2O6M

H98Q mutant of the homing endonuclease I-PPOI complexed with DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Mutability of an HNH nuclease imidazole general base and exchange of a deprotonation mechanism.

Eastberg, J.H.Eklund, J.Monnat, R.Stoddard, B.L.

(2007) Biochemistry 46: 7215-7225

  • DOI: 10.1021/bi700418d
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Several unique protein folds that catalyze the hydrolysis of phosphodiester bonds have arisen independently in nature, including the PD(D/E)XK superfamily (typified by type II restriction endonucleases and many recombination and repair enzymes) and t ...

    Several unique protein folds that catalyze the hydrolysis of phosphodiester bonds have arisen independently in nature, including the PD(D/E)XK superfamily (typified by type II restriction endonucleases and many recombination and repair enzymes) and the HNH superfamily (found in an equally wide array of enzymes, including bacterial colicins and homing endonucleases). Whereas the identity and position of catalytic residues within the PD(D/E)XK superfamily are highly variable, the active sites of HNH nucleases are much more strongly conserved. In this study, the ability of an HNH nuclease to tolerate a mutation of its most conserved catalytic residue (its histidine general base), and the mechanism of the most active enzyme variant, were characterized. Conversion of this residue into several altered chemistries, glutamine, lysine, or glutamate, resulted in measurable activity. The histidine to glutamine mutant displays the highest residual activity and a pH profile similar to that of the wild-type enzyme. This activity is dependent on the presence of a neighboring imidazole ring, which has taken over as a less efficient general base for the reaction. This result implies that mutational pathways to alternative HNH-derived catalytic sites do exist but are not as extensively or successfully diverged or reoptimized in nature as variants of the PD(D/E)XK nuclease superfamily. This is possibly due to multiple steric constraints placed on the compact HNH motif, which is simultaneously involved in protein folding, DNA binding, and catalysis, as well as the use of a planar, aromatic imidazole group as a general base.


    Organizational Affiliation

    Fred Hutchinson Cancer Research Center and Graduate Program in Molecular and Cellular Biology, University of Washington, 1100 Fairview Avenue North, A3-025, Seattle, Washington 98109, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Intron-encoded endonuclease I-PpoIA, B163Physarum polycephalumMutation(s): 1 
Gene Names: I-PpoI
EC: 3.1
Find proteins for Q94702 (Physarum polycephalum)
Explore Q94702 
Go to UniProtKB:  Q94702
Protein Feature View
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  • Reference Sequence

Find similar nucleic acids by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*DTP*DTP*DGP*DAP*DCP*DTP*DCP*DTP*DCP*DTP*DTP*DAP*DAP*DGP*DAP*DGP*DAP*DGP*DTP*DCP*DA)-3'C, D21N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Download CCD File 
C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.211 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.85α = 90
b = 113.85β = 90
c = 88.88γ = 120
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-10-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance