P04390 (T2E5_ECOLX) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Type-2 restriction enzyme EcoRV
Short name=R.EcoRV
EC=3.1.21.4

Alternative name(s):
Endonuclease EcoRV
Type II restriction enzyme EcoRV

Gene names

Name:

ecoRVR

Organism

Escherichia coli

Taxonomic identifier

562 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	245 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	Recognizes the double-stranded sequence GATATC and cleaves after T-3.
Catalytic activity	Endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates.
Cofactor	Binds 2 magnesium ions per subunit.
Subunit structure	Homodimer.

Ontologies

Keywords
Biological process	Restriction system
Ligand	Magnesium Metal-binding
Molecular function	Endonuclease Hydrolase Nuclease
Technical term	3D-structure
Gene Ontology (GO)
Biological_process	DNA restriction-modification system Inferred from electronic annotation. Source: UniProtKB-KW nucleic acid phosphodiester bond hydrolysis Inferred from electronic annotation. Source: GOC
Molecular_function	DNA binding Inferred from electronic annotation. Source: InterPro Type II site-specific deoxyribonuclease activity Inferred from electronic annotation. Source: EC metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed

Chain

2 – 245

244

Type-2 restriction enzyme EcoRV

PRO_0000077305

Sites

Active site

74

1

Active site

90

1

Active site

92

1

Metal binding

45

1

Magnesium 2

Metal binding

74

1

Magnesium 1

Metal binding

74

1

Magnesium 2

Metal binding

90

1

Magnesium 1

Experimental info

Mutagenesis

70

1

N → Q: Decrease in activity.

Mutagenesis

73

1

P → A or G: Loss of activity.

Mutagenesis

74

1

D → A: Loss of activity.

Mutagenesis

74

1

D → E: Decrease in activity.

Mutagenesis

90

1

D → A, N, E or T: Loss of activity.

Mutagenesis

183

1

S → A or T: Decrease in activity.

Mutagenesis

183

1

S → I: Loss of activity.

Mutagenesis

185

1

N → D, A or Q: Loss of activity.

Mutagenesis

186

1

T → S or N: Loss of activity.

Mutagenesis

187

1

T → S or N: No loss of activity.

Mutagenesis

188

1

N → A, Q or T: Decrease in activity.

Mutagenesis

188

1

N → D: Loss of activity.

Mutagenesis

190

1

G → A: No loss of activity.

Secondary structure

1

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245

Helix Strand Turn

Details...

Helix

3 – 17

15

Beta strand

20 – 25

6

Beta strand

30 – 32

3

Helix

37 – 58

22

Beta strand

62 – 64

3

Beta strand

67 – 70

4

Beta strand

74 – 78

5

Beta strand

86 – 98

13

Beta strand

106 – 112

7

Turn

113 – 115

3

Beta strand

116 – 118

3

Beta strand

119 – 123

5

Helix

125 – 127

3

Beta strand

128 – 140

13

Turn

145 – 148

4

Helix

153 – 158

6

Beta strand

162 – 172

11

Helix

173 – 176

4

Beta strand

177 – 183

7

Turn

184 – 187

4

Beta strand

188 – 191

4

Helix

196 – 201

6

Helix

209 – 217

9

Helix

223 – 226

4

Beta strand

227 – 229

3

Helix

233 – 241

9

Sequences

	Sequence		Length	Mass (Da)
	P04390 [UniParc]. Last modified January 23, 2007. Version 3. Checksum: 7DB7EC640A746281	FASTA	245	28,650
	10 20 30 40 50 60 MSLRSDLINA LYDENQKYDV CGIISAEGKI YPLGSDTKVL STIFELFSRP IINKIAEKHG 70 80 90 100 110 120 YIVEEPKQQN HYPDFTLYKP SEPNKKIAID IKTTYTNKEN EKIKFTLGGY TSFIRNNTKN 130 140 150 160 170 180 IVYPFDQYIA HWIIGYVYTR VATRKSSLKT YNINELNEIP KPYKGVKVFL QDKWVIAGDL 190 200 210 220 230 240 AGSGNTTNIG SIHAHYKDFV EGKGIFDSED EFLDYWRNYE RTSQLRNDKY NNISEYRNWI YRGRK

