5AHO

Crystal structure of human 5' exonuclease Apollo


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Structures of the Snm1A and Snm1B/Apollo Nuclease Domains Reveal a Potential Basis for Their Distinct DNA Processing Activities.

Allerston, C.K.Lee, S.Y.Newman, J.A.Schofield, C.J.Mchugh, P.J.Gileadi, O.

(2015) Nucleic Acids Res. 43: 11047

  • DOI: 10.1093/nar/gkv1256
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The human SNM1A and SNM1B/Apollo proteins are members of an extended family of eukaryotic nuclease containing a motif related to the prokaryotic metallo-β-lactamase (MBL) fold. SNM1A is a key exonuclease during replication-dependent and transcription ...

    The human SNM1A and SNM1B/Apollo proteins are members of an extended family of eukaryotic nuclease containing a motif related to the prokaryotic metallo-β-lactamase (MBL) fold. SNM1A is a key exonuclease during replication-dependent and transcription-coupled interstrand crosslink repair, while SNM1B/Apollo is required for maintaining telomeric overhangs. Here, we report the crystal structures of SNM1A and SNM1B at 2.16 Å. While both proteins contain a typical MBL-β-CASP domain, a region of positive charge surrounds the active site of SNM1A, which is absent in SNM1B and explains the greater apparent processivity of SNM1A. The structures of both proteins also reveal a putative, wide DNA-binding groove. Extensive mutagenesis of this groove, coupled with detailed biochemical analysis, identified residues that did not impact on SNM1A catalytic activity, but drastically reduced its processivity. Moreover, we identified a key role for this groove for efficient digestion past DNA interstrand crosslinks, facilitating the key DNA repair reaction catalysed by SNM1A. Together, the architecture and dimensions of this groove, coupled to the surrounding region of high positive charge, explain the remarkable ability of SNM1A to accommodate and efficiently digest highly distorted DNA substrates, such as those containing DNA lesions.


    Organizational Affiliation

    Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive, University of Oxford, Oxford OX3 7DQ, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
5' EXONUCLEASE APOLLO
A
336Homo sapiensMutation(s): 0 
Gene Names: DCLRE1B (SNM1B)
EC: 3.1.-.-
Find proteins for Q9H816 (Homo sapiens)
Go to Gene View: DCLRE1B
Go to UniProtKB:  Q9H816
Small Molecules
Ligands 3 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
TLA
Query on TLA

Download SDF File 
Download CCD File 
A
L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.206 
  • Space Group: P 41 3 2
Unit Cell:
Length (Å)Angle (°)
a = 143.092α = 90.00
b = 143.092β = 90.00
c = 143.092γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
SCALAdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-02-18
    Type: Initial release
  • Version 1.1: 2016-02-24
    Type: Database references
  • Version 1.2: 2018-01-24
    Type: Structure summary