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P04390

- T2E5_ECOLX

UniProt

P04390 - T2E5_ECOLX

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Protein

Type-2 restriction enzyme EcoRV

Gene

ecoRVR

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

Functioni

Recognizes the double-stranded sequence GATATC and cleaves after T-3.

Catalytic activityi

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

Cofactori

Binds 2 magnesium ions per subunit.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi45 – 451Magnesium 2
Active sitei74 – 741
Metal bindingi74 – 741Magnesium 1
Metal bindingi74 – 741Magnesium 2
Active sitei90 – 901
Metal bindingi90 – 901Magnesium 1
Active sitei92 – 921

GO - Molecular functioni

  1. DNA binding Source: InterPro
  2. metal ion binding Source: UniProtKB-KW
  3. Type II site-specific deoxyribonuclease activity Source: UniProtKB-EC

GO - Biological processi

  1. DNA restriction-modification system Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Hydrolase, Nuclease

Keywords - Biological processi

Restriction system

Keywords - Ligandi

Magnesium, Metal-binding

Protein family/group databases

REBASEi995. EcoRV.

Names & Taxonomyi

Protein namesi
Recommended name:
Type-2 restriction enzyme EcoRV (EC:3.1.21.4)
Short name:
R.EcoRV
Alternative name(s):
Endonuclease EcoRV
Type II restriction enzyme EcoRV
Gene namesi
Name:ecoRVR
OrganismiEscherichia coli
Taxonomic identifieri562 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi70 – 701N → Q: Decrease in activity. 1 Publication
Mutagenesisi73 – 731P → A or G: Loss of activity. 1 Publication
Mutagenesisi74 – 741D → A: Loss of activity. 1 Publication
Mutagenesisi74 – 741D → E: Decrease in activity. 1 Publication
Mutagenesisi90 – 901D → A, N, E or T: Loss of activity. 1 Publication
Mutagenesisi183 – 1831S → A or T: Decrease in activity. 1 Publication
Mutagenesisi183 – 1831S → I: Loss of activity. 1 Publication
Mutagenesisi185 – 1851N → D, A or Q: Loss of activity. 1 Publication
Mutagenesisi186 – 1861T → S or N: Loss of activity. 1 Publication
Mutagenesisi187 – 1871T → S or N: No loss of activity. 1 Publication
Mutagenesisi188 – 1881N → A, Q or T: Decrease in activity. 1 Publication
Mutagenesisi188 – 1881N → D: Loss of activity. 1 Publication
Mutagenesisi190 – 1901G → A: No loss of activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed
Chaini2 – 245244Type-2 restriction enzyme EcoRVPRO_0000077305Add
BLAST

Proteomic databases

PRIDEiP04390.

Interactioni

Subunit structurei

Homodimer.

Structurei

Secondary structure

1
245
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi3 – 1715
Beta strandi20 – 256
Beta strandi30 – 323
Helixi37 – 5822
Beta strandi62 – 643
Beta strandi67 – 704
Beta strandi74 – 785
Beta strandi86 – 9813
Beta strandi106 – 1127
Turni113 – 1153
Beta strandi116 – 1183
Beta strandi119 – 1235
Helixi125 – 1273
Beta strandi128 – 14013
Turni145 – 1484
Helixi153 – 1586
Beta strandi162 – 17211
Helixi173 – 1764
Beta strandi177 – 1837
Turni184 – 1874
Beta strandi188 – 1914
Helixi196 – 2016
Helixi209 – 2179
Helixi223 – 2264
Beta strandi227 – 2293
Helixi233 – 2419

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1AZ0X-ray2.00A/B2-245[»]
1AZ3X-ray2.40A/B2-245[»]
1AZ4X-ray2.40A/B2-245[»]
1B94X-ray1.90A/B2-245[»]
1B95X-ray2.05A/B2-245[»]
1B96X-ray2.30A/B2-245[»]
1B97X-ray1.90A/B2-245[»]
1BGBX-ray2.00A/B2-245[»]
1BSSX-ray2.15A/B2-245[»]
1BSUX-ray2.00A/B2-245[»]
1BUAX-ray2.15A/B2-245[»]
1EO3X-ray2.00A/B1-245[»]
1EO4X-ray1.90A/B1-245[»]
1EONX-ray1.60A/B1-245[»]
1EOOX-ray2.16A/B1-245[»]
1EOPX-ray2.60A/B1-245[»]
1RV5X-ray2.10A/B2-245[»]
1RVAX-ray2.00A/B2-245[»]
1RVBX-ray2.10A/B2-245[»]
1RVCX-ray2.10A/B2-245[»]
1RVEX-ray2.50A/B1-245[»]
1STXX-ray2.10A/B2-245[»]
1SUZX-ray1.80A/B2-245[»]
1SX5X-ray1.50A/B2-245[»]
1SX8X-ray2.15A/B2-245[»]
2B0DX-ray2.00A/B1-245[»]
2B0EX-ray1.90A/B1-245[»]
2GE5X-ray2.40A/B2-220[»]
2RVEX-ray3.00A/B2-245[»]
4RVEX-ray3.00A/B/C2-245[»]
ProteinModelPortaliP04390.
SMRiP04390. Positions 2-245.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP04390.

Family & Domainsi

Family and domain databases

Gene3Di3.40.600.10. 1 hit.
InterProiIPR011337. DNA_rep_MutH/RE_typeII.
IPR011335. Restrct_endonuc-II-like.
IPR015314. Restrct_endonuc_II_EcoRV.
IPR019755. Restrct_endonuc_II_EcoRV_Pbac.
[Graphical view]
PfamiPF09233. Endonuc-EcoRV. 1 hit.
[Graphical view]
PIRSFiPIRSF000995. RE_EcoRV. 1 hit.
SUPFAMiSSF52980. SSF52980. 1 hit.

Sequencei

Sequence statusi: Complete.

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

P04390 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MSLRSDLINA LYDENQKYDV CGIISAEGKI YPLGSDTKVL STIFELFSRP
60 70 80 90 100
IINKIAEKHG YIVEEPKQQN HYPDFTLYKP SEPNKKIAID IKTTYTNKEN
110 120 130 140 150
EKIKFTLGGY TSFIRNNTKN IVYPFDQYIA HWIIGYVYTR VATRKSSLKT
160 170 180 190 200
YNINELNEIP KPYKGVKVFL QDKWVIAGDL AGSGNTTNIG SIHAHYKDFV
210 220 230 240
EGKGIFDSED EFLDYWRNYE RTSQLRNDKY NNISEYRNWI YRGRK
Length:245
Mass (Da):28,650
Last modified:January 23, 2007 - v3
Checksum:i7DB7EC640A746281
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X00530 Genomic DNA. Translation: CAA25208.1.
M19941 Genomic DNA. Translation: AAA24615.1.
PIRiA00784. NDECR5.
RefSeqiNP_863580.1. NC_005019.1.
WP_011117659.1. NC_019982.1.
YP_007316617.1. NC_019982.1.

Genome annotation databases

GeneIDi14401263.
1446621.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X00530 Genomic DNA. Translation: CAA25208.1 .
M19941 Genomic DNA. Translation: AAA24615.1 .
PIRi A00784. NDECR5.
RefSeqi NP_863580.1. NC_005019.1.
WP_011117659.1. NC_019982.1.
YP_007316617.1. NC_019982.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
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 2-245 [» ]
1BSU X-ray 2.00 A/B 2-245 [» ]
1BUA X-ray 2.15 A/B 2-245 [» ]
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 1-245 [» ]
1EOP X-ray 2.60 A/B 1-245 [» ]
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 2-245 [» ]
1SUZ X-ray 1.80 A/B 2-245 [» ]
1SX5 X-ray 1.50 A/B 2-245 [» ]
1SX8 X-ray 2.15 A/B 2-245 [» ]
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 2-220 [» ]
2RVE X-ray 3.00 A/B 2-245 [» ]
4RVE X-ray 3.00 A/B/C 2-245 [» ]
ProteinModelPortali P04390.
SMRi P04390. Positions 2-245.
ModBasei Search...
MobiDBi Search...

Protein family/group databases

REBASEi 995. EcoRV.

Proteomic databases

PRIDEi P04390.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

GeneIDi 14401263.
1446621.

Miscellaneous databases

EvolutionaryTracei P04390.

Family and domain databases

Gene3Di 3.40.600.10. 1 hit.
InterProi IPR011337. DNA_rep_MutH/RE_typeII.
IPR011335. Restrct_endonuc-II-like.
IPR015314. Restrct_endonuc_II_EcoRV.
IPR019755. Restrct_endonuc_II_EcoRV_Pbac.
[Graphical view ]
Pfami PF09233. Endonuc-EcoRV. 1 hit.
[Graphical view ]
PIRSFi PIRSF000995. RE_EcoRV. 1 hit.
SUPFAMi SSF52980. SSF52980. 1 hit.
ProtoNeti Search...

Publicationsi

  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.

Entry informationi

Entry nameiT2E5_ECOLX
AccessioniPrimary (citable) accession number: P04390
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 20, 1987
Last sequence update: January 23, 2007
Last modified: October 1, 2014
This is version 118 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure

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