https://proteopedia.org/api.php?action=feedcontributions&feedformat=atom&user=Silky+Srivastava 2026-10-07T14:47:00Z User contributions MediaWiki 1.43.8 https://proteopedia.org/index.php?title=8HG1:_Structure_of_Monkeypox_DNA_Polymerase&diff=4396805 2025-11-30T17:50:43Z

<p>Silky Srivastava: </p> <hr /> <div>=Structure of DNA Polymerase Holoenzyme of Monkeypox Virus=<br /> &lt;StructureSection load='8hg1' size='350' side='right' caption='Cryo-EM structure of MPXV polymerase holoenzyme in replicating state' scene=''&gt;<br /> <br /> ==Introduction==<br /> 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.<br /> ----<br /> <br /> <br /> <br /> ==Biological Function==<br /> 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.<br /> ----<br /> <br /> <br /> <br /> ==Overall Architecture==<br /> <br /> '''Components of holoenzyme:''' 1 &lt;scene name='10/1096888/Dna_polymerase_f8/1'&gt;F8&lt;/scene&gt; , 1 &lt;scene name='33/330227/A22/1'&gt;A22&lt;/scene&gt; , 1 &lt;scene name='33/330227/E4/2'&gt;E4&lt;/scene&gt; , &lt;scene name='33/330227/Primer/2'&gt;primer&lt;/scene&gt;–&lt;scene name='33/330227/Template/1'&gt;template&lt;/scene&gt; DNA , incoming &lt;scene name='33/330227/Dttp/1'&gt;dTTP&lt;/scene&gt;.<br /> <br /> '''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).<br /> <br /> '''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).<br /> <br /> '''E4 (uracil-DNA glycosylase homolog):''' ~218 residues, resembles VACV D4 and contacts F8 Exo directly.<br /> <br /> ----<br /> <br /> <br /> <br /> ==DNA Binding &amp; Active Site==<br /> <br /> '''Bound nucleic acids:''' 22-nt template strand + 14-nt primer strand in the structure, incoming dTTP and a catalytic Mg²⁺ are observed.<br /> <br /> '''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.<br /> <br /> '''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.<br /> ----<br /> <br /> <br /> <br /> ==Processivity Mechanism — “forward sliding clamp”==<br /> <br /> '''Key observation:''' A22–E4 folds back and, together with F8 NTD/Exo, forms a closed ring/channel that encircles the single-stranded template.<br /> <br /> '''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.<br /> <br /> '''Supporting biochemistry:''' Primer-extension assays show F8 alone is distributive (incorporates &lt;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.<br /> ----<br /> <br /> <br /> <br /> ==Significant Structural Features==<br /> <br /> Fingers domain rotates (~17°) toward palm in replicating state — brings R634 / K661 closer to incoming dNTP triphosphate.<br /> <br /> Thumb wraps around duplex. DNA duplex remains B-form over the 14 base pairs modeled.<br /> <br /> A22’s Mid domain resembles ligase folds but has substitutions that likely prevent ATP binding, supporting an inactive structural role.<br /> <br /> 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.<br /> ----<br /> <br /> <br /> ==References==<br /> Peng, X., Zhang, Y., Sun, L., Peng, R., Zhao, Y., Chen, Y., Lu, X., Yang, H., &amp; Rao, Z. (2023). Structure of the monkeypox virus DNA polymerase holoenzyme. Science, 380(6652), 703–709. https://doi.org/10.1126/science.ade6360<br /> &lt;/StructureSection&gt;<br /> ----<br /> <br /> <br /> <br /> ===Note===<br /> This page was prepared as part of the internal assessment for course BI3323-Aug2025.</div>

Silky Srivastava https://proteopedia.org/index.php?title=8HG1:_Structure_of_Monkeypox_DNA_Polymerase&diff=4396442 2025-11-30T13:18:59Z

<p>Silky Srivastava: </p> <hr /> <div>=Structure of DNA Polymerase Holoenzyme of Monkeypox Virus=<br /> &lt;StructureSection load='8hg1' size='350' side='right' caption='testing' scene=''&gt;<br /> <br /> ==Introduction==<br /> 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.<br /> ----<br /> <br /> <br /> <br /> ==Biological Function==<br /> 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.<br /> ----<br /> <br /> <br /> <br /> ==Overall Architecture==<br /> <br /> '''Components of holoenzyme:''' 1 &lt;scene name='10/1096888/Dna_polymerase_f8/1'&gt;F8&lt;/scene&gt; , 1 &lt;scene name='33/330227/A22/1'&gt;A22&lt;/scene&gt; , 1 &lt;scene name='33/330227/E4/2'&gt;E4&lt;/scene&gt; , &lt;scene name='33/330227/Primer/2'&gt;primer&lt;/scene&gt;–&lt;scene name='33/330227/Template/1'&gt;template&lt;/scene&gt; DNA , incoming &lt;scene name='33/330227/Dttp/1'&gt;dTTP&lt;/scene&gt;.<br /> <br /> '''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).<br /> <br /> '''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).<br /> <br /> '''E4 (uracil-DNA glycosylase homolog):''' ~218 residues, resembles VACV D4 and contacts F8 Exo directly.<br /> <br /> ----<br /> <br /> <br /> <br /> ==DNA Binding &amp; Active Site==<br /> <br /> '''Bound nucleic acids:''' 22-nt template strand + 14-nt primer strand in the structure, incoming dTTP and a catalytic Mg²⁺ are observed.<br /> <br /> '''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.<br /> <br /> '''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.<br /> ----<br /> <br /> <br /> <br /> ==Processivity Mechanism — “forward sliding clamp”==<br /> <br /> '''Key observation:''' A22–E4 folds back and, together with F8 NTD/Exo, forms a closed ring/channel that encircles the single-stranded template.<br /> <br /> '''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.<br /> <br /> '''Supporting biochemistry:''' Primer-extension assays show F8 alone is distributive (incorporates &lt;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.<br /> ----<br /> <br /> <br /> <br /> ==Significant Structural Features==<br /> <br /> Fingers domain rotates (~17°) toward palm in replicating state — brings R634 / K661 closer to incoming dNTP triphosphate.<br /> <br /> Thumb wraps around duplex. DNA duplex remains B-form over the 14 base pairs modeled.<br /> <br /> A22’s Mid domain resembles ligase folds but has substitutions that likely prevent ATP binding, supporting an inactive structural role.<br /> <br /> 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.<br /> ----<br /> <br /> <br /> ==References==<br /> Peng, X., Zhang, Y., Sun, L., Peng, R., Zhao, Y., Chen, Y., Lu, X., Yang, H., &amp; Rao, Z. (2023). Structure of the monkeypox virus DNA polymerase holoenzyme. Science, 380(6652), 703–709. https://doi.org/10.1126/science.ade6360<br /> &lt;/StructureSection&gt;<br /> ----<br /> <br /> <br /> <br /> ===Note===<br /> This page was prepared as part of the internal assessment for course BI3323-Aug2025.</div>

