3FHD

Crystal structure of the Shutoff and Exonuclease Protein from Kaposis Sarcoma Associated Herpesvirus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of the shutoff and exonuclease protein from the oncogenic Kaposi's sarcoma-associated herpesvirus

Dahlroth, S.L.Gurmu, D.Schmitzberger, F.Engman, H.Haas, J.Erlandsen, H.Nordlund, P.

(2009) FEBS J 276: 6636-6645

  • DOI: 10.1111/j.1742-4658.2009.07374.x
  • Primary Citation of Related Structures:  
    3FHD

  • PubMed Abstract: 
  • The Kaposi's sarcoma-associated herpesvirus protein SOX (shut off and exonuclease) and its Epstein-Barr virus homolog, BGLF5, are active during the early lytic phase and belong to the alkaline nuclease family. Both proteins have been shown to be bifunctional, being responsible for DNA maturation as well as host shutoff at the mRNA level ...

    The Kaposi's sarcoma-associated herpesvirus protein SOX (shut off and exonuclease) and its Epstein-Barr virus homolog, BGLF5, are active during the early lytic phase and belong to the alkaline nuclease family. Both proteins have been shown to be bifunctional, being responsible for DNA maturation as well as host shutoff at the mRNA level. We present the crystal structure of SOX determined at 1.85 A resolution. By modeling DNA binding, we have identified catalytic residues that explain the preferred 5'-exonuclease activity of the alkaline nucleases. The presence of a crevice suitable for binding duplex DNA supports a role for herpes alkaline nucleases in recombination events preceding packaging of viral DNA. Direct interaction with dsDNA is supported by oligonucleotide binding data. Mutations specifically affecting host shutoff map to a surface region of the N-terminal domain, implying an essential role in protein-protein interactions, and link the RNase activity of the enzyme to mRNA degradation pathways.


    Organizational Affiliation

    Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ORF 37A508Human herpesvirus 8 type MMutation(s): 0 
Gene Names: orf37
EC: 3.1
UniProt
Find proteins for P88925 (Human herpesvirus 8 type M)
Explore P88925 
Go to UniProtKB:  P88925
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP88925
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.247α = 95.48
b = 48.905β = 106.86
c = 67.294γ = 104.27
Software Package:
Software NamePurpose
SOLVEphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-11-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2011-07-27
    Changes: Database references