5Y6Z

Crystal structure of the coxsackievirus A16 polymerase elongation complex

Summary for 5Y6Z

• Entry DOI: 10.2210/pdb5y6z/pdb
• Descriptor: Genome polyprotein, Template RNA (33-MER), Product RNA (14-MER), ... (7 entities in total)
• Functional Keywords: polymerase, transferase-rna complex, transferase/rna
• Biological source: Coxsackievirus A16; More
• Cellular location: Host cytoplasmic vesicle membrane ; Peripheral membrane protein ; Cytoplasmic side : L7WS61
• Total number of polymer chains: 6
• Total formula weight: 138442.66

Authors

Bi, P.,Shu, B.,Gong, P. (deposition date: 2017-08-15, release date: 2017-12-27, Last modification date: 2023-11-22)

Primary citation

Bi, P.,Shu, B.,Gong, P.
Crystal structure of the coxsackievirus A16 RNA-dependent RNA polymerase elongation complex reveals novel features in motif A dynamics
Virol Sin, 32:548-552, 2017

PubMed Abstract: The RNA-dependent RNA polymerases (RdRPs) encoded by RNA viruses represent a unique class of nucleic acid polymerases. Unlike other classes of single-subunit polymerases, viral RdRPs have evolved a unique conformational change in their palm domain to close the active site during catalysis. The hallmark of this conformational change is the backbone shift of the polymerase motif A from an "open" state to a "closed" state, allowing two universally conserved aspartic acid residues to orient toward each other for divalent metal binding and catalysis. The "closed" motif A conformation was only observed upon the binding of correct NTP in RdRP catalytic complexes or under rare conditions such as induced by a bound lutetium ion or a bound glutamate molecule. By solving the crystal structure of the catalytic elongation complex of the coxsackievirus RdRP, we in this work observed for the first time the "closed" motif A conformation in the absence of an NTP substrate or other conformational-change-inducing factors. This observation emphasizes the intrinsic dynamic features of viral RdRP motif A, and solidifies the structural basis for how this important structural element participates in catalytic events of the RdRPs.

PubMed: 29164396
DOI: 10.1007/s12250-017-4066-8

Experimental method

X-RAY DIFFRACTION (2.5 Å)