Silky Srivastava https://proteopedia.org/index.php?title=Structure_of_mpxv&diff=4396397 2025-11-30T12:44:51Z

<p>Silky Srivastava: Structure of mpxv moved to 8HG1: Structure of Monkeypox DNA Polymerase</p> <hr /> <div>#REDIRECT [[8HG1: Structure of Monkeypox DNA Polymerase]]</div>

Silky Srivastava https://proteopedia.org/index.php?title=8HG1:_Structure_of_Monkeypox_DNA_Polymerase&diff=4396396 2025-11-30T12:44:51Z

<p>Silky Srivastava: Structure of mpxv moved to 8HG1: Structure of Monkeypox DNA Polymerase</p> <hr /> <div>=Structure of DNA Polymerase Holoenzyme of Monkeypox Virus=<br /> &lt;StructureSection load='8hg1' size='350' side='right' caption='testing' scene=''&gt;<br /> <br /> ==Introduction==<br /> 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.<br /> ----<br /> <br /> <br /> <br /> ==Biological Function==<br /> 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.<br /> ----<br /> <br /> <br /> <br /> ==Overall Architecture==<br /> <br /> '''Components of holoenzyme:''' 1 &lt;scene name='33/330227/Dna_polymerase_f8/1'&gt;F8&lt;/scene&gt; , 1 &lt;scene name='33/330227/A22/1'&gt;A22&lt;/scene&gt; , 1 &lt;scene name='33/330227/E4/2'&gt;E4&lt;/scene&gt; , &lt;scene name='33/330227/Primer/2'&gt;primer&lt;/scene&gt;–&lt;scene name='33/330227/Template/1'&gt;template&lt;/scene&gt; DNA , incoming &lt;scene name='33/330227/Dttp/1'&gt;dTTP&lt;/scene&gt;.<br /> <br /> '''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).<br /> <br /> '''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).<br /> <br /> '''E4 (uracil-DNA glycosylase homolog):''' ~218 residues, resembles VACV D4 and contacts F8 Exo directly.<br /> <br /> ----<br /> <br /> <br /> <br /> ==DNA Binding &amp; Active Site==<br /> <br /> '''Bound nucleic acids:''' 22-nt template strand + 14-nt primer strand in the structure, incoming dTTP and a catalytic Mg²⁺ are observed.<br /> <br /> '''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.<br /> <br /> '''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.<br /> ----<br /> <br /> <br /> <br /> ==Processivity Mechanism — “forward sliding clamp”==<br /> <br /> '''Key observation:''' A22–E4 folds back and, together with F8 NTD/Exo, forms a closed ring/channel that encircles the single-stranded template.<br /> <br /> '''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.<br /> <br /> '''Supporting biochemistry:''' Primer-extension assays show F8 alone is distributive (incorporates &lt;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.<br /> ----<br /> <br /> <br /> <br /> ==Significant Structural Features==<br /> <br /> Fingers domain rotates (~17°) toward palm in replicating state — brings R634 / K661 closer to incoming dNTP triphosphate.<br /> <br /> Thumb wraps around duplex. DNA duplex remains B-form over the 14 base pairs modeled.<br /> <br /> A22’s Mid domain resembles ligase folds but has substitutions that likely prevent ATP binding, supporting an inactive structural role.<br /> <br /> 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.<br /> ----<br /> <br /> <br /> ==References==<br /> Peng, X., Zhang, Y., Sun, L., Peng, R., Zhao, Y., Chen, Y., Lu, X., Yang, H., &amp; Rao, Z. (2023). Structure of the monkeypox virus DNA polymerase holoenzyme. Science, 380(6652), 703–709. https://doi.org/10.1126/science.ade6360<br /> &lt;/StructureSection&gt;<br /> ----<br /> <br /> <br /> <br /> ===Note===<br /> This page was prepared as part of the internal assessment for course BI3323-Aug2025.</div>

Silky Srivastava https://proteopedia.org/index.php?title=8HG1:_Structure_of_Monkeypox_DNA_Polymerase&diff=4396358 2025-11-30T12:21:44Z

<p>Silky Srivastava: </p> <hr /> <div>=Structure of DNA Polymerase Holoenzyme of Monkeypox Virus=<br /> &lt;StructureSection load='8hg1' size='350' side='right' caption='testing' scene=''&gt;<br /> <br /> ==Introduction==<br /> 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.<br /> ----<br /> <br /> <br /> <br /> ==Biological Function==<br /> 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.<br /> ----<br /> <br /> <br /> <br /> ==Overall Architecture==<br /> <br /> '''Components of holoenzyme:''' 1 &lt;scene name='33/330227/Dna_polymerase_f8/1'&gt;F8&lt;/scene&gt; , 1 &lt;scene name='33/330227/A22/1'&gt;A22&lt;/scene&gt; , 1 &lt;scene name='33/330227/E4/2'&gt;E4&lt;/scene&gt; , &lt;scene name='33/330227/Primer/2'&gt;primer&lt;/scene&gt;–&lt;scene name='33/330227/Template/1'&gt;template&lt;/scene&gt; DNA , incoming &lt;scene name='33/330227/Dttp/1'&gt;dTTP&lt;/scene&gt;.<br /> <br /> '''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).<br /> <br /> '''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).<br /> <br /> '''E4 (uracil-DNA glycosylase homolog):''' ~218 residues, resembles VACV D4 and contacts F8 Exo directly.<br /> <br /> ----<br /> <br /> <br /> <br /> ==DNA Binding &amp; Active Site==<br /> <br /> '''Bound nucleic acids:''' 22-nt template strand + 14-nt primer strand in the structure, incoming dTTP and a catalytic Mg²⁺ are observed.<br /> <br /> '''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.<br /> <br /> '''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.<br /> ----<br /> <br /> <br /> <br /> ==Processivity Mechanism — “forward sliding clamp”==<br /> <br /> '''Key observation:''' A22–E4 folds back and, together with F8 NTD/Exo, forms a closed ring/channel that encircles the single-stranded template.<br /> <br /> '''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.<br /> <br /> '''Supporting biochemistry:''' Primer-extension assays show F8 alone is distributive (incorporates &lt;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.<br /> ----<br /> <br /> <br /> <br /> ==Significant Structural Features==<br /> <br /> Fingers domain rotates (~17°) toward palm in replicating state — brings R634 / K661 closer to incoming dNTP triphosphate.<br /> <br /> Thumb wraps around duplex. DNA duplex remains B-form over the 14 base pairs modeled.<br /> <br /> A22’s Mid domain resembles ligase folds but has substitutions that likely prevent ATP binding, supporting an inactive structural role.<br /> <br /> 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.<br /> ----<br /> <br /> <br /> ==References==<br /> Peng, X., Zhang, Y., Sun, L., Peng, R., Zhao, Y., Chen, Y., Lu, X., Yang, H., &amp; Rao, Z. (2023). Structure of the monkeypox virus DNA polymerase holoenzyme. Science, 380(6652), 703–709. https://doi.org/10.1126/science.ade6360<br /> &lt;/StructureSection&gt;<br /> ----<br /> <br /> <br /> <br /> ===Note===<br /> This page was prepared as part of the internal assessment for course BI3323-Aug2025.</div>

