Crystallographic structure of the nuclease domain of 3'hExo, a DEDDh family member, bound to rAMP

Experimental Data Snapshot

  • Resolution: 1.59 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 

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Crystallographic Structure of the Nuclease Domain of 3'Hexo, a Deddh Family Member, Bound to Ramp

Cheng, Y.Patel, D.

(2004) J Mol Biol 343: 305

  • DOI: https://doi.org/10.1016/j.jmb.2004.08.055
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    A human 3'-5'-exoribonuclease (3'hExo) has recently been identified and shown to be responsible for histone mRNA degradation. Functionally, 3'hExo and a stem-loop binding protein (SLBP) target opposite faces of a unique highly conserved stem-loop RNA scaffold towards the 3' end of histone mRNA, which is composed of a 6 bp stem and a 4 nt loop, followed by an ACCCA sequence. Its Caenorhabditis elegans homologue, ERI-1, has been shown to degrade small interfering RNA in vitro and to function as a negative regulator of RNA interference in neuronal cells. We have determined the structure of the nuclease domain (Nuc) of 3'hExo complexed with rAMP in the presence of Mg2+ at 1.6 A resolution. The Nuc domain adopts an alpha/beta globular fold, with four acidic residues coordinating a binuclear metal cluster within the active site, whose topology is related to DEDDh exonuclease family members, despite a very low level of primary sequence identity. The two magnesium cations in the Nuc active site are coordinated to D134, E136, D234 and D298, and together with H293, which can potentially act as a general base, provide a platform for hydrolytic cleavage of bound RNA in the 3' --> 5' direction. The bound rAMP is positioned within a deep active-site pocket, with its purine ring close-packed with the hydrophobic F185 and L189 side-chains and its sugar 2'-OH and 3'-OH groups hydrogen bonded to backbone atoms of Nuc. There are striking similarities between the active sites of Nuc and epsilon186, an Escherichia coli DNA polymerase III proofreading domain, providing a common hydrolytic cleavage mechanism for RNA degradation and DNA editing, respectively.

  • Organizational Affiliation

    Structural Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA.

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3'-5' EXONUCLEASE ERI1204Homo sapiensMutation(s): 0 
EC: 3.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IV48 (Homo sapiens)
Explore Q8IV48 
Go to UniProtKB:  Q8IV48
GTEx:  ENSG00000104626 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IV48
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
Experimental Data & Validation

Experimental Data

  • Resolution: 1.59 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.6α = 90
b = 101.6β = 90
c = 100.4γ = 120
Software Package:
Software NamePurpose

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-09-30
    Type: Initial release
  • Version 1.1: 2011-06-02
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance