3UXU | pdb_00003uxu

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

• PDB DOI: https://doi.org/10.2210/pdb3UXU/pdb

• Classification: RECOMBINATION
• Organism(s): Sulfolobus spindle-shaped virus 1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2011-12-05 Released: 2012-05-16 
• Deposition Author(s): Eilers, B.J., Young, M.J., Lawrence, C.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.71 Å
• R-Value Free: 
  0.214 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

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

• PubMed: 22593158 
• DOI: https://doi.org/10.1128/JVI.00547-12
• Primary Citation 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. An intramolecular disulfide bond contributes significant thermostability in vitro.

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Organizational Affiliation: 
• Thermal Biology Institute, Montana State University, Bozeman, Montana, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 20.12 kDa 
• Atom Count: 1,367 
• Modeled Residue Count: 159 
• Deposited Residue Count: 169 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable integrase	A	169	Sulfolobus spindle-shaped virus 1	Mutation(s): 2  Gene Names: d335 EC: 3.1 (UniProt), 2.7.7 (UniProt)
UniProt
Find proteins for P20214 (Sulfolobus spindle-shape virus 1) Explore P20214  Go to UniProtKB:  P20214

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.71 Å
• R-Value Free:  0.214 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.963	α = 90
b = 73.963	β = 90
c = 176.251	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
AutoSol	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-16 
Deposition Author(s): Eilers, B.J., Young, M.J., Lawrence, C.M.

Revision History  

• 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
• Version 1.3: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary