3TD7

Crysal structure of the mimivirus sulfhydryl oxidase R596


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Exploring ORFan domains in giant viruses: structure of mimivirus sulfhydryl oxidase R596.

Hakim, M.Ezerina, D.Alon, A.Vonshak, O.Fass, D.

(2012) Plos One 7: e50649-e50649

  • DOI: 10.1371/journal.pone.0050649

  • PubMed Abstract: 
  • The mimivirus genome contains many genes that lack homologs in the sequence database and are thus known as ORFans. In addition, mimivirus genes that encode proteins belonging to known fold families are in some cases fused to domain-sized segments tha ...

    The mimivirus genome contains many genes that lack homologs in the sequence database and are thus known as ORFans. In addition, mimivirus genes that encode proteins belonging to known fold families are in some cases fused to domain-sized segments that cannot be classified. One such ORFan region is present in the mimivirus enzyme R596, a member of the Erv family of sulfhydryl oxidases. We determined the structure of a variant of full-length R596 and observed that the carboxy-terminal region of R596 assumes a folded, compact domain, demonstrating that these ORFan segments can be stable structural units. Moreover, the R596 ORFan domain fold is novel, hinting at the potential wealth of protein structural innovation yet to be discovered in large double-stranded DNA viruses. In the context of the R596 dimer, the ORFan domain contributes to formation of a broad cleft enriched with exposed aromatic groups and basic side chains, which may function in binding target proteins or localization of the enzyme within the virus factory or virions. Finally, we find evidence for an intermolecular dithiol/disulfide relay within the mimivirus R596 dimer, the first such extended, intersubunit redox-active site identified in a viral sulfhydryl oxidase.


    Organizational Affiliation

    Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FAD-linked sulfhydryl oxidase R596
A
295Acanthamoeba polyphaga mimivirusMutation(s): 4 
EC: 1.8.3.2
Find proteins for Q5UP54 (Acanthamoeba polyphaga mimivirus)
Go to UniProtKB:  Q5UP54
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download SDF File 
Download CCD File 
A
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.227 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 91.306α = 90.00
b = 91.306β = 90.00
c = 200.790γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
EDNAdata collection
SCALAdata scaling
XDSdata reduction
PHENIXphasing
PHENIXmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2011-08-10 
  • Released Date: 2012-09-05 
  • Deposition Author(s): Hakim, M., Fass, D.

Revision History 

  • Version 1.0: 2012-09-05
    Type: Initial release
  • Version 1.1: 2016-12-14
    Type: Database references
  • Version 1.2: 2017-08-23
    Type: Data collection