3GWL | pdb_00003gwl

Crystal structure of ASFV pB119L, a viral sulfhydryl oxidase

• PDB DOI: https://doi.org/10.2210/pdb3GWL/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): African swine fever virus BA71V
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-04-01 Released: 2009-07-07 
• Deposition Author(s): Hakim, M., Fass, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.261 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.212 (DCC) 

Literature

Dimer interface migration in a viral sulfhydryl oxidase

Hakim, M., Fass, D.

(2009) J Mol Biology 391: 758-768

• PubMed: 19576902 
• DOI: https://doi.org/10.1016/j.jmb.2009.06.070
• Primary Citation Related Structures: 
  3GWL, 3GWN


• PubMed Abstract: 
  

  Large double-stranded DNA viruses, including poxviruses and mimiviruses, encode enzymes to catalyze the formation of disulfide bonds in viral proteins produced in the cell cytosol, an atypical location for oxidative protein folding. These viral disulfide catalysts belong to a family of sulfhydryl oxidases that are dimers of a small five-helix fold containing a Cys-X-X-Cys motif juxtaposed to a flavin adenine dinucleotide cofactor. We report that the sulfhydryl oxidase pB119L from African swine fever virus (ASFV) uses for self-assembly surface different from that observed in homologs from mammals, plants, and fungi. Within a protein family, different packing interfaces for the same oligomerization state are extremely rare. We find that the alternate dimerization mode seen in ASFV pB119L is not characteristic of all viral sulfhydryl oxidases, as the flavin-binding domain from a mimivirus sulfhydryl oxidase assumes the same dimer structure as the known eukaryotic enzymes. ASFV pB119L demonstrates the potential of large double-stranded DNA viruses, which have faster mutation rates than their hosts and the tendency to incorporate host genes, to pioneer new protein folds and self-assembly modes.

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Organizational Affiliation: 
• Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 27.38 kDa 
• Atom Count: 2,085 
• Modeled Residue Count: 208 
• Deposited Residue Count: 212 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FAD-linked sulfhydryl oxidase	A, B	106	African swine fever virus BA71V	Mutation(s): 0  Gene Names: 9GL, B119L, Ba71V-073 EC: 1.8.3.2
UniProt
Find proteins for Q65163 (African swine fever virus (strain Badajoz 1971 Vero-adapted)) Explore Q65163  Go to UniProtKB:  Q65163

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	C [auth A], D [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.261 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.212 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.45	α = 90
b = 69	β = 90
c = 83.68	γ = 90

Software Package:

Software Name	Purpose
SOLVE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-07 
Deposition Author(s): Hakim, M., Fass, D.

Revision History  

• Version 1.0: 2009-07-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2016-12-07
  Changes: Database references
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary