3SPL

Crystal structure of aprataxin ortholog Hnt3 in complex with DNA and AMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 

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This is version 1.1 of the entry. See complete history


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

  • DOI: 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 ...

    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.


    Organizational Affiliation

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



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Aprataxin-like proteinA, B, C, D204Schizosaccharomyces pombe 972h-Mutation(s): 1 
Gene Names: hnt3SPCC18.09c
EC: 3.6.1.71 (UniProt), 3.6.1.72 (UniProt)
UniProt
Find proteins for O74859 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore O74859 
Go to UniProtKB:  O74859
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO74859
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*TP*AP*TP*TP*CP*CP*GP*AP*TP*AP*GP*TP*GP*AP*C)-3')E, G 15N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (5'-D(*GP*TP*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*AP*TP*GP*AP*G)-3')F, H 17N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AMP
Query on AMP

Download Ideal Coordinates CCD File 
BA [auth D],
J [auth A],
P [auth B],
V [auth C]
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
CA [auth D],
DA [auth D],
EA [auth D],
FA [auth D],
K [auth A],
CA [auth D],
DA [auth D],
EA [auth D],
FA [auth D],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
W [auth C],
X [auth C],
Y [auth C],
Z [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth D],
I [auth A],
O [auth B],
U [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 220.956α = 90
b = 220.956β = 90
c = 135.154γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

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