Monkeypox DNA Polymerase: Difference between revisions

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==Overall Architecture==
==Overall Architecture==


'''Stoichiometry:''' 1 <scene name='33/330227/Dna_polymerase_f8/1'>F8</scene> : 1 <scene name='33/330227/A22/1'>A22</scene> : 1 <scene name='33/330227/E4/2'>E4</scene> + <scene name='33/330227/Primer/2'>primer</scene>–<scene name='33/330227/Template/1'>template</scene> DNA + incoming <scene name='33/330227/Dttp/1'>dTTP</scene>.
'''Components of holoenzyme:''' 1 <scene name='33/330227/Dna_polymerase_f8/1'>F8</scene> , 1 <scene name='33/330227/A22/1'>A22</scene> , 1 <scene name='33/330227/E4/2'>E4</scene> , <scene name='33/330227/Primer/2'>primer</scene>–<scene name='33/330227/Template/1'>template</scene> DNA , incoming <scene name='33/330227/Dttp/1'>dTTP</scene>.


'''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).
'''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 modules but lacks canonical ligase activity (putative active site is nonfunctional).
'''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.
'''E4 (uracil-DNA glycosylase homolog):''' ~218 residues, resembles VACV D4 and contacts F8 Exo directly.
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'''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.
'''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 coordinating catalysis / substrate:''' 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.
'''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.
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