Reviewed, UniProtKB/Swiss-Prot P00642 (T2E1_ECOLX)

Names and origin

Protein names

Recommended name:
    Type-2 restriction enzyme EcoRI
      Short name=R.EcoRI
    EC=3.1.21.4
Alternative name(s):
    Type II restriction enzyme EcoRI
    Endonuclease EcoRI

Gene names

Name:

ecoRIR

Encoded on

Plasmid pMB1 Ref.1
Plasmid pMB4 Ref.2

Organism

Escherichia coli

Taxonomic identifier

562 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	277 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 GAATTC and cleaves after G-1.
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 Direct protein sequencing Plasmid
Gene Ontology (GO)
Biological process	DNA restriction-modification system Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	DNA binding Inferred from electronic annotation. Source: InterPro Type II site-specific deoxyribonuclease activity Inferred from electronic annotation. Source: EC magnesium 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 – 277

276

Type-2 restriction enzyme EcoRI

PRO_0000077303

Sites

Active site

91

1

Active site

111

1

Active site

113

1

Metal binding

91

1

Magnesium 1

Metal binding

91

1

Magnesium 2

Metal binding

111

1

Magnesium 1

Experimental info

Mutagenesis

144

1

E → D: Only nicks double strand DNA. Ref.7

Mutagenesis

144

1

E → Q: Inactivates the enzyme. Ref.7

Secondary structure

1

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277

Helix Strand Turn

Details...

Helix

20 – 31

12

Helix

35 – 49

15

Beta strand

55 – 59

5

Helix

63 – 73

11

Beta strand

94 – 98

5

Beta strand

104 – 114

11

Helix

118 – 123

6

Turn

129 – 132

4

Beta strand

134 – 136

3

Helix

142 – 146

5

Helix

147 – 156

10

Turn

157 – 159

3

Beta strand

160 – 162

3

Beta strand

165 – 171

7

Beta strand

179 – 182

4

Beta strand

188 – 191

4

Turn

196 – 198

3

Helix

201 – 203

3

Helix

205 – 208

4

Beta strand

213 – 215

3

Beta strand

221 – 223

3

Beta strand

225 – 227

3

Beta strand

230 – 232

3

Beta strand

236 – 239

4

Helix

248 – 265

18

Helix

267 – 269

3

Helix

271 – 275

5

Sequences

	Sequence		Length	Mass (Da)
	P00642-1 [UniParc]. Last modified January 23, 2007. Version 2. Checksum: 83EDC82868261B4B	FASTA	277	31,059
	10 20 30 40 50 60 MSNKKQSNRL TEQHKLSQGV IGIFGDYAKA HDLAVGEVSK LVKKALSNEY PQLSFRYRDS 70 80 90 100 110 120 IKKTEINEAL KKIDPDLGGT LFVSNSSIKP DGGIVEVKDD YGEWRVVLVA EAKHQGKDII 130 140 150 160 170 180 NIRNGLLVGK RGDQDLMAAG NAIERSHKNI SEIANFMLSE SHFPYVLFLE GSNFLTENIS 190 200 210 220 230 240 ITRPDGRVVN LEYNSGILNR LDRLTAANYG MPINSNLCIN KFVNHKDKSI MLQAASIYTQ 250 260 270 GDGREWDSKI MFEIMFDIST TSLRVLGRDL FEQLTSK

References

[1]	"Sequence analysis of the DNA encoding the Eco RI endonuclease and methylase." Greene P.J., Gupta M., Boyer H.W., Brown W.E., Rosenberg J.M. J. Biol. Chem. 256:2143-2153(1981) [PubMed: 6257703] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"DNA sequences of structural genes for Eco RI DNA restriction and modification enzymes." Newman A.K., Rubin R.A., Kim S.-H., Modrich P. J. Biol. Chem. 256:2131-2139(1981) [PubMed: 6257701] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: C.
[3]	"Partial NH2- and COOH-terminal sequence analyses of Eco RI DNA restriction and modification enzymes." Rubin R.A., Modrich P., Vanaman T.C. J. Biol. Chem. 256:2140-2142(1981) [PubMed: 6257702] [Abstract] Cited for: PROTEIN SEQUENCE OF N-TERMINUS, PROTEIN SEQUENCE OF C-TERMINUS.
[4]	"Structure of the DNA-Eco RI endonuclease recognition complex at 3-A resolution." McClarin J.A., Frederick C.A., Wang B.-C., Greene P., Boyer H.W., Grable J., Rosenberg J.M. Science 234:1526-1541(1986) [PubMed: 3024321] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS).
[5]	"Refinement of Eco RI endonuclease crystal structure: a revised protein chain tracing." Kim Y., Grable J.C., Love R., Greene P.J., Rosenberg J.M. Science 249:1307-1309(1990) [PubMed: 2399465] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS).
[6]	"Structure and function of restriction endonucleases." Rosenberg J.M. Curr. Opin. Struct. Biol. 1:104-113(1991) Cited for: REVIEW.
[7]	"Probing the role of glutamic acid 144 in the EcoRI endonuclease using aspartic acid and glutamine replacements." Hager P.W., Reich N.O., Day J.P., Coche T.G., Boyer H.W., Rosenberg J.M., Greene P.J. J. Biol. Chem. 265:21520-21526(1990) [PubMed: 2254311] [Abstract] Cited for: MUTAGENESIS OF GLU-144.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

J01675 Genomic DNA. Translation: AAA26371.1.

PIR

NDECP4. B92308.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1CKQ	X-ray	1.85	A	2-277	[»]
1CL8	X-ray	1.80	A	2-277	[»]
1ERI	X-ray	2.50	A	2-277	[»]
1QC9	X-ray	3.00	A/B/C	2-277	[»]
1QPS	X-ray	2.50	A	17-277	[»]
1QRH	X-ray	2.50	A	17-277	[»]
1QRI	X-ray	2.60	A	17-277	[»]
2OXV	X-ray	1.95	A	1-277	[»]

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-16997N.

Protein family/group databases

REBASE

993. EcoRI.

Enzyme and pathway databases

BRENDA

3.1.21.4. 246.

Family and domain databases

InterPro

IPR011335. Restrict_endonuc_II-like_core.
IPR004221. Restrict_endonuc_II_EcoRI.
IPR011336. Restrict_endonuc_II_EcoRI/MunI.
IPR018131. Restrict_endonuc_II_EcoRI_Pbac.
[Graphical view]

Gene3D

G3DSA:3.40.580.10. Restrict_endonuc_II_EcoRI/MunI. 1 hit.

Pfam

PF02963. EcoRI. 1 hit.
[Graphical view]

PIRSF

PIRSF001002. Restrict_endonuc_II_EcoRI. 1 hit.

ProDom

PD039825. Restrict_endonuc_II_EcoRI. 1 hit.
[Graphical view] [Entries sharing at least one domain]

ProtoNet

Search...

Entry information

Entry name

T2E1_ECOLX

Accession

Primary (citable) accession number: P00642

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	January 23, 2007
Last modified:	December 15, 2009
This is version 90 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)