1AK0

P1 NUCLEASE IN COMPLEX WITH A SUBSTRATE ANALOG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Recognition of single-stranded DNA by nuclease P1: high resolution crystal structures of complexes with substrate analogs.

Romier, C.Dominguez, R.Lahm, A.Dahl, O.Suck, D.

(1998) Proteins 32: 414-424


  • PubMed Abstract: 
  • The reaction mechanism of nuclease P1 from Penicillium citrinum has been investigated using single-stranded dithiophosphorylated di-, tetra-, and hexanucleotides as substrate analogs. The complexes crystallize in tetragonal and orthorhombic space gro ...

    The reaction mechanism of nuclease P1 from Penicillium citrinum has been investigated using single-stranded dithiophosphorylated di-, tetra-, and hexanucleotides as substrate analogs. The complexes crystallize in tetragonal and orthorhombic space groups and have been solved by molecular replacement. The high resolution structures give a clear picture of base recognition by P1 nuclease at its two nucleotide-binding sites, especially the 1.8 A structure of a P1-tetranucleotide complex which can be considered a P1-product complex. The observed binding modes are in agreement with a catalytic mechanism where the two closely spaced zinc ions activate the attacking water while the third, more exposed zinc ion stabilizes the leaving 03' oxyanion. Stacking as well as hydrogen bonding interactions with the base 5' to the cleaved phosphodiester bond are important elements of substrate binding and recognition. Modelling of a productive P1-substrate complex based on the solved structures suggests steric hindrance as the likely reason for the resistance of Rp-phosphorothioates and phosphorodithioates. Differences with the highly homologous nuclease S1 from Aspergillus oryzae are discussed.


    Related Citations: 
    • Crystal Structure of Penicillium Citrinum P1 Nuclease at 2.8 A Resolution
      Volbeda, A.,Lahm, A.,Sakiyama, F.,Suck, D.
      (1991) Embo J. 10: 1607


    Organizational Affiliation

    European Molecular Biology Laboratory, Heidelberg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
P1 NUCLEASE
A
270Penicillium citrinumEC: 3.1.30.1
Find proteins for P24289 (Penicillium citrinum)
Go to UniProtKB:  P24289
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
THS
Query on THS

Download SDF File 
Download CCD File 
A
THYMIDINE-5'-(DITHIO)PHOSPHATE
C10 H15 N2 O6 P S2
KMPXQZWMYQHTNT-XLPZGREQSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ADS
Query on ADS

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-(DITHIO)PHOSPHATE
C10 H14 N5 O5 P S2
RPDDEEQJNPPYRG-CPTYKQRNSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 41.980α = 90.00
b = 74.040β = 90.00
c = 102.130γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
XDSdata scaling
X-PLORphasing
X-PLORrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1997-05-28 
  • Released Date: 1997-12-03 
  • Deposition Author(s): Romier, C., Suck, D.

Revision History 

  • Version 1.0: 1997-12-03
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance