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Solution structure of the 2A protease from a common cold agent, human rhinovirus C2, strain W12.

Lee W, Watters KE, Troupis AT, Reinen NM, Suchy FP, Moyer KL, Frederick RO, Tonelli M, Aceti DJ, Palmenberg AC, Markley JL - PLoS ONE (2014)

Bottom Line: The catalytic triad consists of conserved Cys (C105), His (H34), and Asp (D18) residues.The backbone of C2 2Apro superimposed closely (1.41-1.81 Å rmsd) with those of orthologs from RV-A2, coxsackie B4 (CB4), and enterovirus 71 (EV71) having sequence identities between 40% and 60%.Comparison of the structures suggest that the differential functional properties of C2 2Apro stem from its unique surface charge, high proportion of surface aromatics, and sequence surrounding the di-tyrosine flap.

View Article: PubMed Central - PubMed

Affiliation: National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, Madison, Wisconsin, United States of America.

ABSTRACT
Human rhinovirus strains differ greatly in their virulence, and this has been correlated with the differing substrate specificity of the respective 2A protease (2Apro). Rhinoviruses use their 2Apro to cleave a spectrum of cellular proteins important to virus replication and anti-host activities. These enzymes share a chymotrypsin-like fold stabilized by a tetra-coordinated zinc ion. The catalytic triad consists of conserved Cys (C105), His (H34), and Asp (D18) residues. We used a semi-automated NMR protocol developed at NMRFAM to determine the solution structure of 2Apro (C105A variant) from an isolate of the clinically important rhinovirus C species (RV-C). The backbone of C2 2Apro superimposed closely (1.41-1.81 Å rmsd) with those of orthologs from RV-A2, coxsackie B4 (CB4), and enterovirus 71 (EV71) having sequence identities between 40% and 60%. Comparison of the structures suggest that the differential functional properties of C2 2Apro stem from its unique surface charge, high proportion of surface aromatics, and sequence surrounding the di-tyrosine flap.

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Cross-eyed stereoscopic representations of 2Apro structures.(A) Superimposition of backbones of the four proteases showing their structural similarity. Pairwise rmsd values for C2 relative to both A2 and CB4 proteases are both 1.809 Å, while to EV71 protease is 1.4 Å. Poisson-Boltzmann electrostatic potential surfaces are illustrated by PyMOL [29] for (B) C2, (C) A2,(D) CB4 and (E) EV71 2Apro. Each structure is shown in the same orientation. (F) Comparison of the positions of the bll−cll and cll−dll loops in the structures of C2 (blue), A2 (red), CB4 (green), and EV71 (orange) 2Apro.
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pone-0097198-g008: Cross-eyed stereoscopic representations of 2Apro structures.(A) Superimposition of backbones of the four proteases showing their structural similarity. Pairwise rmsd values for C2 relative to both A2 and CB4 proteases are both 1.809 Å, while to EV71 protease is 1.4 Å. Poisson-Boltzmann electrostatic potential surfaces are illustrated by PyMOL [29] for (B) C2, (C) A2,(D) CB4 and (E) EV71 2Apro. Each structure is shown in the same orientation. (F) Comparison of the positions of the bll−cll and cll−dll loops in the structures of C2 (blue), A2 (red), CB4 (green), and EV71 (orange) 2Apro.

Mentions: Superimposition of the 3D structures of C2 and CB4 2Apro (Figure 8A; NMR model 1) gave a lower pairwise backbone rmsd (1.809 Å) than might have been expected from the 41% sequence identity. Superimposition of C2 and EV71 2Apro models (40% sequence identity) yielded the lowest pairwise rmsd (1.4 Å). When electrostatic potential surfaces were generated with the contouring value set to ±10 kT/e (Figure 8 B,C,D,E), all four enzymes exhibited similar negative charge surface distributions (red) despite the overall sequence differences. However, the C2 enzyme (Figure 8B) lacks several intensely basic surface patches (blue) displayed by A2 (Figure 8C), CB4 (Figure 8D) and EV71 (Figure 8E). Examples of sequence differences at aligned positions that result in a more acidic pI for the C2 sequence overall (4.62) than for A2 (5.43), CB4 (5.20), or EV71 (6.04) include C2 G39/A2 R40 and C2 L63/A2 K64. Actually, the C2 enzyme has the most acidic pI of known 2Apro sequences [8], [9].