References

[1]	"Characterization of the genes coding for the Eco RV restriction and modification system of Escherichia coli." Bougueleret L., Schwarzstein M., Tsugita A., Zabeau M. Nucleic Acids Res. 12:3659-3676(1984) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"The EcoRV restriction-modification system: genes, enzymes, synthetic substrates." Kraev A.S., Kravets A.N., Chernov B.K., Skryabin K.G., Baev A.A. Mol. Biol. (Mosk.) 19:236-242(1985) Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]	"Site-directed mutagenesis studies with EcoRV restriction endonuclease to identify regions involved in recognition and catalysis." Thielking V., Selent U., Koehler E., Wolfes H., Pieper U., Geiger R., Urbanke C., Winkler F.K., Pingoud A. Biochemistry 30:6416-6422(1991) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS.
[4]	"The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments." Winkler F.K., Banner D.W., Oefner C., Tsernoglou D., Brown R., Heathman S.P., Bryan R.K., Martin P.D., Petratos K., Wilson K.S. EMBO J. 12:1781-1795(1993) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS).
[5]	"Mg2+ binding to the active site of EcoRV endonuclease: a crystallographic study of complexes with substrate and product DNA at 2 A resolution." Kostrewa D., Winkler F.K. Biochemistry 34:683-696(1995) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
[6]	"Conformational transitions and structural deformability of EcoRV endonuclease revealed by crystallographic analysis." Perona J.J., Martin A.M. J. Mol. Biol. 273:207-225(1997) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
[7]	"Recognition of flanking DNA sequences by EcoRV endonuclease involves alternative patterns of water-mediated contacts." Horton N.C., Perona J.J. J. Biol. Chem. 273:21721-21729(1998) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
[8]	"Role of protein-induced bending in the specificity of DNA recognition: crystal structure of EcoRV endonuclease complexed with d(AAAGAT) + d(ATCTT)." Horton N.C., Perona J.J. J. Mol. Biol. 277:779-787(1998) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS).
[9]	"Structural analysis of a mutational hot-spot in the EcoRV restriction endonuclease: a catalytic role for a main chain carbonyl group." Thomas M.P., Brady R.L., Halford S.E., Sessions R.B., Baldwin G.S. Nucleic Acids Res. 27:3438-3445(1999) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF GLN-69 MUTANTS.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X00530 Genomic DNA. Translation: CAA25208.1.
M19941 Genomic DNA. Translation: AAA24615.1.

PIR

NDECR5. A00784.

RefSeq

NP_863580.1. NC_005019.1.
YP_007316617.1. NC_019982.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1AZ0	X-ray	2.00	A/B	2-245	[»]
1AZ3	X-ray	2.40	A/B	2-245	[»]
1AZ4	X-ray	2.40	A/B	2-245	[»]
1B94	X-ray	1.90	A/B	2-245	[»]
1B95	X-ray	2.05	A/B	2-245	[»]
1B96	X-ray	2.30	A/B	2-245	[»]
1B97	X-ray	1.90	A/B	2-245	[»]
1BGB	X-ray	2.00	A/B	2-245	[»]
1BSS	X-ray	2.15	A/B	2-244	[»]
1BSU	X-ray	2.00	A/B	2-244	[»]
1BUA	X-ray	2.15	A/B	2-244	[»]
1EO3	X-ray	2.00	A/B	1-245	[»]
1EO4	X-ray	1.90	A/B	1-245	[»]
1EON	X-ray	1.60	A/B	1-245	[»]
1EOO	X-ray	2.16	A/B	2-244	[»]
1EOP	X-ray	2.60	A/B	2-244	[»]
1RV5	X-ray	2.10	A/B	2-245	[»]
1RVA	X-ray	2.00	A/B	2-245	[»]
1RVB	X-ray	2.10	A/B	2-245	[»]
1RVC	X-ray	2.10	A/B	2-245	[»]
1RVE	X-ray	2.50	A/B	1-245	[»]
1STX	X-ray	2.10	A/B	2-244	[»]
1SUZ	X-ray	1.80	A/B	2-244	[»]
1SX5	X-ray	1.50	A/B	2-244	[»]
1SX8	X-ray	2.15	A/B	2-244	[»]
2B0D	X-ray	2.00	A/B	1-245	[»]
2B0E	X-ray	1.90	A/B	1-245	[»]
2GE5	X-ray	2.40	A/B	2-219	[»]
2RVE	X-ray	3.00	A/B	2-245	[»]
4RVE	X-ray	3.00	A/B/C	2-245	[»]

ProteinModelPortal

P04390.

SMR

P04390. Positions 2-245.

ModBase

Search...

Protein family/group databases

REBASE

995. EcoRV.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

GeneID

14401263.
1446621.

Phylogenomic databases

ProtClustDB

CLSK918372.

Family and domain databases

Gene3D

3.40.600.10. 1 hit.

InterPro

IPR011337. DNA_rep_MutH/RE_typeII.
IPR011335. Restrct_endonuc-II-like.
IPR015314. Restrct_endonuc_II_EcoRV.
IPR019755. Restrct_endonuc_II_EcoRV_Pbac.
[Graphical view]

Pfam

PF09233. Endonuc-EcoRV. 1 hit.
[Graphical view]

PIRSF

PIRSF000995. RE_EcoRV. 1 hit.

SUPFAM

SSF52980. Restrict_endonuc_II-like_core. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

P04390.

Entry information

Entry name

T2E5_ECOLX

Accession

Primary (citable) accession number: P04390

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 20, 1987
Last sequence update:	January 23, 2007
Last modified:	April 3, 2013
This is version 110 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program