3OQG

Restriction endonuclease HPY188I in complex with substrate DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Hpy188I-DNA pre- and post-cleavage complexes--snapshots of the GIY-YIG nuclease mediated catalysis.

Sokolowska, M.Czapinska, H.Bochtler, M.

(2011) Nucleic Acids Res 39: 1554-1564

  • DOI: 10.1093/nar/gkq821
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The GIY-YIG nuclease domain is present in all kingdoms of life and has diverse functions. It is found in the eukaryotic flap endonuclease and Holliday junction resolvase Slx1-Slx4, the prokaryotic nucleotide excision repair proteins UvrC and Cho, and ...

    The GIY-YIG nuclease domain is present in all kingdoms of life and has diverse functions. It is found in the eukaryotic flap endonuclease and Holliday junction resolvase Slx1-Slx4, the prokaryotic nucleotide excision repair proteins UvrC and Cho, and in proteins of 'selfish' genetic elements. Here we present the structures of the ternary pre- and post-cleavage complexes of the type II GIY-YIG restriction endonuclease Hpy188I with DNA and a surrogate or catalytic metal ion, respectively. Our structures suggest that GIY-YIG nucleases catalyze DNA hydrolysis by a single substitution reaction. They are consistent with a previous proposal that a tyrosine residue (which we expect to occur in its phenolate form) acts as a general base for the attacking water molecule. In contrast to the earlier proposal, our data identify the general base with the GIY and not the YIG tyrosine. A conserved glutamate residue (Glu149 provided in trans in Hpy188I) anchors a single metal cation in the active site. This metal ion contacts the phosphate proS oxygen atom and the leaving group 3'-oxygen atom, presumably to facilitate its departure. Taken together, our data reveal striking analogy in the absence of homology between GIY-YIG and ββα-Me nucleases.


    Organizational Affiliation

    International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hpy188IA, B180Helicobacter pylori 118Mutation(s): 0 
Gene Names: hpy188IR
Find proteins for Q9KJ88 (Helicobacter pylori)
Explore Q9KJ88 
Go to UniProtKB:  Q9KJ88
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsLengthOrganism
DNA 5'-D(*GP*AP*TP*CP*TP*GP*AP*AP*C)-3'C9N/A
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsLengthOrganism
DNA 5'-D(*GP*TP*TP*CP*AP*GP*AP*TP*C)-3'D9N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A,BL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.236α = 90
b = 65.236β = 90
c = 220.63γ = 90
Software Package:
Software NamePurpose
SHELXCDphasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMmodel building
ARP/wARPmodel building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-10-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Refinement description