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Polyhedra structures and the evolution of the insect viruses.

Ji X, Axford D, Owen R, Evans G, Ginn HM, Sutton G, Stuart DI - J. Struct. Biol. (2015)

Bottom Line: These structures illustrate the effect of 400 million years of evolution on a system where the crystal lattice is the functionally conserved feature in the face of massive sequence variability.By spreading the contacts over so much of the protein surface the lattice remains robust in the face of many individual changes.Overall these unusual structural constraints seem to have skewed the molecule's evolution so that surface residues are almost as conserved as the internal residues.

View Article: PubMed Central - PubMed

Affiliation: Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, Oxfordshire OX3 7BN, United Kingdom.

No MeSH data available.


Related in: MedlinePlus

Purine binding. The bottom panel helps orient the reader to the position of the depicted in the other panels. Side and face-on views of a unit cell are shown, with smoothed maps representing polyhedrin trimers similar to Fig. 2. In the side view the 2 trimers closest to the viewer are shown only as outlines so that the close proximity of the NTPs to the surface of the unit cell can be clearly seen. To improve clarity the positions of the ATP (magenta) and GTP (blue) moieties for just CPV1 are shown in this panel. As a reference the positions of the CPV1 ATP and GTP have been replicated across the other panels. The yellow box shows the area represented in other 9 panels. For the nine cypovirus types the same viewpoint is shown. Protein chains are coloured separately and consistently between types. Side chains of residues which either interact with nucleotides or occupy nucleotide pockets are shown. The view has narrow clipping planes to facilitate interpretation. The positions of the calcium ion in CPV5 and C142 in CPV17 are indicated.
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f0020: Purine binding. The bottom panel helps orient the reader to the position of the depicted in the other panels. Side and face-on views of a unit cell are shown, with smoothed maps representing polyhedrin trimers similar to Fig. 2. In the side view the 2 trimers closest to the viewer are shown only as outlines so that the close proximity of the NTPs to the surface of the unit cell can be clearly seen. To improve clarity the positions of the ATP (magenta) and GTP (blue) moieties for just CPV1 are shown in this panel. As a reference the positions of the CPV1 ATP and GTP have been replicated across the other panels. The yellow box shows the area represented in other 9 panels. For the nine cypovirus types the same viewpoint is shown. Protein chains are coloured separately and consistently between types. Side chains of residues which either interact with nucleotides or occupy nucleotide pockets are shown. The view has narrow clipping planes to facilitate interpretation. The positions of the calcium ion in CPV5 and C142 in CPV17 are indicated.

Mentions: The purines are found at three 2-fold axes on the facets such that there are eight symmetry equivalent purine clusters per facet (Fig. 4). Each has complex interactions with the neighbouring protein, including variable regions V1, V3, V4, V2c and V5 contributed by four different polypeptide chains, forming diverse interactions between the facets of unit cells in different polyhedra (Fig. S6). In CPV18 purine binding is almost identical to CPV1 in that GTP hydrogen bonds with V2c and V1 while ATP is supported by two V4 regions from different polypeptide chains. The ATP and GTP bases stack with each other and with the phenol ring of Y172. There are two substitutions in the binding pocket, K154H and R155V. Residue 155 interacts via the main chain nitrogen, and is thus sequence independent, whilst at residue 154 both the lysine and histidine side chain NH groups hydrogen bond with ATP phosphates.


Polyhedra structures and the evolution of the insect viruses.

Ji X, Axford D, Owen R, Evans G, Ginn HM, Sutton G, Stuart DI - J. Struct. Biol. (2015)

Purine binding. The bottom panel helps orient the reader to the position of the depicted in the other panels. Side and face-on views of a unit cell are shown, with smoothed maps representing polyhedrin trimers similar to Fig. 2. In the side view the 2 trimers closest to the viewer are shown only as outlines so that the close proximity of the NTPs to the surface of the unit cell can be clearly seen. To improve clarity the positions of the ATP (magenta) and GTP (blue) moieties for just CPV1 are shown in this panel. As a reference the positions of the CPV1 ATP and GTP have been replicated across the other panels. The yellow box shows the area represented in other 9 panels. For the nine cypovirus types the same viewpoint is shown. Protein chains are coloured separately and consistently between types. Side chains of residues which either interact with nucleotides or occupy nucleotide pockets are shown. The view has narrow clipping planes to facilitate interpretation. The positions of the calcium ion in CPV5 and C142 in CPV17 are indicated.
© Copyright Policy - CC BY
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4597613&req=5

f0020: Purine binding. The bottom panel helps orient the reader to the position of the depicted in the other panels. Side and face-on views of a unit cell are shown, with smoothed maps representing polyhedrin trimers similar to Fig. 2. In the side view the 2 trimers closest to the viewer are shown only as outlines so that the close proximity of the NTPs to the surface of the unit cell can be clearly seen. To improve clarity the positions of the ATP (magenta) and GTP (blue) moieties for just CPV1 are shown in this panel. As a reference the positions of the CPV1 ATP and GTP have been replicated across the other panels. The yellow box shows the area represented in other 9 panels. For the nine cypovirus types the same viewpoint is shown. Protein chains are coloured separately and consistently between types. Side chains of residues which either interact with nucleotides or occupy nucleotide pockets are shown. The view has narrow clipping planes to facilitate interpretation. The positions of the calcium ion in CPV5 and C142 in CPV17 are indicated.
Mentions: The purines are found at three 2-fold axes on the facets such that there are eight symmetry equivalent purine clusters per facet (Fig. 4). Each has complex interactions with the neighbouring protein, including variable regions V1, V3, V4, V2c and V5 contributed by four different polypeptide chains, forming diverse interactions between the facets of unit cells in different polyhedra (Fig. S6). In CPV18 purine binding is almost identical to CPV1 in that GTP hydrogen bonds with V2c and V1 while ATP is supported by two V4 regions from different polypeptide chains. The ATP and GTP bases stack with each other and with the phenol ring of Y172. There are two substitutions in the binding pocket, K154H and R155V. Residue 155 interacts via the main chain nitrogen, and is thus sequence independent, whilst at residue 154 both the lysine and histidine side chain NH groups hydrogen bond with ATP phosphates.

Bottom Line: These structures illustrate the effect of 400 million years of evolution on a system where the crystal lattice is the functionally conserved feature in the face of massive sequence variability.By spreading the contacts over so much of the protein surface the lattice remains robust in the face of many individual changes.Overall these unusual structural constraints seem to have skewed the molecule's evolution so that surface residues are almost as conserved as the internal residues.

View Article: PubMed Central - PubMed

Affiliation: Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, Oxfordshire OX3 7BN, United Kingdom.

No MeSH data available.


Related in: MedlinePlus