Exaptation of Inactivated Host Enzymes for Structural Roles in Orthopoxviruses and Novel Folds of Virus Proteins Revealed by Protein Structure Modeling

Mutz, Pascal; Resch, Wolfgang; Faure, Guilhem; Senkevich, Tatiana G.; Koonin, Eugene V.; Moss, Bernard

doi:10.1128/mbio.00408-23

Cited by 11 publications

(7 citation statements)

References 94 publications

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“…For example, ab initio modeling has been used to broadly identify pathogen mimics of host proteins, 9 to identify evolutionary connections among pathogen effectors, 10 to expand an understanding of immunoglobulin gene family evolution, 11 and to provide insight into the distant cellular origins of structural proteins found in viruses. 12 In this study, we use AlphaFold to enable searches for hidden homology in viral proteomes and inform the mechanistic study of host-pathogen interfaces.…”

Section: Introductionmentioning

confidence: 99%

Structural homology screens reveal host-derived poxvirus protein families impacting inflammasome activity

et al. 2023

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Section: Introductionmentioning

confidence: 99%

Structural homology screens reveal host-derived poxvirus protein families impacting inflammasome activity

et al. 2023

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“…67-310) corresponding to an inactive DNA ligase composed of a catalytic subdomain followed by an Oligonucleotide/oligosaccharide-Binding (OB)-fold domain [27]. The ligase domain had been identified in the MPXV processivity factor protein A20 [23] and in the Alphafold 2 predicted protein structures of orthopoxviruses [28]. The Alphafold 2 prediction of A20 could be fitted reliably into the electron density after adjustment of the relative orientation of the…”

Section: Resultsmentioning

confidence: 99%

Structure and flexibility of the DNA polymerase holoenzyme of vaccinia virus

Burmeister,

Boutin,

Balestra

et al. 2024

PLoS Pathog

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The year 2022 was marked by the mpox outbreak caused by the human monkeypox virus (MPXV), which is approximately 98% identical to the vaccinia virus (VACV) at the sequence level with regard to the proteins involved in DNA replication. We present the production in the baculovirus-insect cell system of the VACV DNA polymerase holoenzyme, which consists of the E9 polymerase in combination with its co-factor, the A20-D4 heterodimer. This led to the 3.8 Å cryo-electron microscopy (cryo-EM) structure of the DNA-free form of the holoenzyme. The model of the holoenzyme was constructed from high-resolution structures of the components of the complex and the A20 structure predicted by AlphaFold 2. The structures do not change in the context of the holoenzyme compared to the previously determined crystal and NMR structures, but the E9 thumb domain became disordered. The E9-A20-D4 structure shows the same compact arrangement with D4 folded back on E9 as observed for the recently solved MPXV holoenzyme structures in the presence and the absence of bound DNA. A conserved interface between E9 and D4 is formed by a cluster of hydrophobic residues. Small-angle X-ray scattering data show that other, more open conformations of E9-A20-D4 without the E9-D4 contact exist in solution using the flexibility of two hinge regions in A20. Biolayer interferometry (BLI) showed that the E9-D4 interaction is indeed weak and transient in the absence of DNA although it is very important, as it has not been possible to obtain viable viruses carrying mutations of key residues within the E9-D4 interface.

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“…67-310) composed more precisely of a catalytic subdomain followed by an OB-domain. The ligase domain has been identified in the MPXV processivity factor protein A22 [18] and in the Alphafold 2 predicted protein structures of orthopoxviruses [22]. The Alphafold 2 prediction of A20 could be fitted reliably into the electron density adjusting the relative orientation of the domains A20 1-50 (Fig 2c), ligase domain and A20 304-426 although for the final structure a model based on the very similar MPXV A22 structure has been used.…”

Section: Resultsmentioning

confidence: 99%

Structure and flexibility of the DNA polymerase holoenzyme of vaccinia virus

Burmeister,

Boutin,

Balestra

et al. 2023

Preprint

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The year 2022 was marked by the mpox outbreak caused by human monkeypox virus (MPXV), which is about 98 % identical to vaccinia virus (VACV) at the sequence level regarding the proteins involved in DNA replication. We present the strategy for the production of the VACV DNA polymerase holoenzyme composed of the E9 polymerase associated with its co-factor, the A20-D4 heterodimer, which led to the 3.8 Å cryo-electron microscopy (cryo-EM) structure of the DNA-free form of the holoenzyme. Model building used high-resolution structures of components of the complex and the A20 structure predicted by AlphaFold 2. The structure of E9 does not change in context of the holoenzyme compared to the crystal structure. As for the MPXV holoenzyme, a contact between E9 and D4 is mediated by a cluster of hydrophobic residues. The holoenzyme structure is quite compact and surprisingly similar to the MPXV holoenzyme in presence of a DNA template, with the exception of a movement of the finger domain and the thumb domain, which becomes ordered in presence of DNA. Even in absence of DNA, the VACV holoenzyme structure is too compact for an agreement with SAXS data. This suggests the presence of more open conformations in solution, which are also predicted by Alphafold 2 indicating hinge regions located within A20. Using biolayer interferometry we showed that indeed, the E9-D4 interaction is weak and transient although very important as it has not been possible to obtain viable viruses carrying mutations of key residues in the E9-D4 interface.

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Exaptation of Inactivated Host Enzymes for Structural Roles in Orthopoxviruses and Novel Folds of Virus Proteins Revealed by Protein Structure Modeling

Abstract: Protein structures are more strongly conserved in evolution than are amino acid sequences. Comparative structural analysis is particularly important for inferring the origins of viral proteins that typically evolve at high rates.

Cited by 11 publications

References 94 publications

Structural homology screens reveal host-derived poxvirus protein families impacting inflammasome activity

Structural homology screens reveal host-derived poxvirus protein families impacting inflammasome activity

Structure and flexibility of the DNA polymerase holoenzyme of vaccinia virus

Structure and flexibility of the DNA polymerase holoenzyme of vaccinia virus

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