8HG1: Structure of Monkeypox DNA Polymerase

Structure of DNA Polymerase Holoenzyme of Monkeypox Virus

spinqualitylabelsall models Cryo-EM structure of MPXV polymerase holoenzyme in replicating state. PDB code 8hg1. Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Introduction The structure represents the monkeypox virus (MPXV) DNA polymerase holoenzyme in a replicating state, resolved by cryo-EM at ~2.8 Å. It contains the catalytic polymerase F8 bound to its processivity cofactors A22 and E4, along with a primer–template DNA duplex and an incoming dTTP. The structure reveals a poxvirus-specific mechanism in which the A22–E4 heterodimer forms a forward sliding clamp that encircles the single-stranded template strand, enabling highly processive DNA synthesis. Biological Function F8 is the B-family DNA polymerase responsible for MPXV genome replication. A22 and E4 form a heterodimeric processivity factor that stabilizes the polymerase on DNA and promotes continuous elongation. Overall Architecture Components of holoenzyme: 1 F8 , 1 A22 , 1 E4 , primer–template DNA , incoming dTTP. F8 (polymerase): 1004 residues traced (last two residues missing); canonical B-family domains — NTD, 3′–5′ Exonuclease (Exo), palm, fingers, thumb — plus five poxvirus-specific insertions (largest named insert2). A22 (processivity factor): three domains — NTD, Middle (Mid), CTD. The Mid shows structural similarity to ligase adenylylation and OB-fold domains but lacks canonical ligase activity (putative active site is nonfunctional). E4 (uracil-DNA glycosylase homolog): ~218 residues, resembles VACV D4 and contacts F8 Exo directly. DNA Binding & Active Site Bound nucleic acids: 22-nt template strand + 14-nt primer strand in the structure, incoming dTTP and a catalytic Mg²⁺ are observed. DNA path: duplex lies in groove between palm and thumb. Single-stranded 5′ template exits through a channel formed by F8 NTD + Exo and E4, perpendicular to the duplex. Residues involved: conserved Asp residues D549 (motif A- F8) and D753 (motif C- A22) coordinate the catalytic metal; Y554 of F8 stacks the incoming ribose (steric gate against rNTPs); R634 and K661 stabilize triphosphate. These motifs closely mirror canonical B-family polymerases. Processivity Mechanism — “forward sliding clamp” Key observation: A22–E4 folds back and, together with F8 NTD/Exo, forms a closed ring/channel that encircles the single-stranded template. Functional consequence: This encirclement prevents template dissociation and enables high processivity — a distinct forward sliding-clamp mode (encircling ss-template) versus PCNA-type backward clamps (encircling dsDNA) used in many other systems. Supporting biochemistry: Primer-extension assays show F8 alone is distributive (incorporates <14 nt), while addition/assembly with A22–E4 yields full-length extension (60 nt template) in a concentration-dependent manner; alanine scanning of E4 residues (e.g., W36, R39, N165) confirms residues critical for processivity. Significant Structural Features Fingers domain rotates (~17°) toward palm in replicating state — brings R634 / K661 closer to incoming dNTP triphosphate. Thumb wraps around duplex. DNA duplex remains B-form over the 14 base pairs modeled. A22’s Mid domain resembles ligase folds but has substitutions that likely prevent ATP binding, supporting an inactive structural role. 47 F8 residues directly contact DNA (29 to template strand, 18 to primer strand), mostly interacting with phosphodiester backbone rather than bases — explains sequence-independent elongation. References Peng, X., Zhang, Y., Sun, L., Peng, R., Zhao, Y., Chen, Y., Lu, X., Yang, H., & Rao, Z. (2023). Structure of the monkeypox virus DNA polymerase holoenzyme. Science, 380(6652), 703–709. https://doi.org/10.1126/science.ade6360

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This page was prepared as part of the internal assessment for course BI3323-Aug2025.

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Silky Srivastava, Michal Harel