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Structure paper

TitleDirect observation of backtracking by influenza A and B polymerases upon consecutive incorporation of the nucleoside analog T1106.
Journal, issue, pagesCell Rep, Vol. 42, Issue 1, Page 111901, Year 2023
Publish dateJan 31, 2023
AuthorsTomas Kouba / Anna Dubankova / Petra Drncova / Elisa Donati / Pietro Vidossich / Valentina Speranzini / Alex Pflug / Johanna Huchting / Chris Meier / Marco De Vivo / Stephen Cusack /
PubMed AbstractThe antiviral pseudo-base T705 and its de-fluoro analog T1106 mimic adenine or guanine and can be competitively incorporated into nascent RNA by viral RNA-dependent RNA polymerases. Although ...The antiviral pseudo-base T705 and its de-fluoro analog T1106 mimic adenine or guanine and can be competitively incorporated into nascent RNA by viral RNA-dependent RNA polymerases. Although dispersed, single pseudo-base incorporation is mutagenic, consecutive incorporation causes polymerase stalling and chain termination. Using a template encoding single and then consecutive T1106 incorporation four nucleotides later, we obtained a cryogenic electron microscopy structure of stalled influenza A/H7N9 polymerase. This shows that the entire product-template duplex backtracks by 5 nt, bringing the singly incorporated T1106 to the +1 position, where it forms an unexpected T1106:U wobble base pair. Similar structures show that influenza B polymerase also backtracks after consecutive T1106 incorporation, regardless of whether prior single incorporation has occurred. These results give insight into the unusual mechanism of chain termination by pyrazinecarboxamide base analogs. Consecutive incorporation destabilizes the proximal end of the product-template duplex, promoting irreversible backtracking to a more energetically favorable overall configuration.
External linksCell Rep / PubMed:36596301
MethodsEM (single particle)
Resolution2.34 - 3.12 Å
Structure data

EMDB-14144, PDB-7qtl:
Influenza A/H7N9 polymerase elongation complex
Method: EM (single particle) / Resolution: 2.48 Å

EMDB-14222, PDB-7r0e:
Early transcription elongation state of influenza A/H7N9 polymerase backtracked due to double incoproation of nucleotide analogue T1106 and with singly incoporated T1106 at the +1 position
Method: EM (single particle) / Resolution: 2.51 Å

EMDB-14240, PDB-7r1f:
Early transcription elongation state of influenza B polymerase backtracked due to double incoproation of nucleotide analogue T1106
Method: EM (single particle) / Resolution: 2.58 Å

EMDB-14857, PDB-7zpl:
Symmetric dimer of influenza A/H7N9 polymerase bound to 5' vRNA hook
Method: EM (single particle) / Resolution: 3.12 Å

EMDB-14858, PDB-7zpm:
Influenza A/H7N9 polymerase apo-protein dimer complex
Method: EM (single particle) / Resolution: 2.81 Å

EMDB-15984, PDB-8bdr:
Early transcription elongation state of influenza B/Mem polymerase backtracked due to double incoproation of nucleotide analogue T1106 and with singly incoporated T1106 at the U +1 position
Method: EM (single particle) / Resolution: 2.7 Å

EMDB-15996, PDB-8be0:
Early transcription elongation state of influenza B/Mem polymerase backtracked due to double incoproation of nucleotide analogue T1106 and with singly incoporated T1106 at the C +1 position
Method: EM (single particle) / Resolution: 2.34 Å

EMDB-16006, PDB-8bek:
Early transcription elongation state of influenza A/H7N9 backtracked polymerase with singly incoporated T1106 at the U +1 position
Method: EM (single particle) / Resolution: 2.86 Å

EMDB-16013, PDB-8bf5:
Early transcription elongation state of influenza A/H7N9 polymerase stalled with incoming GTP analogue
Method: EM (single particle) / Resolution: 2.96 Å

Chemicals

ChemComp-2TM:
5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine

ChemComp-MG:
Unknown entry

ChemComp-GTA:
P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE

ChemComp-HOH:
WATER

ChemComp-G2P:
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / GMP-CPP, energy-carrying molecule analogue*YM

Source
  • influenza a virus (a/zhejiang/dtid-zju01/2013(h7n9))
  • influenza a virus
  • influenza b virus (b/memphis/13/2003)
  • influenza b virus
  • influenza b virus (b/acre/117700/2012)
  • influenza b virus (b/kaliningrad/rii06/2012)
KeywordsVIRAL PROTEIN / Influenza / viral RNA-dependent RNA polymerase; cap-dependent transcription / viral RNA-dependent RNA polymerase; antiviral drug; nucleoside analogue; T705 (favipiravir); T1106; cap-dependent transcription; backtracking; / H7N9 / viral RNA-dependent RNA polymerase / viral RNA-dependent RNA polymerase; / nucleoside analogue

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