1AK0

P1 NUCLEASE IN COMPLEX WITH A SUBSTRATE ANALOG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


This is version 2.0 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

  • Primary Citation of Related Structures:  
    1AK0

  • 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 groups and have been solved by molecular replacement ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
P1 NUCLEASEA270Penicillium citrinumMutation(s): 0 
EC: 3.1.30.1
UniProt
Find proteins for P24289 (Penicillium citrinum)
Explore P24289 
Go to UniProtKB:  P24289
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseB2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADS (Subject of Investigation/LOI)
Query on ADS

Download Ideal Coordinates CCD File 
I [auth A]ADENOSINE-5'-(DITHIO)PHOSPHATE
C10 H14 N5 O5 P S2
RPDDEEQJNPPYRG-CPTYKQRNSA-N
 Ligand Interaction
THS (Subject of Investigation/LOI)
Query on THS

Download Ideal Coordinates CCD File 
J [auth A], K [auth A], L [auth A]THYMIDINE-5'-(DITHIO)PHOSPHATE
C10 H15 N2 O6 P S2
KMPXQZWMYQHTNT-XLPZGREQSA-N
 Ligand Interaction
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A], D [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A], F [auth A], G [auth A], H [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.98α = 90
b = 74.04β = 90
c = 102.13γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 1997-12-03
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary