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P04390

- T2E5_ECOLX

UniProt

P04390 - T2E5_ECOLX

Protein

Type-2 restriction enzyme EcoRV

Gene

ecoRVR

Organism
Escherichia coli
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 118 (01 Oct 2014)
      Sequence version 3 (23 Jan 2007)
      Previous versions | rss
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    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

    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.

    P04390-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSLRSDLINA LYDENQKYDV CGIISAEGKI YPLGSDTKVL STIFELFSRP    50
    IINKIAEKHG YIVEEPKQQN HYPDFTLYKP SEPNKKIAID IKTTYTNKEN 100
    EKIKFTLGGY TSFIRNNTKN IVYPFDQYIA HWIIGYVYTR VATRKSSLKT 150
    YNINELNEIP KPYKGVKVFL QDKWVIAGDL AGSGNTTNIG SIHAHYKDFV 200
    EGKGIFDSED EFLDYWRNYE RTSQLRNDKY NNISEYRNWI YRGRK 245
    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