability to promote DNA repair. Ref.9

Mutagenesis

69

1

R → Q or A: Loss of ability to promote DNA repair. Great loss of Holliday junction resolvase activity. No effect on DNA binding. Ref.9

Mutagenesis

70

1

D → N: Reduces junction resolution 80-fold. No effect on DNA binding. Ref.7 Ref.8

Mutagenesis

72

1

D → N: Loss of ability to resolve junctions. No effect on DNA binding. Ref.8

Mutagenesis

73

1

N → A: Slight reduction in ability to promote DNA repair. Great reduction in Holliday junction resolution activity. Ref.9

Mutagenesis

76

1

K → Q: Loss of ability to promote DNA repair. Loss of Holliday junction resolvase activity. No effect on DNA binding. Ref.9

Mutagenesis

76

1

K → R: Loss of ability to promote DNA repair. Less than 2% activity of Holliday junction resolvase. No effect on DNA binding. Ref.9

Mutagenesis

80

1

D → N: Slight reduction in ability to resolve junctions. No effect on DNA binding. Ref.8

Mutagenesis

87

1

F → Y or V: No effect on ability to promote DNA repair. Ref.9

Mutagenesis

90

1

D → N: Slight reduction in ability to resolve junctions. No effect on DNA binding. Ref.8

Mutagenesis

91

1

D → N: Loss of ability to resolve junctions. No effect on DNA binding. Ref.8

Mutagenesis

101

1

K → Q: No effect on ability to promote DNA repair. Ref.9

Mutagenesis

111

1

E → Q: No effect on resolvase activity or DNA binding. Ref.8

Mutagenesis

116

1

E → Q: No effect on resolvase activity or DNA binding. Ref.8

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

120

Helix Strand Turn

Details...

Beta strand

3 – 9

7

Helix

14 – 17

4

Beta strand

18 – 23

6

Beta strand

25 – 27

3

Helix

29 – 44

16

Beta strand

55 – 62

8

Beta strand

64 – 67

4

Helix

72 – 84

13

Beta strand

87 – 89

3

Helix

91 – 93

3

Beta strand

94 – 102

9

Beta strand

109 – 116

8

Sequences

	Sequence		Length	Mass (Da)
	P0AG74 [UniParc]. Last modified December 20, 2005. Version 1. Checksum: 38401669E8819EA6	FASTA	120	13,846
	10 20 30 40 50 60 MNTYSITLPW PPSNNRYYRH NRGRTHVSAE GQAYRDNVAR IIKNAMLDIG LAMPVKIRIE 70 80 90 100 110 120 CHMPDRRRRD LDNLQKAAFD ALTKAGFWLD DAQVVDYRVV KMPVTKGGRL ELTITEMGNE