Silky Srivastava https://proteopedia.org/index.php?title=8HG1:_Structure_of_Monkeypox_DNA_Polymerase&diff=4396347 2025-11-30T12:12:45Z

<p>Silky Srivastava: New page: =Structure of DNA Polymerase Holoenzyme of Monkeypox Virus= &lt;StructureSection load=&#039;8hg1&#039; size=&#039;350&#039; side=&#039;right&#039; caption=&#039;testing&#039; scene=&#039;&#039;&gt; ==Introduction== The structure represents the...</p> <hr /> <div>=Structure of DNA Polymerase Holoenzyme of Monkeypox Virus=<br /> &lt;StructureSection load='8hg1' size='350' side='right' caption='testing' scene=''&gt;<br /> <br /> ==Introduction==<br /> 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.<br /> ----<br /> <br /> <br /> <br /> ==Biological Function==<br /> 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.<br /> ----<br /> <br /> <br /> <br /> ==Overall Architecture==<br /> <br /> '''Components of holoenzyme:''' 1 &lt;scene name='33/330227/Dna_polymerase_f8/1'&gt;F8&lt;/scene&gt; , 1 &lt;scene name='33/330227/A22/1'&gt;A22&lt;/scene&gt; , 1 &lt;scene name='33/330227/E4/2'&gt;E4&lt;/scene&gt; , &lt;scene name='33/330227/Primer/2'&gt;primer&lt;/scene&gt;–&lt;scene name='33/330227/Template/1'&gt;template&lt;/scene&gt; DNA , incoming &lt;scene name='33/330227/Dttp/1'&gt;dTTP&lt;/scene&gt;.<br /> <br /> '''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).<br /> <br /> '''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).<br /> <br /> '''E4 (uracil-DNA glycosylase homolog):''' ~218 residues, resembles VACV D4 and contacts F8 Exo directly.<br /> <br /> ----<br /> <br /> <br /> <br /> ==DNA Binding &amp; Active Site==<br /> <br /> '''Bound nucleic acids:''' 22-nt template strand + 14-nt primer strand in the structure, incoming dTTP and a catalytic Mg²⁺ are observed.<br /> <br /> '''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.<br /> <br /> '''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.<br /> ----<br /> <br /> <br /> <br /> ==Processivity Mechanism — “forward sliding clamp”==<br /> <br /> '''Key observation:''' A22–E4 folds back and, together with F8 NTD/Exo, forms a closed ring/channel that encircles the single-stranded template.<br /> <br /> '''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.<br /> <br /> '''Supporting biochemistry:''' Primer-extension assays show F8 alone is distributive (incorporates &lt;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.<br /> ----<br /> The following figure shows two binding modes of processivity factors with polymerases. The processivity factors bound with template in poxvirus function as a “forward sliding clamp” (i) or dsDNA products in eukaryotes as a “backward sliding clamp” (ii).<br /> <br /> [[Image:MPXV.png|700px]]<br /> <br /> <br /> <br /> ==Significant Structural Features==<br /> <br /> Fingers domain rotates (~17°) toward palm in replicating state — brings R634 / K661 closer to incoming dNTP triphosphate.<br /> <br /> Thumb wraps around duplex. DNA duplex remains B-form over the 14 base pairs modeled.<br /> <br /> A22’s Mid domain resembles ligase folds but has substitutions that likely prevent ATP binding, supporting an inactive structural role.<br /> <br /> 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.<br /> ----<br /> <br /> <br /> ==References==<br /> Peng, X., Zhang, Y., Sun, L., Peng, R., Zhao, Y., Chen, Y., Lu, X., Yang, H., &amp; Rao, Z. (2023). Structure of the monkeypox virus DNA polymerase holoenzyme. Science, 380(6652), 703–709. https://doi.org/10.1126/science.ade6360<br /> &lt;/StructureSection&gt;<br /> ----<br /> <br /> <br /> <br /> ===Note===<br /> This page was prepared as part of the internal assessment for course BI3323-Aug2025.</div>

Silky Srivastava https://proteopedia.org/index.php?title=Monkeypox_DNA_Polymerase&diff=4396077 2025-11-30T02:31:36Z

<p>Silky Srivastava: Removing all content from page</p> <hr /> <div></div>

Silky Srivastava https://proteopedia.org/index.php?title=Talk:Sandbox_Aryan_20221057_BI3323-Aug2025&diff=4396073 2025-11-30T02:11:14Z

<p>Silky Srivastava: Talk:8HG1: Monkeypox DNA Polymerase moved to Talk:Monkeypox DNA Polymerase</p> <hr /> <div>#REDIRECT [[Talk:Monkeypox DNA Polymerase]]</div>

Silky Srivastava https://proteopedia.org/index.php?title=Talk:Monkeypox_DNA_Polymerase&diff=4396072 2025-11-30T02:11:14Z

<p>Silky Srivastava: Talk:8HG1: Monkeypox DNA Polymerase moved to Talk:Monkeypox DNA Polymerase</p> <hr /> <div>==Your Heading Here (maybe something like 'Structure')==<br /> &lt;StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page '''Sandboxes'''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> <br /> == Function ==<br /> <br /> == Disease ==<br /> <br /> == Relevance ==<br /> <br /> == Structural highlights ==<br /> <br /> This is a sample scene created with SAT to &lt;scene name=&quot;/12/3456/Sample/1&quot;&gt;color&lt;/scene&gt; by Group, and another to make &lt;scene name=&quot;/12/3456/Sample/2&quot;&gt;a transparent representation&lt;/scene&gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br /> <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Silky Srivastava https://proteopedia.org/index.php?title=Sandbox_Aryan_20221057_BI3323-Aug2025&diff=4396071 2025-11-30T02:11:14Z

<p>Silky Srivastava: 8HG1: Monkeypox DNA Polymerase moved to Monkeypox DNA Polymerase</p> <hr /> <div>#REDIRECT [[Monkeypox DNA Polymerase]]</div>

Silky Srivastava https://proteopedia.org/index.php?title=Monkeypox_DNA_Polymerase&diff=4396070 2025-11-30T02:11:14Z

