Structural and Functional Characterization of K339T Substitution Identified in the PB2 Subunit Cap-binding Pocket of Influenza A Virus

Liu, Yong; Qin, Kun; Meng, Geng; Zhang, Jinfang; Zhou, Jianfang; Zhao, Guangyu; Luo, Ming; Zheng, Xiaofeng

doi:10.1074/jbc.m112.392878

Cited by 35 publications

(36 citation statements)

References 49 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…When PB2cap binding interactions are placed in the context of the full-length viral polymerase assembly, the interactions with the β-phosphate will be visible with more clarity. Like 5EG8, the sidechain of His432 assumes two conformations (Figures 1a and 2), whereas the sidechain of Asn429 assumes only one conformation when bound to m 7 GTP, like the single conformation observed in 4ENF (Figures 1b and 2) [10,11]. Lastly, it was observed that sidechains of Phe404, Met431, and Gln406 form a hydrophobic pocket to accommodate the methyl group at position 7 of the cap (Figure 2).…”

Section: Structure Of Mutant Pb2cap From A/california/07/2009 (H1n1) mentioning

confidence: 85%

“…In addition, interactions with α, β, and γ-phosphates in the cap are different in 4CB4 versus 5EG7. Comparisons between 5EG7 and PB2cap from A/Hong Kong/1/68 (H3N2) bound to m 7 GTP (PDB code: 4EQK) [11] revealed similar interactions with the cap, except the side chain of Phe323 is shifted in 4EQK, reducing T-shaped interactions with the guanine moiety (Figure 3b,g) [10].…”

Section: Structural Comparisons Between 5eg7 and Other Structuresmentioning

confidence: 99%

“…Alternatively, the structure of PB2cap from A/PR/8/34 (H1N1) (PDB code: 4ENF) [11] does not feature multiple conformations of Lys376, Asn429, or His432 (Figure 1b). This comparison suggests that the sidechain orientation of binding site residues may be slightly different in unliganded PB2scap from different strains of H1N1 influenza A virus, despite highly conserved amino acid sequences [10].…”

Section: Data Processing and Refinementmentioning

confidence: 99%

“…In addition to the comparison mentioned in Section 2.4, additional B-factor and RMSD comparisons were drawn between 5WOP [13] and 5EG7 [10], 4ENF [11] (Table 2 and Figure 5). These comparisons indicate that these structural changes are universal across different strains.…”

Section: Structural Comparisons Between Other Pb2cap Structuresmentioning

confidence: 99%

“…Figure 6. B-putty drawings [26] of 5WOP Chain A [13], 5EG7 [10], 4ENF [11], 4CB5, and 4CB7 Chain A [12]. The diameter of the tubes is proportional to the B-factor.…”

Section: Structural Comparisons Between Other Pb2cap Structuresmentioning

confidence: 99%

See 4 more Smart Citations

Characterization of the PB2 Cap Binding Domain Accelerates Inhibitor Design

et al. 2018

Self Cite

View full text Add to dashboard Cite

X-ray crystallographic structural determinations of the PB2 cap binding domain (PB2cap) have improved the conformational characterization of the RNA-dependent RNA polymerase machinery (PA, PB2, and PB1) of the influenza virus. Geometrically, the catalytic PB1 subunit resembles the palm of a human hand. PA lies near the thumb region, and PB2 lies near the finger region. PB2 binds the cap moiety in the pre-mRNA of the host cell, while the endonuclease of PA cleaves the pre-mRNA 10-13 nucleotides downstream. The truncated RNA piece performs as a primer for PB1 to synthesize the viral mRNA. Precisely targeting PB2cap with a small molecule inhibitor will halt viral proliferation via interference of the cap-snatching activity. Wild-type and mutant PB2cap from A/California/07/2009 H1N1 were expressed in Escherichia coli, purified by nickel affinity and size exclusion chromatography, crystallized, and subjected to X-ray diffraction experiments. The crystal of mutant PB2cap liganded with m 7 GTP was prepared by co-crystallization. Structures were solved by the molecular replacement method, refined, and deposited in the Protein Data Bank (PDB). Structural determination and comparative analyses of these structures revealed the functions of Glu361, Lys376, His357, Phe404, Phe323, Lys339, His432, Asn429, Gln406, and Met401 in PB2cap, and the dissociation of the influenza A PB2cap C-terminal subdomain (residues 446-479) upon ligand binding. Understanding the role of these residues will aid in the ultimate development of a small-molecule inhibitor that binds both Influenza A and B virus PB2cap.

show abstract

Section: Structure Of Mutant Pb2cap From A/california/07/2009 (H1n1) mentioning

confidence: 85%

Section: Structural Comparisons Between 5eg7 and Other Structuresmentioning

confidence: 99%

Section: Data Processing and Refinementmentioning

confidence: 99%

Section: Structural Comparisons Between Other Pb2cap Structuresmentioning

confidence: 99%

“…Figure 6. B-putty drawings [26] of 5WOP Chain A [13], 5EG7 [10], 4ENF [11], 4CB5, and 4CB7 Chain A [12]. The diameter of the tubes is proportional to the B-factor.…”

Section: Structural Comparisons Between Other Pb2cap Structuresmentioning

confidence: 99%

See 3 more Smart Citations

Characterization of the PB2 Cap Binding Domain Accelerates Inhibitor Design

et al. 2018

Self Cite

View full text Add to dashboard Cite

show abstract

Structure and Function of Influenza Virus Ribonucleoprotein

Tang

Shaw

2018

Subcellular Biochemistry

View full text Add to dashboard Cite

Influenza is a negative-sense single-stranded RNA virus with segmented genome. Each segment is encapsidated by a ribonucleoprotein (RNP) complex composed of RNA-dependent RNA polymerase (RdRP) and multiple copies of nucleoprotein (NP). The RNP complex plays a crucial role in viral life cycle, supporting and regulating transcription and replication of viral genome in infected cells. The structural characterization of RdRP and RNP in recent years has shed light on its functions and mechanism of action. In this review, we summarize current understanding on the structure of RNP complex, as well as the structure of each subunit. Crucial functions of RNP are also discussed.

show abstract

Common and unique features of viral RNA-dependent polymerases

Velthuis

2014

Cell. Mol. Life Sci.

224

210

View full text Add to dashboard Cite

Eukaryotes and bacteria can be infected with a wide variety of RNA viruses. On average, these pathogens share little sequence similarity and use different replication and transcription strategies. Nevertheless, the members of nearly all RNA virus families depend on the activity of a virally encoded RNA-dependent polymerase for the condensation of nucleotide triphosphates. This review provides an overview of our current understanding of the viral RNA-dependent polymerase structure and the biochemistry and biophysics that is involved in replicating and transcribing the genetic material of RNA viruses.

show abstract

Structural and Functional Characterization of K339T Substitution Identified in the PB2 Subunit Cap-binding Pocket of Influenza A Virus

Cited by 35 publications

References 49 publications

Characterization of the PB2 Cap Binding Domain Accelerates Inhibitor Design

Characterization of the PB2 Cap Binding Domain Accelerates Inhibitor Design

Structure and Function of Influenza Virus Ribonucleoprotein

Common and unique features of viral RNA-dependent polymerases

Contact Info

Product

Resources

About