3SPD

Crystal structure of aprataxin ortholog Hnt3 in complex with DNA

• PDB DOI: https://doi.org/10.2210/pdb3SPD/pdb
• NAKB: 3SPD

• Classification: HYDROLASE/DNA
• Organism(s): Schizosaccharomyces pombe 972h-
• Expression System: Escherichia coli
• Mutation(s): Yes 


• 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: 1.91 Å
• R-Value Free: 0.211 
• R-Value Work: 0.175 
• R-Value Observed: 0.176 

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: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 115.9 kDa 
• Atom Count: 8,860 
• Modelled Residue Count: 856 
• Deposited Residue Count: 880 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

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

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*AP*TP*TP*CP*CP*GP*AP*TP*AP*GP*TP*GP*AP*C)-3')	E, G	15	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*TP*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*AP*TP*GP*AP*G)-3')	F, H	17	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	AA [auth D], BA [auth D], J [auth A], K [auth A], L [auth A], M [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], T [auth C], U [auth C], V [auth C], W [auth C], Y [auth D], Z [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	I [auth A], N [auth B], S [auth C], X [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 0.211 
• R-Value Work: 0.175 
• R-Value Observed: 0.176 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 220.409	α = 90
b = 220.409	β = 90
c = 135.031	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	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
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description