<p>Silky Srivastava: 8HG1: Monkeypox DNA Polymerase moved to Monkeypox DNA Polymerase</p> <hr /> <div>=Structure of DNA Polymerase Holoenzyme of Monkeypox Virus=<br /> &lt;StructureSection load='8hg1' size='350' side='right' caption='testing' scene=''&gt;<br /> <br /> ==Introduction==<br /> 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.<br /> ----<br /> <br /> <br /> <br /> ==Biological Function==<br /> 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.<br /> ----<br /> <br /> <br /> <br /> ==Overall Architecture==<br /> <br /> '''Components of holoenzyme:''' 1 &lt;scene name='33/330227/Dna_polymerase_f8/1'&gt;F8&lt;/scene&gt; , 1 &lt;scene name='33/330227/A22/1'&gt;A22&lt;/scene&gt; , 1 &lt;scene name='33/330227/E4/2'&gt;E4&lt;/scene&gt; , &lt;scene name='33/330227/Primer/2'&gt;primer&lt;/scene&gt;–&lt;scene name='33/330227/Template/1'&gt;template&lt;/scene&gt; DNA , incoming &lt;scene name='33/330227/Dttp/1'&gt;dTTP&lt;/scene&gt;.<br /> <br /> '''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).<br /> <br /> '''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).<br /> <br /> '''E4 (uracil-DNA glycosylase homolog):''' ~218 residues, resembles VACV D4 and contacts F8 Exo directly.<br /> <br /> ----<br /> <br /> <br /> <br /> ==DNA Binding &amp; Active Site==<br /> <br /> '''Bound nucleic acids:''' 22-nt template strand + 14-nt primer strand in the structure, incoming dTTP and a catalytic Mg²⁺ are observed.<br /> <br /> '''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.<br /> <br /> '''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.<br /> ----<br /> <br /> <br /> <br /> ==Processivity Mechanism — “forward sliding clamp”==<br /> <br /> '''Key observation:''' A22–E4 folds back and, together with F8 NTD/Exo, forms a closed ring/channel that encircles the single-stranded template.<br /> <br /> '''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.<br /> <br /> '''Supporting biochemistry:''' Primer-extension assays show F8 alone is distributive (incorporates &lt;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.<br /> ----<br /> The following figure shows two binding modes of processivity factors with polymerases. The processivity factors bound with template in poxvirus function as a “forward sliding clamp” (i) or dsDNA products in eukaryotes as a “backward sliding clamp” (ii).<br /> <br /> [[Image:MPXV.png|700px]]<br /> <br /> <br /> <br /> ==Significant Structural Features==<br /> <br /> Fingers domain rotates (~17°) toward palm in replicating state — brings R634 / K661 closer to incoming dNTP triphosphate.<br /> <br /> Thumb wraps around duplex. DNA duplex remains B-form over the 14 base pairs modeled.<br /> <br /> A22’s Mid domain resembles ligase folds but has substitutions that likely prevent ATP binding, supporting an inactive structural role.<br /> <br /> 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.<br /> ----<br /> <br /> <br /> ==References==<br /> Peng, X., Zhang, Y., Sun, L., Peng, R., Zhao, Y., Chen, Y., Lu, X., Yang, H., &amp; Rao, Z. (2023). Structure of the monkeypox virus DNA polymerase holoenzyme. Science, 380(6652), 703–709. https://doi.org/10.1126/science.ade6360<br /> &lt;/StructureSection&gt;<br /> ----<br /> <br /> <br /> <br /> ===Note===<br /> This page was prepared as part of the internal assessment for course BI3323-Aug2025.</div>

Silky Srivastava https://proteopedia.org/index.php?title=Help_talk:Sandboxes&diff=4396068 2025-11-30T02:04:53Z

<p>Silky Srivastava: Help talk:Sandboxes moved to Talk:8HG1: Monkeypox DNA Polymerase</p> <hr /> <div>#REDIRECT [[Talk:8HG1: Monkeypox DNA Polymerase]]</div>

Silky Srivastava https://proteopedia.org/index.php?title=Talk:Monkeypox_DNA_Polymerase&diff=4396067 2025-11-30T02:04:52Z

<p>Silky Srivastava: Help talk:Sandboxes moved to Talk:8HG1: Monkeypox DNA Polymerase</p> <hr /> <div>==Your Heading Here (maybe something like 'Structure')==<br /> &lt;StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page '''Sandboxes'''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> <br /> == Function ==<br /> <br /> == Disease ==<br /> <br /> == Relevance ==<br /> <br /> == Structural highlights ==<br /> <br /> This is a sample scene created with SAT to &lt;scene name=&quot;/12/3456/Sample/1&quot;&gt;color&lt;/scene&gt; by Group, and another to make &lt;scene name=&quot;/12/3456/Sample/2&quot;&gt;a transparent representation&lt;/scene&gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br /> <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Silky Srivastava https://proteopedia.org/index.php?title=Help:Sandboxes&diff=4396066 2025-11-30T02:04:52Z

<p>Silky Srivastava: Help:Sandboxes moved to 8HG1: Monkeypox DNA Polymerase</p> <hr /> <div>#REDIRECT [[8HG1: Monkeypox DNA Polymerase]]</div>

Silky Srivastava https://proteopedia.org/index.php?title=Monkeypox_DNA_Polymerase&diff=4396065 2025-11-30T02:04:52Z

<p>Silky Srivastava: Help:Sandboxes moved to 8HG1: Monkeypox DNA Polymerase</p> <hr /> <div>=Structure of DNA Polymerase Holoenzyme of Monkeypox Virus=<br /> &lt;StructureSection load='8hg1' size='350' side='right' caption='testing' scene=''&gt;<br /> <br /> ==Introduction==<br /> 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.<br /> ----<br /> <br /> <br /> <br /> ==Biological Function==<br /> 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.<br /> ----<br /> <br /> <br /> <br /> ==Overall Architecture==<br /> <br /> '''Components of holoenzyme:''' 1 &lt;scene name='33/330227/Dna_polymerase_f8/1'&gt;F8&lt;/scene&gt; , 1 &lt;scene name='33/330227/A22/1'&gt;A22&lt;/scene&gt; , 1 &lt;scene name='33/330227/E4/2'&gt;E4&lt;/scene&gt; , &lt;scene name='33/330227/Primer/2'&gt;primer&lt;/scene&gt;–&lt;scene name='33/330227/Template/1'&gt;template&lt;/scene&gt; DNA , incoming &lt;scene name='33/330227/Dttp/1'&gt;dTTP&lt;/scene&gt;.<br /> <br /> '''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).<br /> <br /> '''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).<br /> <br /> '''E4 (uracil-DNA glycosylase homolog):''' ~218 residues, resembles VACV D4 and contacts F8 Exo directly.<br /> <br /> ----<br /> <br /> <br /> <br /> ==DNA Binding &amp; Active Site==<br /> <br /> '''Bound nucleic acids:''' 22-nt template strand + 14-nt primer strand in the structure, incoming dTTP and a catalytic Mg²⁺ are observed.<br /> <br /> '''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.<br /> <br /> '''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.<br /> ----<br /> <br /> <br /> <br /> ==Processivity Mechanism — “forward sliding clamp”==<br /> <br /> '''Key observation:''' A22–E4 folds back and, together with F8 NTD/Exo, forms a closed ring/channel that encircles the single-stranded template.<br /> <br /> '''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.<br /> <br /> '''Supporting biochemistry:''' Primer-extension assays show F8 alone is distributive (incorporates &lt;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.<br /> ----<br /> The following figure shows two binding modes of processivity factors with polymerases. The processivity factors bound with template in poxvirus function as a “forward sliding clamp” (i) or dsDNA products in eukaryotes as a “backward sliding clamp” (ii).<br /> <br /> [[Image:MPXV.png|700px]]<br /> <br /> <br /> <br /> ==Significant Structural Features==<br /> <br /> Fingers domain rotates (~17°) toward palm in replicating state — brings R634 / K661 closer to incoming dNTP triphosphate.<br /> <br /> Thumb wraps around duplex. DNA duplex remains B-form over the 14 base pairs modeled.<br /> <br /> A22’s Mid domain resembles ligase folds but has substitutions that likely prevent ATP binding, supporting an inactive structural role.<br /> <br /> 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.<br /> ----<br /> <br /> <br /> ==References==<br /> Peng, X., Zhang, Y., Sun, L., Peng, R., Zhao, Y., Chen, Y., Lu, X., Yang, H., &amp; Rao, Z. (2023). Structure of the monkeypox virus DNA polymerase holoenzyme. Science, 380(6652), 703–709. https://doi.org/10.1126/science.ade6360<br /> &lt;/StructureSection&gt;<br /> ----<br /> <br /> <br /> <br /> ===Note===<br /> This page was prepared as part of the internal assessment for course BI3323-Aug2025.</div>

