Jelly roll fold

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Jelly-roll fold
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beta strands are labeled with their traditional designations (for historical reasons, sheet A is not used), highlighting the packing of the BIDG and CHEF four-stranded sheets.[1]

The jelly roll or Swiss roll fold is a

Structural Classification of Proteins (SCOP) database.[5]

Structure

The basic jelly roll structure consists of eight

hydrophobic interface [Where citation... uniprot]. The strands are traditionally labeled B through I for the historical reason that the first solved structure, of a jelly roll capsid protein from the tomato bushy stunt virus, had an additional strand A outside the fold's common core.[6][7] The sheets are composed of strands BIDG and CHEF, folded such that strand B packs opposite strand C, I opposite H, etc.[4][8]

Viral proteins

The full assembled capsid structure of the satellite tobacco mosaic virus, with the monomer shown above at the bottom of the highlighted pentamer. The remainder of the protein chains are shown in purple and the RNA in the interior of the capsid is shown in brown. The axis of the jelly roll in this single jelly roll capsid is parallel to the capsid surface. From PDB: 4OQ9​.[1]

A large number of

capsids from proteins containing either a single or a double jelly roll fold. This shared capsid architecture is thought to reflect ancient evolutionary relationships, possibly dating to before the last universal common ancestor (LUCA) of cellular life.[8][9][10] Other viral lineages use evolutionarily unrelated proteins to build their enclosed capsids, which likely evolved independently at least twice[9][11] and possibly many times, with links to proteins of cellular origin.[12]

Single jelly roll capsid proteins

Single jelly roll capsid (JRC) proteins are found in at least sixteen distinct viral

double-stranded DNA viruses with single-JRC capsids are the Papillomaviridae and Polyomaviridae, both of which have fairly small capsids; in these viruses, the architecture of the assembled capsid orients the axis of the jelly roll parallel or "horizontally" relative to the capsid surface.[11] A large-scale analysis of viral capsid components suggested that the single horizontal jelly roll is the most common fold among capsid proteins, accounting for about 28% of known examples.[12]

Another group of viruses uses single jelly roll proteins in their capsids, but in the vertical rather than horizontal orientation. These viruses are evolutionarily related to the large group of double jelly-roll viruses known as the

extremophilic prokaryotes.[14][12]

Double jelly roll proteins

bacteriophage PM2. The two distinct jelly roll domains are shown in red and blue, with the remaining protein sequence in orange. Double jelly rolls are oriented with the "vertical" axis perpendicular to the capsid surface, which is at the bottom in this image. From PDB: 2W0C​.[17]
A pseudohexameric trimer of double jelly roll proteins; the jelly rolls are in red and blue and the loops and helices are colored to distinguish the three monomers in the assembly. The viewer is looking down from the exterior toward the capsid surface. From PDB: 2W0C​.[17]

Double jelly roll capsid proteins consist of two single jelly roll folds connected by a short linker region. They are found in both

domains of life, and spanning a large capsid size range.[4][11][18] In the double jelly roll capsid architecture, the jelly roll axis is oriented perpendicular or "vertically" relative to the capsid surface.[19]

Double jelly roll proteins are believed to have evolved from single jelly roll proteins by

nucleocytoplasmic large DNA viruses (NCLDV).[24]

Initially, it was believed that double jelly roll proteins are unique to viruses, because they were not observed in cellular proteins.[11] However, in 2022, comparison of protein structures revealed several families of bona fide cellular proteins with the double jelly roll fold [25]

Non-capsid proteins

Single jelly rolls also occur in non-capsid viral proteins, including minor components of the assembled

plasmodesmata channels have the single jelly-roll fold and have evolved from the capsid proteins of small icosahedral viruses.[26]

Cellular proteins

Both single and double jelly roll folds are found in proteins of cellular origin.

N-terminal domain of nucleoplasmins possesses a single jelly roll fold and assembled into a pentamer.[27] Similar structures have since been reported in additional groups of chromatin remodeling proteins.[28] Jelly roll motifs with identical beta-sheet connectivity are also found in tumor necrosis factor ligands[29] and proteins from the bacterium Yersinia pseudotuberculosis that belong to a class of viral and bacterial proteins known as superantigens.[30][31]

More broadly, the members of the extremely diverse cupin superfamily are also often described as jelly rolls; though the common core of the cupin domain structure contains only six beta strands, many cupins have eight.[32] Examples include the non-heme dioxygenase enzymes[33][34] (including alpha-ketoglutarate-dependent hydroxylases) and JmjC-family histone demethylases.[35][36]

Cellular proteins with the double jelly roll fold include glycoside hydrolases of the DUF2961 family, peptide:N-glycosidase F (PNGases F) and peptidylglycine alpha-amidating monooxygenase.[25]

A notable difference between PNGases F and the other double jelly roll proteins is the absence of the α-helices, which follow the F and F' strands in capsid proteins and DUF2961. The equivalent regions are variable in the PNGases F and contain either long loops or insertions. By contrast, jelly-roll domains of DUF2961 proteins contain an insertion of short β-hairpins upstream of the G and G' strands of the double jelly roll fold. Importantly, DUF2961 family proteins form trimers resembling viral capsomers.[25]

Evolution

Comparative studies of proteins classified as jelly roll and

Greek key structures suggest that the Greek key proteins evolved significantly earlier than their more topologically complex jelly roll counterparts.[5] Structural bioinformatics studies comparing virus capsid jelly-roll proteins to other proteins of known structure indicates that the capsid proteins form a well-separated cluster, suggesting that they are subject to a distinctive set of evolutionary constraints.[4] One of the most notable features of viral capsid jelly roll proteins is their ability to form oligomers in a repeated tiling pattern to produce a closed protein shell; the cellular proteins that are most similar in fold and topology are mostly also oligomers.[4] It has been proposed that viral jelly-roll capsid proteins have evolved from cellular jelly-roll proteins, potentially on several independent occasions, at the earliest stages of cellular evolution.[12]

History and nomenclature

The name "jelly roll" was first used for the structure composed of an elaboration on the

cupin fold, a JmjC fold, or a double-stranded beta helix.[34]

References

  1. ^
    PMID 25195746
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  2. ^
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  3. ^
    PMID 1447783
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  4. ^
    PMID 23408879
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  5. ^
    PMID 24244135
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  6. S2CID 4341051
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  7. PMID 6854630
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  8. ^
    PMID 15574324
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  9. ^
    S2CID 2767388
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  10. PMID 21450811
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  11. ^
    PMID 22440622
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  12. ^
    PMID 28265094
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  13. PMID 23850154
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  17. ^
    PMID 18775333
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  18. PMID 28716906
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  19. ^
    S2CID 31542714
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  20. PMID 32132243
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  21. S2CID 221182789
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  22. PMID 29636073
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  23. PMID 21742267
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  24. PMID 23812617
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  25. ^
    PMID 35078938
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  26. PMID 37319262
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  27. PMID 11684019
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  28. PMID 25813344
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  29. PMID 11796220
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  30. PMID 14725774
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  31. S2CID 39174409
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  32. PMID 11264412
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  33. PMID 17301803
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  34. ^
    PMID 23142576
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  35. S2CID 15273763
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  36. S2CID 2616900
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External links
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