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Holliday junction resolvases encoded by homologous rusA genes in Escherichia coli K-12 and phage 82." Mahdi A.A., Sharples G.J., Mandal T.N., Lloyd R.G. J. Mol. Biol. 257:561-573(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[2]	"Sequence of minutes 4-25 of Escherichia coli." Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M., Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D., Namath A., Oefner P., Roberts D., Schramm S., Davis R.W. Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[3]	"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.
[4]	"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.
[5]	"Processing of intermediates in recombination and DNA repair: identification of a new endonuclease that specifically cleaves Holliday junctions." Sharples G.J., Chan S.N., Mahdi A.A., Whitby M.C., Lloyd R.G. EMBO J. 13:6133-6142(1994) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 1-9, CHARACTERIZATION.
[6]	"Sequence specificity and biochemical characterization of the RusA Holliday junction resolvase of Escherichia coli." Chan S.N., Harris L., Bolt E.L., Whitby M.C., Lloyd R.G. J. Biol. Chem. 272:14873-14882(1997) [PubMed] [Europe PMC] [Abstract] Cited for: CHARACTERIZATION, SUBUNIT.
[7]	"Structural recognition and distortion by the DNA junction-resolving enzyme RusA." Giraud-Panis M.-J.E., Lilley D.M.J. J. Mol. Biol. 278:117-133(1998) [PubMed] [Europe PMC] [Abstract] Cited for: CLEAVAGE SPECIFICITY, DNA-BINDING, MUTAGENESIS OF ASP-70.
[8]	"Identification of three aspartic acid residues essential for catalysis by the RusA holliday junction resolvase." Bolt E.L., Sharples G.J., Lloyd R.G. J. Mol. Biol. 286:403-415(1999) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF ASP-70; ASP-72; ASP-80; ASP-90; ASP-91; GLU-111 AND GLU-116.
[9]	"Analysis of conserved basic residues associated with DNA binding (Arg69) and catalysis (Lys76) by the RusA holliday junction resolvase." Bolt E.L., Sharples G.J., Lloyd R.G. J. Mol. Biol. 304:165-176(2000) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF ARG-16; TYR-17; ARG-19; ARG-58; ARG-68; ARG-69; ASN-73; LYS-76; PHE-87 AND LYS-101.
[10]	"The structure of Escherichia coli RusA endonuclease reveals a new Holliday junction DNA binding fold." Rafferty J.B., Bolt E.L., Muranova T.A., Sedelnikova S.E., Leonard P., Pasquo A., Baker P.J., Rice D.W., Sharples G.J., Lloyd R.G. Structure 11:1557-1567(2003) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS), SUBUNIT.
[11]	"RusA Holliday junction resolvase: DNA complex structure -- insights into selectivity and specificity." Macmaster R., Sedelnikova S., Baker P.J., Bolt E.L., Lloyd R.G., Rafferty J.B. Nucleic Acids Res. 34:5577-5584(2006) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.2 ANGSTROMS) OF MUTANT ASN-70 IN COMPLEX WITH DNA, SUBUNIT.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X92587 Genomic DNA. Translation: CAA63321.1.
U82598 Genomic DNA. Translation: AAB40746.1.
U00096 Genomic DNA. Translation: AAC73651.1.
AP009048 Genomic DNA. Translation: BAE76325.1.

PIR

S66590.

RefSeq

NP_415082.1. NC_000913.2.
YP_488837.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1Q8R	X-ray	1.90	A/B	1-120	[»]
2H8C	X-ray	3.10	A/B/C/D	1-120	[»]
2H8E	X-ray	1.20	A	1-120	[»]

ProteinModelPortal

P0AG74.

SMR

P0AG74. Positions 1-118.

ModBase

Search...

Protein-protein interaction databases

IntAct

P0AG74. 1 interaction.

STRING

511145.b0550.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC73651; AAC73651; b0550.
BAE76325; BAE76325; BAE76325.

GeneID

12932535.
945174.

KEGG

ecj:Y75_p0535.
eco:b0550.

PATRIC

32116262. VBIEscCol129921_0571.

Organism-specific databases

EchoBASE

EB4170.

EcoGene

EG20283. rusA.

Phylogenomic databases

eggNOG

COG4570.

HOGENOM

HOG000119986.

KO

K01160.

OMA

GIHYISD.

ProtClustDB

PRK09786.

Enzyme and pathway databases

BioCyc

EcoCyc:G6306-MONOMER.
ECOL316407:JW0538-MONOMER.

Gene expression databases

Genevestigator

P0AG74.

Family and domain databases

Gene3D

3.30.1330.70. 1 hit.

InterPro

IPR016281. Endonuclease_RusA.
IPR008822. Endonuclease_RusA-like.
[Graphical view]

Pfam

PF05866. RusA. 1 hit.
[Graphical view]

PIRSF

PIRSF001007. RusA. 1 hit.

SUPFAM

SSF103084. RusA-like. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

P0AG74.

Entry information

Entry name

RUSA_ECOLI

Accession

Primary (citable) accession number: P0AG74
Secondary accession number(s): P40116, Q2MBN1

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 20, 2005
Last sequence update:	December 20, 2005
Last modified:	May 1, 2013
This is version 68 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program