Silky Srivastava https://proteopedia.org/index.php?title=Monkeypox_DNA_Polymerase&diff=4396064 2025-11-30T02:01:52Z

<p>Silky Srivastava: </p> <hr /> <div>=Structure of DNA Polymerase Holoenzyme of Monkeypox Virus=<br /> &lt;StructureSection load='8hg1' size='350' side='right' caption='testing' scene=''&gt;<br /> <br /> ==Introduction==<br /> 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.<br /> ----<br /> <br /> <br /> <br /> ==Biological Function==<br /> 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.<br /> ----<br /> <br /> <br /> <br /> ==Overall Architecture==<br /> <br /> '''Components of holoenzyme:''' 1 &lt;scene name='33/330227/Dna_polymerase_f8/1'&gt;F8&lt;/scene&gt; , 1 &lt;scene name='33/330227/A22/1'&gt;A22&lt;/scene&gt; , 1 &lt;scene name='33/330227/E4/2'&gt;E4&lt;/scene&gt; , &lt;scene name='33/330227/Primer/2'&gt;primer&lt;/scene&gt;–&lt;scene name='33/330227/Template/1'&gt;template&lt;/scene&gt; DNA , incoming &lt;scene name='33/330227/Dttp/1'&gt;dTTP&lt;/scene&gt;.<br /> <br /> '''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).<br /> <br /> '''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).<br /> <br /> '''E4 (uracil-DNA glycosylase homolog):''' ~218 residues, resembles VACV D4 and contacts F8 Exo directly.<br /> <br /> ----<br /> <br /> <br /> <br /> ==DNA Binding &amp; Active Site==<br /> <br /> '''Bound nucleic acids:''' 22-nt template strand + 14-nt primer strand in the structure, incoming dTTP and a catalytic Mg²⁺ are observed.<br /> <br /> '''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.<br /> <br /> '''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.<br /> ----<br /> <br /> <br /> <br /> ==Processivity Mechanism — “forward sliding clamp”==<br /> <br /> '''Key observation:''' A22–E4 folds back and, together with F8 NTD/Exo, forms a closed ring/channel that encircles the single-stranded template.<br /> <br /> '''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.<br /> <br /> '''Supporting biochemistry:''' Primer-extension assays show F8 alone is distributive (incorporates &lt;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.<br /> ----<br /> The following figure shows two binding modes of processivity factors with polymerases. The processivity factors bound with template in poxvirus function as a “forward sliding clamp” (i) or dsDNA products in eukaryotes as a “backward sliding clamp” (ii).<br /> <br /> [[Image:MPXV.png|700px]]<br /> <br /> <br /> <br /> ==Significant Structural Features==<br /> <br /> Fingers domain rotates (~17°) toward palm in replicating state — brings R634 / K661 closer to incoming dNTP triphosphate.<br /> <br /> Thumb wraps around duplex. DNA duplex remains B-form over the 14 base pairs modeled.<br /> <br /> A22’s Mid domain resembles ligase folds but has substitutions that likely prevent ATP binding, supporting an inactive structural role.<br /> <br /> 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.<br /> ----<br /> <br /> <br /> ==References==<br /> Peng, X., Zhang, Y., Sun, L., Peng, R., Zhao, Y., Chen, Y., Lu, X., Yang, H., &amp; Rao, Z. (2023). Structure of the monkeypox virus DNA polymerase holoenzyme. Science, 380(6652), 703–709. https://doi.org/10.1126/science.ade6360<br /> &lt;/StructureSection&gt;<br /> ----<br /> <br /> <br /> <br /> ===Note===<br /> This page was prepared as part of the internal assessment for course BI3323-Aug2025.</div>

Silky Srivastava https://proteopedia.org/index.php?title=Monkeypox_DNA_Polymerase&diff=4396063 2025-11-30T01:51:12Z

<p>Silky Srivastava: </p> <hr /> <div>=Structure of DNA Polymerase Holoenzyme of Monkeypox Virus=<br /> &lt;StructureSection load='8hg1' size='350' side='right' caption='testing' scene=''&gt;<br /> <br /> ==Introduction==<br /> 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.<br /> ----<br /> <br /> <br /> <br /> ==Biological Function==<br /> 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.<br /> ----<br /> <br /> <br /> <br /> ==Overall Architecture==<br /> <br /> '''Stoichiometry:''' 1 &lt;scene name='33/330227/Dna_polymerase_f8/1'&gt;F8&lt;/scene&gt; : 1 &lt;scene name='33/330227/A22/1'&gt;A22&lt;/scene&gt; : 1 &lt;scene name='33/330227/E4/2'&gt;E4&lt;/scene&gt; + &lt;scene name='33/330227/Primer/2'&gt;primer&lt;/scene&gt;–&lt;scene name='33/330227/Template/1'&gt;template&lt;/scene&gt; DNA + incoming &lt;scene name='33/330227/Dttp/1'&gt;dTTP&lt;/scene&gt;.<br /> <br /> '''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).<br /> <br /> '''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).<br /> <br /> '''E4 (uracil-DNA glycosylase homolog):''' ~218 residues, resembles VACV D4 and contacts F8 Exo directly.<br /> <br /> ----<br /> <br /> <br /> <br /> ==DNA Binding &amp; Active Site==<br /> <br /> '''Bound nucleic acids:''' 22-nt template strand + 14-nt primer strand in the structure, incoming dTTP and a catalytic Mg²⁺ are observed.<br /> <br /> '''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.<br /> <br /> '''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.<br /> ----<br /> <br /> <br /> <br /> ==Processivity Mechanism — “forward sliding clamp”==<br /> <br /> '''Key observation:''' A22–E4 folds back and, together with F8 NTD/Exo, forms a closed ring/channel that encircles the single-stranded template.<br /> <br /> '''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.<br /> <br /> '''Supporting biochemistry:''' Primer-extension assays show F8 alone is distributive (incorporates &lt;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.<br /> ----<br /> The following figure shows two binding modes of processivity factors with polymerases. The processivity factors bound with template in poxvirus function as a “forward sliding clamp” (i) or dsDNA products in eukaryotes as a “backward sliding clamp” (ii).<br /> <br /> [[Image:MPXV.png|700px]]<br /> <br /> <br /> <br /> ==Significant Structural Features==<br /> <br /> Fingers domain rotates (~17°) toward palm in replicating state — brings R634 / K661 closer to incoming dNTP triphosphate.<br /> <br /> Thumb wraps around duplex. DNA duplex remains B-form over the 14 base pairs modeled.<br /> <br /> A22’s Mid domain resembles ligase folds but has substitutions that likely prevent ATP binding, supporting an inactive structural role.<br /> <br /> 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.<br /> ----<br /> <br /> <br /> ==References==<br /> Peng, X., Zhang, Y., Sun, L., Peng, R., Zhao, Y., Chen, Y., Lu, X., Yang, H., &amp; Rao, Z. (2023). Structure of the monkeypox virus DNA polymerase holoenzyme. Science, 380(6652), 703–709. https://doi.org/10.1126/science.ade6360<br /> &lt;/StructureSection&gt;<br /> ----<br /> <br /> <br /> <br /> ===Note===<br /> This page was prepared as part of the internal assessment for course BI3323-Aug2025.</div>

