1EVW

L116A MUTANT OF THE HOMING ENDONUCLEASE I-PPOI COMPLEXED TO HOMING SITE DNA.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.273 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Conformational changes and cleavage by the homing endonuclease I-PpoI: a critical role for a leucine residue in the active site.

Galburt, E.A.Chadsey, M.S.Jurica, M.S.Chevalier, B.S.Erho, D.Tang, W.Monnat Jr., R.J.Stoddard, B.L.

(2000) J.Mol.Biol. 300: 877-887

  • DOI: 10.1006/jmbi.2000.3874
  • Primary Citation of Related Structures:  1EVX

  • PubMed Abstract: 
  • The homing endonuclease I-PpoI severely bends its DNA target, resulting in significant deformations of the minor and major groove near the scissile phosphate groups. To study the role of conformational changes within the protein catalyst and the DNA ...

    The homing endonuclease I-PpoI severely bends its DNA target, resulting in significant deformations of the minor and major groove near the scissile phosphate groups. To study the role of conformational changes within the protein catalyst and the DNA substrate, we have determined the structure of the enzyme in the absence of bound DNA, performed gel retardation analyses of DNA binding and bending, and have mutagenized a leucine residue that contacts an adenine nucleotide at the site of cleavage. The structure of the L116A/DNA complex has been determined and the effects of the mutation on affinity and catalysis have been measured. The wild-type protein displays a rigid-body rotation of its individual subunits upon DNA binding. Homing site DNA is not detectably bent in the absence of protein, but is sharply bent in both the wild-type and L116A complexes. These results indicate that binding involves a large distortion of the DNA and a smaller change in protein conformation. Leucine 116 is critical for binding and catalysis: it appears to be important for forming a well-ordered protein-DNA complex at the cleavage site, for maximal deformation of the DNA, and for desolvation of the nucleotide bases that are partially unstacked in the enzyme complex.


    Organizational Affiliation

    Fred Hutchinson Cancer Research Center and the Graduate Programs in Molecular and Cell Biology and Biomolecular Structure and Design, 1100 Fairview Ave. N. A3-023, Seattle, WA, 98109, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
I-PPOI HOMING ENDONUCLEASE
A, B, C, D
163Physarum polycephalumEC: 3.1.-.-
Find proteins for Q94702 (Physarum polycephalum)
Go to UniProtKB:  Q94702
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*GP*GP*CP*TP*AP*CP*CP*TP*TP*AP*A)-3')E,G12N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(P*GP*AP*GP*AP*GP*TP*CP*A)-3')M,N8N/A
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*GP*AP*CP*TP*CP*TP*CP*TP*TP*AP*A)-3')F,H12N/A
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (5'-D(P*GP*GP*TP*AP*GP*CP*CP*A)-3')O,P8N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B, N, P
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DNAKd: 0.01 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.273 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 182.000α = 90.00
b = 73.100β = 95.40
c = 92.700γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
X-PLORrefinement
AMoREphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-08-03
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance