4NLW

Poliovirus Polymerase - G289A/C290I Loop Mutant

Summary for 4NLW

• Entry DOI: 10.2210/pdb4nlw/pdb
• Related: 4NLO 4NLP 4NLQ 4NLR 4NLS 4NLT 4NLU 4NLV 4NLX 4NLY
• Descriptor: RNA-directed RNA polymerase 3D-POL, ACETIC ACID, PENTAETHYLENE GLYCOL, ... (5 entities in total)
• Functional Keywords: polymerase, rna dependent rna polymerase, rdrp, virus, viral protein, hydrolase
• Biological source: Human poliovirus 1
• Cellular location: Capsid protein VP0: Virion. Capsid protein VP4: Virion. Capsid protein VP2: Virion. Capsid protein VP3: Virion. Capsid protein VP1: Virion. Protein 2B: Host cytoplasmic vesicle membrane; Peripheral membrane protein; Cytoplasmic side (Potential). Protein 2C: Host cytoplasmic vesicle membrane; Peripheral membrane protein; Cytoplasmic side (Potential). Protein 3A: Host cytoplasmic vesicle membrane; Peripheral membrane protein; Cytoplasmic side (Potential). Protein 3AB: Host cytoplasmic vesicle membrane; Peripheral membrane protein; Cytoplasmic side (Potential). Viral protein genome-linked: Virion. Protease 3C: Host cytoplasm. Protein 3CD: Host cytoplasmic vesicle membrane; Peripheral membrane protein; Cytoplasmic side (Potential). RNA-directed RNA polymerase: Host cytoplasmic vesicle membrane; Peripheral membrane protein; Cytoplasmic side (Potential): P03300
• Total number of polymer chains: 1
• Total formula weight: 53603.74

Authors

Sholders, A.J.,Peersen, O.B. (deposition date: 2013-11-14, release date: 2014-01-22, Last modification date: 2023-09-20)

Primary citation

Sholders, A.J.,Peersen, O.B.
Distinct conformations of a putative translocation element in poliovirus polymerase.
J.Mol.Biol., 426:1407-1419, 2014

PubMed Abstract: The mechanism whereby RNA is translocated by the single subunit viral RNA-dependent RNA polymerases is not yet understood. These enzymes lack homologs of the "O-helix" structures and associated fingers domain movements thought to be responsible for translocation in many DNA-templated polymerases. The structures of multiple picornavirus polymerase elongation complexes suggest that these enzymes use a different molecular mechanism where translocation is not strongly coupled to the opening of the active site following catalysis. Here we present the 2.0- to 2.6-Å-resolution crystal structures and biochemical data for 12 poliovirus polymerase mutants that together show how proper enzyme functions and translocation activity requires conformational flexibility of a loop sequence in the palm domain B-motif. Within the loop, the Ser288-Gly289-Cys290 sequence is shown to play a major role in the catalytic cycle based on RNA binding, processive elongation activity, and single nucleotide incorporation assays. The structures show that Ser288 forms a key hydrogen bond with Asp238, the backbone flexibility of Gly289 is required for translocation competency, and Cys290 modulates the overall elongation activity of the enzyme. Some conformations of the loop represent likely intermediates on the way to forming the catalytically competent closed active site, while others are consistent with a role in promoting translocation of the nascent base pair out of the active site. The loop structure and key residues surrounding it are highly conserved, suggesting that the structural dynamics we observe in poliovirus 3D(pol) are a common feature of viral RNA-dependent RNA polymerases.

PubMed: 24424421
DOI: 10.1016/j.jmb.2013.12.031

Experimental method

X-RAY DIFFRACTION (2.1 Å)