5VSL

Crystal structure of viperin with bound [4Fe-4S] cluster and S-adenosylhomocysteine (SAH)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.972 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural studies of viperin, an antiviral radical SAM enzyme.

Fenwick, M.K.Li, Y.Cresswell, P.Modis, Y.Ealick, S.E.

(2017) Proc. Natl. Acad. Sci. U.S.A. 114: 6806-6811

  • DOI: 10.1073/pnas.1705402114
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Viperin is an IFN-inducible radical S-adenosylmethionine (SAM) enzyme that inhibits viral replication. We determined crystal structures of an anaerobically prepared fragment of mouse viperin (residues 45-362) complexed with S-adenosylhomocysteine (SA ...

    Viperin is an IFN-inducible radical S-adenosylmethionine (SAM) enzyme that inhibits viral replication. We determined crystal structures of an anaerobically prepared fragment of mouse viperin (residues 45-362) complexed with S-adenosylhomocysteine (SAH) or 5'-deoxyadenosine (5'-dAdo) and l-methionine (l-Met). Viperin contains a partial (βα)6-barrel fold with a disordered N-terminal extension (residues 45-74) and a partially ordered C-terminal extension (residues 285-362) that bridges the partial barrel to form an overall closed barrel structure. Cys84, Cys88, and Cys91 located after the first β-strand bind a [4Fe-4S] cluster. The active site architecture of viperin with bound SAH (a SAM analog) or 5'-dAdo and l-Met (SAM cleavage products) is consistent with the canonical mechanism of 5'-deoxyadenosyl radical generation. The viperin structure, together with sequence alignments, suggests that vertebrate viperins are highly conserved and that fungi contain a viperin-like ortholog. Many bacteria and archaebacteria also express viperin-like enzymes with conserved active site residues. Structural alignments show that viperin is similar to several other radical SAM enzymes, including the molybdenum cofactor biosynthetic enzyme MoaA and the RNA methyltransferase RlmN, which methylates specific nucleotides in rRNA and tRNA. The viperin putative active site contains several conserved positively charged residues, and a portion of the active site shows structural similarity to the GTP-binding site of MoaA, suggesting that the viperin substrate may be a nucleoside triphosphate of some type.


    Organizational Affiliation

    Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Radical S-adenosyl methionine domain-containing protein 2
A, B
318Mus musculusMutation(s): 0 
Gene Names: Rsad2 (Vig1)
Find proteins for Q8CBB9 (Mus musculus)
Go to UniProtKB:  Q8CBB9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
A, B
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
SAH
Query on SAH

Download SDF File 
Download CCD File 
A, B
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.972 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.155 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 58.934α = 90.00
b = 73.854β = 90.00
c = 141.872γ = 90.00
Software Package:
Software NamePurpose
Cootmodel building
HKL-2000data collection
HKL-2000data scaling
SHELXDphasing
PHENIXphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney DiseaseUnited StatesDK067081
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM102869
Howard Hughes Medical InstituteUnited States--
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM103403
Department of Energy (United States)United StatesDE-AC02-06CH11357
Wellcome TrustUnited Kingdom101908/Z/13/Z

Revision History 

  • Version 1.0: 2017-06-14
    Type: Initial release
  • Version 1.1: 2017-06-28
    Type: Database references
  • Version 1.2: 2017-07-12
    Type: Database references
  • Version 1.3: 2017-09-27
    Type: Author supporting evidence, Refinement description