Silky Srivastava https://proteopedia.org/index.php?title=Monkeypox_DNA_Polymerase&diff=4396060 2025-11-30T01:20:45Z

<p>Silky Srivastava: </p> <hr /> <div>==Your Heading Here (maybe something like 'Structure')==<br /> &lt;StructureSection load='8hg1' size='350' side='right' caption='testing' scene=''&gt;<br /> <br /> ==Introduction==<br /> 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.<br /> ----<br /> <br /> <br /> <br /> ==Biological Function==<br /> 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.<br /> ----<br /> <br /> <br /> <br /> ==Overall Architecture==<br /> <br /> '''Stoichiometry:''' 1 &lt;scene name='33/330227/Dna_polymerase_f8/1'&gt;F8&lt;/scene&gt; : 1 &lt;scene name='33/330227/A22/1'&gt;A22&lt;/scene&gt; : 1 &lt;scene name='33/330227/E4/2'&gt;E4&lt;/scene&gt; + &lt;scene name='33/330227/Primer/2'&gt;primer&lt;/scene&gt;–&lt;scene name='33/330227/Template/1'&gt;template&lt;/scene&gt; DNA + incoming &lt;scene name='33/330227/Dttp/1'&gt;dTTP&lt;/scene&gt;.<br /> <br /> '''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).<br /> <br /> '''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).<br /> <br /> '''E4 (uracil-DNA glycosylase homolog):''' ~218 residues, resembles VACV D4 and contacts F8 Exo directly.<br /> <br /> ----<br /> <br /> <br /> <br /> ==DNA Binding &amp; Active Site==<br /> <br /> '''Bound nucleic acids:''' 22-nt template strand + 14-nt primer strand in the structure, incoming dTTP and a catalytic Mg²⁺ are observed.<br /> <br /> '''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.<br /> <br /> '''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.<br /> ----<br /> <br /> <br /> <br /> ==Processivity Mechanism — “forward sliding clamp”==<br /> <br /> '''Key observation:''' A22–E4 folds back and, together with F8 NTD/Exo, forms a closed ring/channel that encircles the single-stranded template.<br /> <br /> '''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.<br /> <br /> '''Supporting biochemistry:''' Primer-extension assays show F8 alone is distributive (incorporates &lt;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.<br /> ----<br /> The following figure shows two binding modes of processivity factors with polymerases. The processivity factors bound with template in poxvirus function as a “forward sliding clamp” (i) or dsDNA products in eukaryotes as a “backward sliding clamp” (ii).<br /> <br /> [[Image:MPXV.png|700px]]<br /> <br /> <br /> <br /> ==Significant Structural Features==<br /> <br /> Fingers domain rotates (~17°) toward palm in replicating state — brings R634 / K661 closer to incoming dNTP triphosphate.<br /> <br /> Thumb wraps around duplex. DNA duplex remains B-form over the 14 base pairs modeled.<br /> <br /> A22’s Mid domain resembles ligase folds but has substitutions that likely prevent ATP binding, supporting an inactive structural role.<br /> <br /> 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.<br /> ----<br /> <br /> <br /> <br /> ==References==<br /> Peng, X., Zhang, Y., Sun, L., Peng, R., Zhao, Y., Chen, Y., Lu, X., Yang, H., &amp; Rao, Z. (2023). Structure of the monkeypox virus DNA polymerase holoenzyme. Science, 380(6652), 703–709. https://doi.org/10.1126/science.ade6360<br /> &lt;/StructureSection&gt;</div>

Silky Srivastava https://proteopedia.org/index.php?title=Monkeypox_DNA_Polymerase&diff=4396059 2025-11-30T01:16:50Z

<p>Silky Srivastava: </p> <hr /> <div>==Your Heading Here (maybe something like 'Structure')==<br /> &lt;StructureSection load='8hg1' size='350' side='right' caption='testing' scene=''&gt;<br /> <br /> ==Introduction==<br /> 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.<br /> ----<br /> <br /> <br /> <br /> ==Biological Function==<br /> 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.<br /> ----<br /> <br /> <br /> <br /> ==Overall Architecture==<br /> <br /> '''Stoichiometry:''' 1 &lt;scene name='33/330227/Dna_polymerase_f8/1'&gt;F8&lt;/scene&gt; : 1 &lt;scene name='33/330227/A22/1'&gt;A22&lt;/scene&gt; : 1 &lt;scene name='33/330227/E4/2'&gt;E4&lt;/scene&gt; + &lt;scene name='33/330227/Primer/2'&gt;primer&lt;/scene&gt;–&lt;scene name='33/330227/Template/1'&gt;template&lt;/scene&gt; DNA + incoming &lt;scene name='33/330227/Dttp/1'&gt;dTTP&lt;/scene&gt;.<br /> <br /> '''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).<br /> <br /> '''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).<br /> <br /> '''E4 (uracil-DNA glycosylase homolog):''' ~218 residues, resembles VACV D4 and contacts F8 Exo directly.<br /> <br /> ----<br /> <br /> <br /> <br /> ==DNA Binding &amp; Active Site==<br /> <br /> '''Bound nucleic acids:''' 22-nt template strand + 14-nt primer strand in the structure, incoming dTTP and a catalytic Mg²⁺ are observed.<br /> <br /> '''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.<br /> <br /> '''Residues coordinating catalysis / substrate:''' conserved Asp residues D549 (motif A- F8) and D753 (motif C- A22) coordinate the catalytic metal; Y554 stacks the incoming ribose (steric gate against rNTPs); R634 and K661 stabilize triphosphate. These motifs closely mirror canonical B-family polymerases.<br /> ----<br /> <br /> <br /> <br /> ==Processivity Mechanism — “forward sliding clamp”==<br /> <br /> '''Key observation:''' A22–E4 folds back and, together with F8 NTD/Exo, forms a closed ring/channel that encircles the single-stranded template.<br /> <br /> '''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.<br /> <br /> '''Supporting biochemistry:''' Primer-extension assays show F8 alone is distributive (incorporates &lt;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.<br /> ----<br /> The following figure shows two binding modes of processivity factors with polymerases. The processivity factors bound with template in poxvirus function as a “forward sliding clamp” (i) or dsDNA products in eukaryotes as a “backward sliding clamp” (ii).<br /> [[Image:MPXV.png|700px]]<br /> <br /> <br /> <br /> ==Significant Structural Features==<br /> <br /> Fingers domain rotates (~17°) toward palm in replicating state — brings R634 / K661 closer to incoming dNTP triphosphate.<br /> <br /> Thumb wraps around duplex. DNA duplex remains B-form over the 14 base pairs modeled.<br /> <br /> A22’s Mid domain resembles ligase folds but has substitutions that likely prevent ATP binding, supporting an inactive structural role.<br /> <br /> 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.<br /> ----<br /> <br /> <br /> <br /> ==References==<br /> Peng, X., Zhang, Y., Sun, L., Peng, R., Zhao, Y., Chen, Y., Lu, X., Yang, H., &amp; Rao, Z. (2023). Structure of the monkeypox virus DNA polymerase holoenzyme. Science, 380(6652), 703–709. https://doi.org/10.1126/science.ade6360<br /> &lt;/StructureSection&gt;</div>

Silky Srivastava https://proteopedia.org/index.php?title=Monkeypox_DNA_Polymerase&diff=4396058 2025-11-30T01:14:24Z

<p>Silky Srivastava: </p> <hr /> <div>==Your Heading Here (maybe something like 'Structure')==<br /> &lt;StructureSection load='8hg1' size='350' side='right' caption='testing' scene=''&gt;<br /> <br /> ==Introduction==<br /> 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.<br /> ----<br /> <br /> <br /> <br /> ==Biological Function==<br /> 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.<br /> ----<br /> <br /> <br /> <br /> ==Overall Architecture==<br /> <br /> '''Stoichiometry:''' 1 &lt;scene name='33/330227/Dna_polymerase_f8/1'&gt;F8&lt;/scene&gt; : 1 &lt;scene name='33/330227/A22/1'&gt;A22&lt;/scene&gt; : 1 &lt;scene name='33/330227/E4/2'&gt;E4&lt;/scene&gt; + &lt;scene name='33/330227/Primer/2'&gt;primer&lt;/scene&gt;–&lt;scene name='33/330227/Template/1'&gt;template&lt;/scene&gt; DNA + incoming &lt;scene name='33/330227/Dttp/1'&gt;dTTP&lt;/scene&gt;.<br /> <br /> '''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).<br /> <br /> '''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).<br /> <br /> '''E4 (uracil-DNA glycosylase homolog):''' ~218 residues, resembles VACV D4 and contacts F8 Exo directly.<br /> <br /> ----<br /> <br /> <br /> <br /> ==DNA Binding &amp; Active Site==<br /> <br /> '''Bound nucleic acids:''' 22-nt template strand + 14-nt primer strand in the structure, incoming dTTP and a catalytic Mg²⁺ are observed.<br /> <br /> '''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.<br /> <br /> '''Residues coordinating catalysis / substrate:''' conserved Asp residues D549 (motif A- F8) and D753 (motif C- A22) coordinate the catalytic metal; Y554 stacks the incoming ribose (steric gate against rNTPs); R634 and K661 stabilize triphosphate. These motifs closely mirror canonical B-family polymerases.<br /> ----<br /> <br /> <br /> <br /> ==Processivity Mechanism — “forward sliding clamp”==<br /> <br /> '''Key observation:''' A22–E4 folds back and, together with F8 NTD/Exo, forms a closed ring/channel that encircles the single-stranded template.<br /> <br /> '''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.<br /> <br /> '''Supporting biochemistry:''' Primer-extension assays show F8 alone is distributive (incorporates &lt;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.<br /> ----<br /> [[Image:MPXV.png|700px]]<br /> <br /> <br /> <br /> ==Significant Structural Features==<br /> <br /> Fingers domain rotates (~17°) toward palm in replicating state — brings R634 / K661 closer to incoming dNTP triphosphate.<br /> <br /> Thumb wraps around duplex. DNA duplex remains B-form over the 14 base pairs modeled.<br /> <br /> A22’s Mid domain resembles ligase folds but has substitutions that likely prevent ATP binding, supporting an inactive structural role.<br /> <br /> 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.<br /> ----<br /> <br /> <br /> <br /> ==References==<br /> Peng, X., Zhang, Y., Sun, L., Peng, R., Zhao, Y., Chen, Y., Lu, X., Yang, H., &amp; Rao, Z. (2023). Structure of the monkeypox virus DNA polymerase holoenzyme. Science, 380(6652), 703–709. https://doi.org/10.1126/science.ade6360<br /> &lt;/StructureSection&gt;</div>

Silky Srivastava https://proteopedia.org/index.php?title=Monkeypox_DNA_Polymerase&diff=4396057 2025-11-30T01:12:57Z

