Structure of Viperin from Trichoderma virens

Experimental Data Snapshot

  • Resolution: 2.79 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.190 

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This is version 1.3 of the entry. See complete history


Reconstitution and substrate specificity for isopentenyl pyrophosphate of the antiviral radical SAM enzyme viperin.

Chakravarti, A.Selvadurai, K.Shahoei, R.Lee, H.Fatma, S.Tajkhorshid, E.Huang, R.H.

(2018) J Biol Chem 293: 14122-14133

  • DOI: https://doi.org/10.1074/jbc.RA118.003998
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Viperin is a radical SAM enzyme that has been shown to possess antiviral activity against a broad spectrum of viruses; however, its molecular mechanism is unknown. We report here that recombinant fungal and archaeal viperin enzymes catalyze the addition of the 5'-deoxyadenosyl radical (5'-dA ) to the double bond of isopentenyl pyrophosphate (IPP), producing a new compound we named adenylated isopentyl pyrophosphate (AIPP). The reaction is specific for IPP, as other pyrophosphate compounds involved in the mevalonate biosynthetic pathway did not react with 5'-dA Enzymatic reactions employing IPP derivatives as substrates revealed that any chemical change in IPP diminishes its ability to be an effective substrate of fungal viperin. Mutational studies disclosed that the hydroxyl group on the side chain of Tyr-245 in fungal viperin is the likely source of hydrogen in the last step of the radical addition, providing mechanistic insight into the radical reaction catalyzed by fungal viperin. Structure-based molecular dynamics (MD) simulations of viperin interacting with IPP revealed a good fit of the isopentenyl motif of IPP to the active site cavity of viperin, unraveling the molecular basis of substrate specificity of viperin for IPP. Collectively, our findings indicate that IPP is an effective substrate of fungal and archaeal viperin enzymes and provide critical insights into the reaction mechanism.

  • Organizational Affiliation

    From the Departments of Biochemistry and.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
298Trichoderma virens Gv29-8Mutation(s): 0 
Gene Names: TRIVIDRAFT_58105
Find proteins for G9MQB8 (Hypocrea virens (strain Gv29-8 / FGSC 10586))
Explore G9MQB8 
Go to UniProtKB:  G9MQB8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG9MQB8
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on FLC

Download Ideal Coordinates CCD File 
AA [auth E]
DA [auth F]
GA [auth G]
JA [auth H]
MA [auth I]
AA [auth E],
DA [auth F],
GA [auth G],
JA [auth H],
MA [auth I],
O [auth A],
PA [auth J],
R [auth B],
SA [auth K],
U [auth C],
VA [auth L],
X [auth D]
C6 H5 O7
Query on SO4

Download Ideal Coordinates CCD File 
BA [auth F]
CA [auth F]
EA [auth G]
FA [auth G]
HA [auth H]
BA [auth F],
CA [auth F],
EA [auth G],
FA [auth G],
HA [auth H],
IA [auth H],
KA [auth I],
LA [auth I],
M [auth A],
N [auth A],
NA [auth J],
OA [auth J],
P [auth B],
Q [auth B],
QA [auth K],
RA [auth K],
S [auth C],
T [auth C],
TA [auth L],
UA [auth L],
V [auth D],
W [auth D],
Y [auth E],
Z [auth E]
O4 S
Experimental Data & Validation

Experimental Data

  • Resolution: 2.79 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 173.884α = 90
b = 209.566β = 90
c = 233.941γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM107533

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-25
    Type: Initial release
  • Version 1.1: 2019-08-07
    Changes: Data collection, Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references