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Protein

Type-2 restriction enzyme EcoRI

Gene

ecoRIR

Organism
Escherichia coli
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Recognizes the double-stranded sequence GAATTC and cleaves after G-1.

Catalytic activityi

Endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates.

Cofactori

Mg2+Note: Binds 2 magnesium ions per subunit.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei91 – 911
Metal bindingi91 – 911Magnesium 1
Metal bindingi91 – 911Magnesium 2
Active sitei111 – 1111
Metal bindingi111 – 1111Magnesium 1
Active sitei113 – 1131

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Hydrolase, Nuclease

Keywords - Biological processi

Restriction system

Keywords - Ligandi

Magnesium, Metal-binding

Protein family/group databases

REBASEi993. EcoRI.

Names & Taxonomyi

Protein namesi
Recommended name:
Type-2 restriction enzyme EcoRI (EC:3.1.21.4)
Short name:
R.EcoRI
Alternative name(s):
Endonuclease EcoRI
Type II restriction enzyme EcoRI
Gene namesi
Name:ecoRIR
Encoded oniPlasmid pMB11 Publication
Plasmid pMB41 Publication
OrganismiEscherichia coli
Taxonomic identifieri562 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi144 – 1441E → D: Only nicks double strand DNA. 1 Publication
Mutagenesisi144 – 1441E → Q: Inactivates the enzyme. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed
Chaini2 – 277276Type-2 restriction enzyme EcoRIPRO_0000077303Add
BLAST

Interactioni

Subunit structurei

Homodimer.

Protein-protein interaction databases

DIPiDIP-16997N.

Structurei

Secondary structure

1
277
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi21 – 3111Combined sources
Helixi35 – 4915Combined sources
Beta strandi55 – 595Combined sources
Helixi63 – 7311Combined sources
Beta strandi94 – 985Combined sources
Beta strandi104 – 11411Combined sources
Helixi118 – 1236Combined sources
Turni129 – 1324Combined sources
Beta strandi134 – 1363Combined sources
Helixi142 – 1454Combined sources
Helixi146 – 15611Combined sources
Turni157 – 1593Combined sources
Beta strandi160 – 1623Combined sources
Beta strandi165 – 1717Combined sources
Helixi172 – 1743Combined sources
Beta strandi179 – 1824Combined sources
Beta strandi184 – 1863Combined sources
Beta strandi188 – 1914Combined sources
Turni196 – 1983Combined sources
Helixi201 – 2033Combined sources
Helixi205 – 2084Combined sources
Beta strandi213 – 2153Combined sources
Beta strandi221 – 2233Combined sources
Beta strandi225 – 2273Combined sources
Beta strandi230 – 2323Combined sources
Beta strandi236 – 2394Combined sources
Helixi248 – 26518Combined sources
Helixi267 – 2693Combined sources
Helixi271 – 2755Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1CKQX-ray1.85A2-277[»]
1CL8X-ray1.80A2-277[»]
1ERIX-ray2.50A2-277[»]
1QC9X-ray3.00A/B/C2-277[»]
1QPSX-ray2.50A17-277[»]
1QRHX-ray2.50A17-277[»]
1QRIX-ray2.60A17-277[»]
2OXVX-ray1.95A1-277[»]
ProteinModelPortaliP00642.
SMRiP00642. Positions 17-277.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP00642.

Family & Domainsi

Family and domain databases

Gene3Di3.40.580.10. 1 hit.
InterProiIPR011335. Restrct_endonuc-II-like.
IPR004221. Restrct_endonuc_II_EcoRI.
IPR011336. Restrct_endonuc_II_EcoRI/MunI.
IPR018131. Restrct_endonuc_II_EcoRI_Pbac.
[Graphical view]
PfamiPF02963. EcoRI. 1 hit.
[Graphical view]
PIRSFiPIRSF001002. Restrict_endonuc_II_EcoRI. 1 hit.
ProDomiPD039825. Restrict_endonuc_II_EcoRI. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SUPFAMiSSF52980. SSF52980. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P00642-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSNKKQSNRL TEQHKLSQGV IGIFGDYAKA HDLAVGEVSK LVKKALSNEY
60 70 80 90 100
PQLSFRYRDS IKKTEINEAL KKIDPDLGGT LFVSNSSIKP DGGIVEVKDD
110 120 130 140 150
YGEWRVVLVA EAKHQGKDII NIRNGLLVGK RGDQDLMAAG NAIERSHKNI
160 170 180 190 200
SEIANFMLSE SHFPYVLFLE GSNFLTENIS ITRPDGRVVN LEYNSGILNR
210 220 230 240 250
LDRLTAANYG MPINSNLCIN KFVNHKDKSI MLQAASIYTQ GDGREWDSKI
260 270
MFEIMFDIST TSLRVLGRDL FEQLTSK
Length:277
Mass (Da):31,059
Last modified:January 23, 2007 - v2
Checksum:i83EDC82868261B4B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J01675 Genomic DNA. Translation: AAA26371.1.
PIRiB92308. NDECP4.
RefSeqiWP_001565219.1. NZ_CCRA01000002.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J01675 Genomic DNA. Translation: AAA26371.1.
PIRiB92308. NDECP4.
RefSeqiWP_001565219.1. NZ_CCRA01000002.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1CKQX-ray1.85A2-277[»]
1CL8X-ray1.80A2-277[»]
1ERIX-ray2.50A2-277[»]
1QC9X-ray3.00A/B/C2-277[»]
1QPSX-ray2.50A17-277[»]
1QRHX-ray2.50A17-277[»]
1QRIX-ray2.60A17-277[»]
2OXVX-ray1.95A1-277[»]
ProteinModelPortaliP00642.
SMRiP00642. Positions 17-277.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-16997N.

Chemistry

BindingDBiP00642.
ChEMBLiCHEMBL5729.

Protein family/group databases

REBASEi993. EcoRI.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Miscellaneous databases

EvolutionaryTraceiP00642.

Family and domain databases

Gene3Di3.40.580.10. 1 hit.
InterProiIPR011335. Restrct_endonuc-II-like.
IPR004221. Restrct_endonuc_II_EcoRI.
IPR011336. Restrct_endonuc_II_EcoRI/MunI.
IPR018131. Restrct_endonuc_II_EcoRI_Pbac.
[Graphical view]
PfamiPF02963. EcoRI. 1 hit.
[Graphical view]
PIRSFiPIRSF001002. Restrict_endonuc_II_EcoRI. 1 hit.
ProDomiPD039825. Restrict_endonuc_II_EcoRI. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SUPFAMiSSF52980. SSF52980. 1 hit.
ProtoNetiSearch...

Publicationsi

  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] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Plasmid: pMB1
  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] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: C.
    Plasmid: pMB4
  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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF GLU-144.

Entry informationi

Entry nameiT2E1_ECOLX
AccessioniPrimary (citable) accession number: P00642
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: January 23, 2007
Last modified: May 27, 2015
This is version 113 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Direct protein sequencing, Plasmid

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. Restriction enzymes and methylases
    Classification of restriction enzymes and methylases and list of entries

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.