3SPL | pdb_00003spl

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

PDB DOI: https://doi.org/10.2210/pdb3SPL/pdb
NAKB: 3SPL

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

Deposited: 2011-07-02 Released: 2011-10-12
Deposition Author(s): Gong, Y., Zhu, D., Ding, J., Dou, C., Ren, X., Jiang, T., Wang, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.216 (Depositor), 0.216 (DCC)
R-Value Work:
0.176 (Depositor), 0.179 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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

PubMed: 21984208 Search on PubMed
DOI: https://doi.org/10.1038/nsmb.2145
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 117.29 kDa
Atom Count: 8,684
Modeled Residue Count: 856
Deposited Residue Count: 880
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

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 EC: 3.6.1.72 (UniProt), 3.6.1.71 (UniProt)
UniProt
Find proteins for O74859 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore O74859 Go to UniProtKB: O74859
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O74859
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 2
DNA (5'-D(TPAPTPTPCPCPGPAPTPAPGPTPGPAP*C)-3')	E, G	15	N/A
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 3
DNA (5'-D(GPTPCPAPCPTPAPTPCPGPGPAPAPTPGPAP*G)-3')	F, H	17	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP Query on AMP Download:Ideal Coordinates CCD File SDF format, chain V [auth C] SDF format, chain P [auth B] SDF format, chain J [auth A] SDF format, chain BA [auth D] MOL2 format, chain V [auth C] MOL2 format, chain P [auth B] MOL2 format, chain J [auth A] MOL2 format, chain BA [auth D] mmCIF format, chain V [auth C] mmCIF format, chain P [auth B] mmCIF format, chain J [auth A] mmCIF format, chain BA [auth D]	BA [auth D], J [auth A], P [auth B], V [auth C]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain BA [auth D] Focus chain J [auth A] Focus chain P [auth B] Focus chain V [auth C] Interactions & Density Focus chain BA [auth D] Focus chain J [auth A] Focus chain P [auth B] Focus chain V [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain Y [auth C] SDF format, chain X [auth C] SDF format, chain W [auth C] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain FA [auth D] SDF format, chain EA [auth D] SDF format, chain DA [auth D] SDF format, chain CA [auth D] MOL2 format, chain Z [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain X [auth C] MOL2 format, chain W [auth C] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain FA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain CA [auth D] mmCIF format, chain Z [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain X [auth C] mmCIF format, chain W [auth C] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain FA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain CA [auth D]	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		Interactions Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain U [auth C] SDF format, chain O [auth B] SDF format, chain I [auth A] SDF format, chain AA [auth D] MOL2 format, chain U [auth C] MOL2 format, chain O [auth B] MOL2 format, chain I [auth A] MOL2 format, chain AA [auth D] mmCIF format, chain U [auth C] mmCIF format, chain O [auth B] mmCIF format, chain I [auth A] mmCIF format, chain AA [auth D]	AA [auth D], I [auth A], O [auth B], U [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain I [auth A] Focus chain O [auth B] Focus chain U [auth C] Interactions & Density Focus chain AA [auth D] Focus chain I [auth A] Focus chain O [auth B] Focus chain U [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.216 (Depositor), 0.216 (DCC)
R-Value Work: 0.176 (Depositor), 0.179 (DCC)
R-Value Observed: 0.178 (Depositor)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 220.956	α = 90
b = 220.956	β = 90
c = 135.154	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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-10-12

Deposition Author(s):

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
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description