1H56

Structural and biochemical characterization of a new magnesium ion binding site near Tyr94 in the restriction endonuclease PvuII


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Work: 0.150 
  • R-Value Observed: 0.150 

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This is version 1.2 of the entry. See complete history


Literature

Structural and Biochemical Characterization of a New Mg(2+) Binding Site Near Tyr94 in the Restriction Endonuclease PvuII.

Spyridaki, A.Matzen, C.Lanio, T.Jeltsch, A.Simoncsits, A.Athanasiadis, A.Scheuring-Vanamee, E.Kokkinidis, M.Pingoud, A.

(2003) J Mol Biol 331: 395

  • DOI: 10.1016/s0022-2836(03)00692-2
  • Primary Citation of Related Structures:  
    1H56

  • PubMed Abstract: 
  • We have determined the crystal structure of the PvuII endonuclease in the presence of Mg(2+). According to the structural data, divalent metal ion binding in the PvuII subunits is highly asymmetric. The PvuII-Mg(2+) complex has two distinct metal ion binding sites, one in each monomer ...

    We have determined the crystal structure of the PvuII endonuclease in the presence of Mg(2+). According to the structural data, divalent metal ion binding in the PvuII subunits is highly asymmetric. The PvuII-Mg(2+) complex has two distinct metal ion binding sites, one in each monomer. One site is formed by the catalytic residues Asp58 and Glu68, and has extensive similarities to a catalytically important site found in all structurally examined restriction endonucleases. The other binding site is located in the other monomer, in the immediate vicinity of the hydroxyl group of Tyr94; it has no analogy to metal ion binding sites found so far in restriction endonucleases. To assign the number of metal ions involved and to better understand the role of Mg(2+) binding to Tyr94 for the function of PvuII, we have exchanged Tyr94 by Phe and characterized the metal ion dependence of DNA cleavage of wild-type PvuII and the Y94F variant. Wild-type PvuII cleaves both strands of the DNA in a concerted reaction. Mg(2+) binding, as measured by the Mg(2+) dependence of DNA cleavage, occurs with a Hill coefficient of 4, meaning that at least two metal ions are bound to each subunit in a cooperative fashion upon formation of the active complex. Quenched-flow experiments show that DNA cleavage occurs about tenfold faster if Mg(2+) is pre-incubated with enzyme or DNA than if preformed enzyme-DNA complexes are mixed with Mg(2+). These results show that Mg(2+) cannot easily enter the active center of the preformed enzyme-DNA complex, but that for fast cleavage the metal ions must already be bound to the apoenzyme and carried with the enzyme into the enzyme-DNA complex. The Y94F variant, in contrast to wild-type PvuII, does not cleave DNA in a concerted manner and metal ion binding occurs with a Hill coefficient of 1. These results indicate that removal of the Mg(2+) binding site at Tyr94 completely disrupts the cooperativity in DNA cleavage. Moreover, in quenched-flow experiments Y94F cleaves DNA about ten times more slowly than wild-type PvuII, regardless of the order of mixing. From these results we conclude that wild-type PvuII cleaves DNA in a fast and concerted reaction, because the Mg(2+) required for catalysis are already bound at the enzyme, one of them at Tyr94. We suggest that this Mg(2+) is shifted to the active center during binding of a specific DNA substrate. These results, for the first time, shed light on the pathway by which metal ions as essential cofactors enter the catalytic center of restriction endonucleases.


    Related Citations: 
    • Crystal Structure of PvuII Endonuclease Reveals Extensive Structural Homologies to EcoRV
      Athanasiadis, A., Vlassi, M., Kotsifaki, D., Tucker, P.A., Wilson, K.S., Kokkinidis, M.
      (1994) Nat Struct Biol 1: 469

    Organizational Affiliation

    Department of Biology, IMBB/FORTH, University of Crete, PO Box 1527, Heraklion, GR-71110, Crete, Greece.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TYPE II RESTRICTION ENZYME PVUIIA, B156Proteus vulgarisMutation(s): 0 
EC: 3.1.21.4
UniProt
Find proteins for P23657 (Proteus hauseri)
Explore P23657 
Go to UniProtKB:  P23657
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23657
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Work: 0.150 
  • R-Value Observed: 0.150 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.18α = 90
b = 105.28β = 90
c = 46.67γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-08-07
    Type: Initial release
  • Version 1.1: 2015-04-15
    Changes: Database references, Derived calculations, Non-polymer description, Other, Source and taxonomy, Version format compliance
  • Version 1.2: 2019-07-24
    Changes: Data collection