5FBC

S1 nuclease from Aspergillus oryzae in complex with 2'-deoxyadenosine-5'-thio-monophosphate (5'dAMP(S)).


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.131 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural and Catalytic Properties of S1 Nuclease from Aspergillus oryzae Responsible for Substrate Recognition, Cleavage, Non-Specificity, and Inhibition.

Koval, T.stergaard, L.H.Lehmbeck, J.Nrgaard, A.Lipovova, P.Duskova, J.Skalova, T.Trundova, M.Kolenko, P.Fejfarova, K.Stransky, J.Svecova, L.Hasek, J.Dohnalek, J.

(2016) PLoS ONE 11: e0168832-e0168832

  • DOI: 10.1371/journal.pone.0168832
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The single-strand-specific S1 nuclease from Aspergillus oryzae is an archetypal enzyme of the S1-P1 family of nucleases with a widespread use for biochemical analyses of nucleic acids. We present the first X-ray structure of this nuclease along with ...

    The single-strand-specific S1 nuclease from Aspergillus oryzae is an archetypal enzyme of the S1-P1 family of nucleases with a widespread use for biochemical analyses of nucleic acids. We present the first X-ray structure of this nuclease along with a thorough analysis of the reaction and inhibition mechanisms and of its properties responsible for identification and binding of ligands. Seven structures of S1 nuclease, six of which are complexes with products and inhibitors, and characterization of catalytic properties of a wild type and mutants reveal unknown attributes of the S1-P1 family. The active site can bind phosphate, nucleosides, and nucleotides in several distinguished ways. The nucleoside binding site accepts bases in two binding modes-shallow and deep. It can also undergo remodeling and so adapt to different ligands. The amino acid residue Asp65 is critical for activity while Asn154 secures interaction with the sugar moiety, and Lys68 is involved in interactions with the phosphate and sugar moieties of ligands. An additional nucleobase binding site was identified on the surface, which explains the absence of the Tyr site known from P1 nuclease. For the first time ternary complexes with ligands enable modeling of ssDNA binding in the active site cleft. Interpretation of the results in the context of the whole S1-P1 nuclease family significantly broadens our knowledge regarding ligand interaction modes and the strategies of adjustment of the enzyme surface and binding sites to achieve particular specificity.


    Organizational Affiliation

    Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology CAS, v. v. i., Biocev, Vestec, Czech Republic.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nuclease S1
A
267Aspergillus oryzae (strain ATCC 42149 / RIB 40)Mutation(s): 0 
Gene Names: nucS
EC: 3.1.30.1
Find proteins for P24021 (Aspergillus oryzae (strain ATCC 42149 / RIB 40))
Go to UniProtKB:  P24021
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-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
AS
Query on AS

Download SDF File 
Download CCD File 
A
2-DEOXY-ADENOSINE -5'-THIO-MONOPHOSPHATE
C10 H14 N5 O5 P S
ULJYSQHUKIZEGB-RRKCRQDMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.131 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 41.894α = 90.00
b = 62.585β = 106.97
c = 48.242γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Cootmodel building
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Youth and Sports of the Czech RepublicCzech RepublicLG14009
BIOCEV: Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University from the European Regional Development FundCzech RepublicCZ.1.05/1.1.00/02.0109
European Community283570/8787

Revision History 

  • Version 1.0: 2016-12-28
    Type: Initial release
  • Version 1.1: 2017-01-11
    Type: Database references