Geminivirus replication enhancer (REn/C3): In silico structure and characterization

Geminiviridae, a family of plant viruses that are recognized as causative agents in many plant diseases, has circular single-stranded DNA genomes that encode six genes, either structural or functional protein. Since it is lacking self-encoded polymerases for replication, Geminivirus must efficiently...

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Bibliographic Details
Main Authors: Wijaya, Nicholas Farrell, Nova, Bastian, Jamsari, Jamsari
Format: Conference Proceeding
Language:English
Subjects:
Confidence intervals
Deoxyribonucleic acid
DNA
Genomes
Phenylalanine
Plant diseases
Proteins
Replication
Sandwich structures
Structural analysis
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Summary:Geminiviridae, a family of plant viruses that are recognized as causative agents in many plant diseases, has circular single-stranded DNA genomes that encode six genes, either structural or functional protein. Since it is lacking self-encoded polymerases for replication, Geminivirus must efficiently utilize its protein in favoring viral replication. Replication enhancer protein (REn or C3) is known to be a major driving force in this function with its mutation leading to reduced viral genome accumulation. However, to this date, only a handful of Geminivirus protein structures have been solved (coat protein and part of replication initiator protein domain). Within the silico-based approach using AlphaFold2, we present the first predicted REn structure, both monomer, and homodimer, with a high confidence level. REn novel structure reveals alpha/beta-2-layer sandwich structure and formed bean-shaped structure from the surface. Three conserved phenylalanine; F29, F69, and F86 form a main hydrophobic core for governing its folding. From electrostatic potential, we proposed two different surfaces, positively charged surface (P-face) and neutral-to-negatively charged surface (Nt-Ng face). By forming a homodimer structure (both bidirectional “crab claw” and “ᆺ” structures), REn doubles its P-face area. We speculate such characteristics will strengthen REn electrostatic interactions with negatively charged proteins (e.g., PCNA and p50PDE domain), increase DNA binding domain from Rep, and act as a shuttle for viral DNA.
ISSN:0094-243X
1551-7616
DOI:10.1063/5.0127753