3UXU

The structure of the catalytic domain of the Sulfolobus Spindle-shaped viral integrase reveals an evolutionarily conserved catalytic core and supports a mechanism of DNA cleavage in trans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The Structure of an Archaeal Viral Integrase Reveals an Evolutionarily Conserved Catalytic Core yet Supports a Mechanism of DNA Cleavage in trans.

Eilers, B.J.Young, M.J.Lawrence, C.M.

(2012) J Virol 86: 8309-8313

  • DOI: 10.1128/JVI.00547-12
  • Primary Citation of Related Structures:  
    3UXU

  • PubMed Abstract: 
  • The first structure of a catalytic domain from a hyperthermophilic archaeal viral integrase reveals a minimal fold similar to that of bacterial HP1 integrase and defines structural elements conserved across three domains of life. However, structural superposition on bacterial Holliday junction complexes and similarities in the C-terminal tail with that of eukaryotic Flp suggest that the catalytic tyrosine and an additional active-site lysine are delivered to neighboring subunits in trans ...

    The first structure of a catalytic domain from a hyperthermophilic archaeal viral integrase reveals a minimal fold similar to that of bacterial HP1 integrase and defines structural elements conserved across three domains of life. However, structural superposition on bacterial Holliday junction complexes and similarities in the C-terminal tail with that of eukaryotic Flp suggest that the catalytic tyrosine and an additional active-site lysine are delivered to neighboring subunits in trans. An intramolecular disulfide bond contributes significant thermostability in vitro.


    Organizational Affiliation

    Thermal Biology Institute, Montana State University, Bozeman, Montana, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Probable integrase A169Sulfolobus spindle-shaped virus 1Mutation(s): 2 
Gene Names: d335
EC: 2.7.7 (UniProt), 3.1 (UniProt)
Find proteins for P20214 (Sulfolobus spindle-shape virus 1)
Explore P20214 
Go to UniProtKB:  P20214
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.963α = 90
b = 73.963β = 90
c = 176.251γ = 120
Software Package:
Software NamePurpose
Blu-Icedata collection
AutoSolphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-16
    Type: Initial release
  • Version 1.1: 2012-07-25
    Changes: Database references
  • Version 1.2: 2017-11-08
    Changes: Refinement description