3SP4

Crystal structure of aprataxin ortholog Hnt3 from Schizosaccharomyces pombe

• PDB DOI: https://doi.org/10.2210/pdb3SP4/pdb

• Classification: HYDROLASE
• Organism(s): Schizosaccharomyces pombe 972h-
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-07-01 Released: 2011-10-12 
• Deposition Author(s): Gong, Y., Zhu, D., Ding, J., Dou, C., Ren, X., Jiang, T., Wang, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.225 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 

Literature

Crystal structures of aprataxin ortholog Hnt3 reveal the mechanism for reversal of 5'-adenylated DNA

Gong, Y., Zhu, D., Ding, J., Dou, C., Ren, X., Gu, L., Jiang, T., Wang, D.

(2011) Nat Struct Mol Biol 18: 1297-1299

• PubMed: 21984208 
• DOI: https://doi.org/10.1038/nsmb.2145
• Primary Citation of Related Structures:  
  3SP4, 3SPD, 3SPL


• PubMed Abstract: 
  

  Aprataxin is a DNA deadenylase that resolves DNA 5'-AMP termini and reverses abortive DNA ligation. The crystal structures of Schizosaccharomyces pombe aprataxin Hnt3 in its apo form and in complex to dsDNA and dsDNA-AMP reveal how Hnt3 recognizes and processes 5'-adenylated DNA in a structure-specific manner. The bound DNA adopts a 5'-flap conformation that facilitates 5'-AMP access to the active site, where AMP cleavage occurs by a canonical catalytic mechanism.

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Organizational Affiliation: 

National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 47.6 kDa 
• Atom Count: 3,770 
• Modelled Residue Count: 406 
• Deposited Residue Count: 408 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aprataxin-like protein	A, B	204	Schizosaccharomyces pombe 972h-	Mutation(s): 0  Gene Names: hnt3, SPCC18.09c
UniProt
Find proteins for O74859 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore O74859  Go to UniProtKB:  O74859

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.225 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.177	α = 90
b = 70.201	β = 90
c = 107.809	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-10-12 
Deposition Author(s): Gong, Y., Zhu, D., Ding, J., Dou, C., Ren, X., Jiang, T., Wang, D.

Revision History  

• Version 1.0: 2011-10-12
  Type: Initial release
  
• Version 1.1: 2013-07-03
  Changes: Database references