A comparative analysis of parechovirus protein structures with other picornaviruses

Figures

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  Figure 1.. Schematic representation of parechovirus genome. Genomic ssRNA has viral protein VPg attached to its 5′ end. 5′ UTR contains clover-leaf and IRES elements necessary for RNA replication and protein synthesis initiation. The 3′ UTR contains a stem-loop structure important for virus replication as well as a polyA-tail. Virus protein-coding regions are highlighted with boxes. P1, P2 and P3 coding regions are delineated above. 2ANPGP protein region is shown in brackets to indicate its presence in 0–2 non-identical copies.

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  Figure 2.. Structural details of parechovirus capsid. (a) Schematic view of parechovirus capsid down a twofold axis of symmetry. The icosahedral capsid consists of 60 protomers, each composed of structural proteins VP0 (orange), VP1 (green) and VP3 (light blue). The enlarged view presents modelled structural proteins for PeV-A3 (PDB ID: 6GV4). Pentagon, triangle and oval indicate fivefold, threefold and twofold symmetry axes, respectively. (b) Radially colour coded (steel blue, 130 Å; sky blue, 135 Å; khaki, 140 Å; orange, 145 Å; firebrick, 150 Å) surface presentation of PeV-A3 capsid resolved by cryo-EM (EMD-0069), antibody fragment density subtracted using UCSF Chimera [41]. Capsid view is the same as in panel (a). (c) Ordered ssRNA at the inner surface of the PeV-A3 capsid beneath the fivefold vertices (EMD-0069). Radially colour coded inner surface of the capsid (blue, 100 Å; light blue, 115 Å; khaki, 130 Å; orange, 140 Å; firebrick, 150 Å) and modelled ssRNA stretches (blue slabs for bases) in contact with VP3 N-terminal residues Leu16 to Arg26 (light blue) viewed down fivefold symmetry axis (PDB ID: 6GV4). Boxed segment is enlarged and slightly rotated in (d) to show RNA base stacking…

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  Figure 3.. Functional motifs in 2AH-NC, 2ANPGP, 2B and 2C. (a) Multiple sequence alignment of regions encompassing the active site amino acid residues in phospholipase A and acyltransferase 3 (PLAAT3) with parechovirus 2AH-NC proteins. Residue positions corresponding to PLAAT3 His23, His35 and NC-box are highlighted in boxes. (b) C-terminal sequences of 2ANPGP ‘self-cleaving’ motifs from parechoviruses and foot-and-mouth disease virus aligned to the position of a break in polyprotein chain. Conserved residues of DxExNPGP motif are highlighted in boxes. (c) Prediction of transmembrane regions in parechovirus 2B proteins made in Phobius [62]. Plots are aligned on the x-axis according to protein sequence alignment. The scale of the y-axis is offset by 0.5. (d) Multiple sequence alignments of functional regions in parecho- and poliovirus 2C proteins. Conserved characteristic motifs are highlighted in boxes and labelled on top. Residues in positions with conservation over 35% are shown in colour. Sequences used in the alignment are indicated in table 1.

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  Figure 4.. Parechovirus 3Cpro homology model and specificity. (a) Structure model of PeV-A1 Harris 3Dpro based on I-TASSER structure prediction [114]. Active site amino acid residues are labelled, and loops β3–β4, β8–β9 and β10–β11 are highlighted in purple, yellow and orange, respectively. (b) Cleavage site sequences in PeV-A1 Harris polyprotein. VP0↓VP3 and VP3↓VP1 sites have been confirmed experimentally [1]; other sites are predicted by homology. The sequence logo on top depicts amino acid residue frequency in positions around the cleavage site [115]. (c) Multiple sequence alignments of loop regions β3-β4, β8-β9, β10-β11 of parechovirus and poliovirus (PV1) 3Cpro. Residues in positions with conservation over 35% are shown in colour. Sequences used in the alignment are indicated in table 1.

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  Figure 5.. PeV-A1 3Dpol homology model-based structure and conservation. (a) Homology model and surface representation of PeV-A1 Harris 3Dpol based on I-TASSER structure prediction [114]. Fingers, palm and thumb domains [127] are coloured in orange, grey and blue, respectively. Conserved motifs A, B, C, D, F and G [128] are highlighted in yellow, green, red, cyan, salmon, olive green and purple, respectively. (b) Binding pocket for template RNA +2 nucleotide. Poliovirus (PV1) 3Dpol with template RNA (PDB ID: 3OL6) is shown in light grey. (c) Interaction with product RNA +3 nucleotide 2′OH. PV1 3Dpol is depicted as in b. (d) PeV-A1 3Dpol homology model coloured by amino acid conservation. (e) Multiple sequence alignment of conserved sequence motifs in PeV-A1 Harris and coxsackievirus A16 (CVA16), PV1, foot-and-mouth disease virus (FMDV) and encephalomyocarditis virus (EMCV) 3Dpol proteins. PDB IDs are given for the proteins with experimentally solved structure. Residues in positions with conservation over 35% are shown in colour.