Solution structure of the 2A protease from a common cold agent, human rhinovirus C2, strain W12.

Lee W, Watters KE, Troupis AT, Reinen NM, Suchy FP, Moyer KL, Frederick RO, Tonelli M, Aceti DJ, Palmenberg AC, Markley JL - PLoS ONE (2014)

Cross-eyed stereoscopic representations of 2Apro structures.(A) Superimposition of backbones of the four proteases showing their structural similarity. Pairwise rmsd values for C2 relative to both A2 and CB4 proteases are both 1.809 Å, while to EV71 protease is 1.4 Å. Poisson-Boltzmann electrostatic potential surfaces are illustrated by PyMOL [29] for (B) C2, (C) A2,(D) CB4 and (E) EV71 2Apro. Each structure is shown in the same orientation. (F) Comparison of the positions of the bll−cll and cll−dll loops in the structures of C2 (blue), A2 (red), CB4 (green), and EV71 (orange) 2Apro.
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Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4061012&req=5

pone-0097198-g008: Cross-eyed stereoscopic representations of 2Apro structures.(A) Superimposition of backbones of the four proteases showing their structural similarity. Pairwise rmsd values for C2 relative to both A2 and CB4 proteases are both 1.809 Å, while to EV71 protease is 1.4 Å. Poisson-Boltzmann electrostatic potential surfaces are illustrated by PyMOL [29] for (B) C2, (C) A2,(D) CB4 and (E) EV71 2Apro. Each structure is shown in the same orientation. (F) Comparison of the positions of the bll−cll and cll−dll loops in the structures of C2 (blue), A2 (red), CB4 (green), and EV71 (orange) 2Apro.
Mentions: Superimposition of the 3D structures of C2 and CB4 2Apro (Figure 8A; NMR model 1) gave a lower pairwise backbone rmsd (1.809 Å) than might have been expected from the 41% sequence identity. Superimposition of C2 and EV71 2Apro models (40% sequence identity) yielded the lowest pairwise rmsd (1.4 Å). When electrostatic potential surfaces were generated with the contouring value set to ±10 kT/e (Figure 8 B,C,D,E), all four enzymes exhibited similar negative charge surface distributions (red) despite the overall sequence differences. However, the C2 enzyme (Figure 8B) lacks several intensely basic surface patches (blue) displayed by A2 (Figure 8C), CB4 (Figure 8D) and EV71 (Figure 8E). Examples of sequence differences at aligned positions that result in a more acidic pI for the C2 sequence overall (4.62) than for A2 (5.43), CB4 (5.20), or EV71 (6.04) include C2 G39/A2 R40 and C2 L63/A2 K64. Actually, the C2 enzyme has the most acidic pI of known 2Apro sequences [8], [9].

Bottom Line: The catalytic triad consists of conserved Cys (C105), His (H34), and Asp (D18) residues.The backbone of C2 2Apro superimposed closely (1.41-1.81 Å rmsd) with those of orthologs from RV-A2, coxsackie B4 (CB4), and enterovirus 71 (EV71) having sequence identities between 40% and 60%.Comparison of the structures suggest that the differential functional properties of C2 2Apro stem from its unique surface charge, high proportion of surface aromatics, and sequence surrounding the di-tyrosine flap.

View Article: PubMed Central - PubMed

Affiliation: National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, Madison, Wisconsin, United States of America.

ABSTRACT
Human rhinovirus strains differ greatly in their virulence, and this has been correlated with the differing substrate specificity of the respective 2A protease (2Apro). Rhinoviruses use their 2Apro to cleave a spectrum of cellular proteins important to virus replication and anti-host activities. These enzymes share a chymotrypsin-like fold stabilized by a tetra-coordinated zinc ion. The catalytic triad consists of conserved Cys (C105), His (H34), and Asp (D18) residues. We used a semi-automated NMR protocol developed at NMRFAM to determine the solution structure of 2Apro (C105A variant) from an isolate of the clinically important rhinovirus C species (RV-C). The backbone of C2 2Apro superimposed closely (1.41-1.81 Å rmsd) with those of orthologs from RV-A2, coxsackie B4 (CB4), and enterovirus 71 (EV71) having sequence identities between 40% and 60%. Comparison of the structures suggest that the differential functional properties of C2 2Apro stem from its unique surface charge, high proportion of surface aromatics, and sequence surrounding the di-tyrosine flap.

Show MeSH
Related in: MedlinePlus