Abstract
Recently, two groups of rhodopsin genes were identified in large double-stranded DNA viruses. The structure and function of viral rhodopsins are unknown. We present functional characterization and high-resolution structure of an Organic Lake Phycodnavirus rhodopsin II (OLPVRII) of group 2. It forms a pentamer, with a symmetrical, bottle-like central channel with the narrow vestibule in the cytoplasmic part covered by a ring of 5 arginines, whereas 5 phenylalanines form a hydrophobic barrier in its exit. The proton donor E42 is placed in the helix B. The structure is unique among the known rhodopsins. Structural and functional data and molecular dynamics suggest that OLPVRII might be a light-gated pentameric ion channel analogous to pentameric ligand-gated ion channels, however, future patch clamp experiments should prove this directly. The data shed light on a fundamentally distinct branch of rhodopsins and may contribute to the understanding of virus-host interactions in ecologically important marine protists.
Highlights
Two groups of rhodopsin genes were identified in large double-stranded DNA viruses
Genomic and metagenomic studies have dramatically expanded the collection of rhodopsin sequences, some of which have been identified in unexpected organisms and habitats, for example, sodium-pumping rhodopsins (NaRs) in Flavobacteria[13,14], and the wide spread and importance of PRbased phototrophy in the marine environment[15] have become evident
While Arg[82] was demonstrated to be a key element in the proton translocation mechanism in bR28, and analogous arginine is found in most microbial rhodopsins, playing important roles in their functioning[29,30,31], we suggest that the strong stabilization of Arg[72] in Organic Lake Phycodnavirus rhodopsin II (OLPVRII) by three Asn side chains may affect its mobility and affect the function of the rhodopsin
Summary
Two groups of rhodopsin genes were identified in large double-stranded DNA viruses. We present functional characterization and high-resolution structure of an Organic Lake Phycodnavirus rhodopsin II (OLPVRII) of group 2. It forms a pentamer, with a symmetrical, bottle-like central channel with the narrow vestibule in the cytoplasmic part covered by a ring of 5 arginines, whereas 5 phenylalanines form a hydrophobic barrier in its exit. Rhodopsins that function as inward proton pumps have been discovered[11,12]. Genomic and metagenomic studies have dramatically expanded the collection of rhodopsin sequences, some of which have been identified in unexpected organisms and habitats, for example, sodium-pumping rhodopsins (NaRs) in Flavobacteria[13,14], and the wide spread and importance of PRbased phototrophy in the marine environment[15] have become evident.
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