<p>Silky Srivastava: </p> <hr /> <div>==Your Heading Here (maybe something like 'Structure')==<br /> &lt;StructureSection load='8hg1' size='350' side='right' caption='testing' scene=''&gt;<br /> <br /> ==Introduction==<br /> 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.<br /> ----<br /> <br /> <br /> <br /> ==Biological Function==<br /> 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.<br /> ----<br /> <br /> <br /> <br /> ==Overall Architecture==<br /> <br /> '''Stoichiometry:''' 1 &lt;scene name='33/330227/Dna_polymerase_f8/1'&gt;F8&lt;/scene&gt; : 1 &lt;scene name='33/330227/A22/1'&gt;A22&lt;/scene&gt; : 1 &lt;scene name='33/330227/E4/2'&gt;E4&lt;/scene&gt; + &lt;scene name='33/330227/Primer/2'&gt;primer&lt;/scene&gt;–&lt;scene name='33/330227/Template/1'&gt;template&lt;/scene&gt; DNA + incoming &lt;scene name='33/330227/Dttp/1'&gt;dTTP&lt;/scene&gt;.<br /> <br /> '''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).<br /> <br /> '''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).<br /> <br /> '''E4 (uracil-DNA glycosylase homolog):''' ~218 residues, resembles VACV D4 and contacts F8 Exo directly.<br /> <br /> ----<br /> <br /> <br /> <br /> ==DNA Binding &amp; Active Site==<br /> <br /> '''Bound nucleic acids:''' 22-nt template strand + 14-nt primer strand in the structure, incoming dTTP and a catalytic Mg²⁺ are observed.<br /> <br /> '''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.<br /> <br /> '''Residues coordinating catalysis / substrate:''' conserved Asp residues D549 (motif A- F8) and D753 (motif C- A22) coordinate the catalytic metal; Y554 stacks the incoming ribose (steric gate against rNTPs); R634 and K661 stabilize triphosphate. These motifs closely mirror canonical B-family polymerases.<br /> ----<br /> <br /> <br /> <br /> ==Processivity Mechanism — “forward sliding clamp”==<br /> <br /> '''Key observation:''' A22–E4 folds back and, together with F8 NTD/Exo, forms a closed ring/channel that encircles the single-stranded template.<br /> <br /> '''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.<br /> <br /> '''Supporting biochemistry:''' Primer-extension assays show F8 alone is distributive (incorporates &lt;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.<br /> ----<br /> [[Image:MPXV.png|700px]]<br /> <br /> <br /> <br /> ==Significant Structural Features==<br /> <br /> Fingers domain rotates (~17°) toward palm in replicating state — brings R634 / K661 closer to incoming dNTP triphosphate.<br /> <br /> Thumb wraps around duplex. DNA duplex remains B-form over the 14 base pairs modeled.<br /> <br /> A22’s Mid domain resembles ligase folds but has substitutions that likely prevent ATP binding, supporting an inactive structural role.<br /> <br /> 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.<br /> ----<br /> <br /> <br /> <br /> ==Refernces==<br /> Peng, X., Zhang, Y., Sun, L., Peng, R., Zhao, Y., Chen, Y., Lu, X., Yang, H., &amp; Rao, Z. (2023). Structure of the monkeypox virus DNA polymerase holoenzyme. Science, 380(6652), 703–709. https://doi.org/10.1126/science.ade6360<br /> &lt;/StructureSection&gt;</div>

Silky Srivastava https://proteopedia.org/index.php?title=File:MPXV.png&diff=4396056 2025-11-30T01:10:41Z

<p>Silky Srivastava: uploaded a new version of &quot;Image:MPXV.png&quot;</p> <hr /> <div></div>

Silky Srivastava https://proteopedia.org/index.php?title=Monkeypox_DNA_Polymerase&diff=4396055 2025-11-30T00:57:32Z

<p>Silky Srivastava: </p> <hr /> <div>==Your Heading Here (maybe something like 'Structure')==<br /> &lt;StructureSection load='8hg1' size='350' side='right' caption='testing' scene=''&gt;<br /> <br /> ==Introduction==<br /> 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.<br /> ----<br /> <br /> <br /> <br /> ==Biological Function==<br /> 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.<br /> ----<br /> <br /> <br /> <br /> ==Overall Architecture==<br /> <br /> '''Stoichiometry:''' 1 &lt;scene name='33/330227/Dna_polymerase_f8/1'&gt;F8&lt;/scene&gt; : 1 &lt;scene name='33/330227/A22/1'&gt;A22&lt;/scene&gt; : 1 &lt;scene name='33/330227/E4/2'&gt;E4&lt;/scene&gt; + &lt;scene name='33/330227/Primer/2'&gt;primer&lt;/scene&gt;–&lt;scene name='33/330227/Template/1'&gt;template&lt;/scene&gt; DNA + incoming &lt;scene name='33/330227/Dttp/1'&gt;dTTP&lt;/scene&gt;.<br /> <br /> '''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).<br /> <br /> '''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).<br /> <br /> '''E4 (uracil-DNA glycosylase homolog):''' ~218 residues, resembles VACV D4 and contacts F8 Exo directly.<br /> <br /> ----<br /> <br /> <br /> <br /> ==DNA Binding &amp; Active Site==<br /> <br /> '''Bound nucleic acids:''' 22-nt template strand + 14-nt primer strand in the structure, incoming dTTP and a catalytic Mg²⁺ are observed.<br /> <br /> '''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.<br /> <br /> '''Residues coordinating catalysis / substrate:''' conserved Asp residues D549 (motif A- F8) and D753 (motif C- A22) coordinate the catalytic metal; Y554 stacks the incoming ribose (steric gate against rNTPs); R634 and K661 stabilize triphosphate. These motifs closely mirror canonical B-family polymerases.<br /> ----<br /> <br /> <br /> <br /> ==Processivity Mechanism — “forward sliding clamp”==<br /> <br /> '''Key observation:''' A22–E4 folds back and, together with F8 NTD/Exo, forms a closed ring/channel that encircles the single-stranded template.<br /> <br /> '''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.<br /> <br /> '''Supporting biochemistry:''' Primer-extension assays show F8 alone is distributive (incorporates &lt;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.<br /> ----<br /> <br /> <br /> <br /> ==Significant Structural Features==<br /> <br /> Fingers domain rotates (~17°) toward palm in replicating state — brings R634 / K661 closer to incoming dNTP triphosphate.<br /> <br /> Thumb wraps around duplex. DNA duplex remains B-form over the 14 base pairs modeled.<br /> <br /> A22’s Mid domain resembles ligase folds but has substitutions that likely prevent ATP binding, supporting an inactive structural role.<br /> <br /> 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.<br /> <br /> &lt;/StructureSection&gt;</div>

Silky Srivastava https://proteopedia.org/index.php?title=File:MPXV.png&diff=4396054 2025-11-30T00:57:05Z

<p>Silky Srivastava: </p> <hr /> <div></div>

Silky Srivastava https://proteopedia.org/index.php?title=Monkeypox_DNA_Polymerase&diff=4396053 2025-11-30T00:18:41Z

<p>Silky Srivastava: </p> <hr /> <div>==Your Heading Here (maybe something like 'Structure')==<br /> &lt;StructureSection load='8hg1' size='350' side='right' caption='testing' scene=''&gt;<br /> <br /> ==Introduction==<br /> 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.<br /> ----<br /> <br /> <br /> <br /> ==Biological Function==<br /> 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.<br /> ----<br /> <br /> <br /> <br /> ==Overall Architecture==<br /> <br /> '''Stoichiometry:''' 1 &lt;scene name='33/330227/Dna_polymerase_f8/1'&gt;F8&lt;/scene&gt; : 1 &lt;scene name='33/330227/A22/1'&gt;A22&lt;/scene&gt; : 1 &lt;scene name='33/330227/E4/2'&gt;E4&lt;/scene&gt; + &lt;scene name='33/330227/Primer/2'&gt;primer&lt;/scene&gt;–&lt;scene name='33/330227/Template/1'&gt;template&lt;/scene&gt; DNA + incoming &lt;scene name='33/330227/Dttp/1'&gt;dTTP&lt;/scene&gt;.<br /> <br /> '''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).<br /> <br /> '''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).<br /> <br /> '''E4 (uracil-DNA glycosylase homolog):''' ~218 residues, resembles VACV D4 and contacts F8 Exo directly.<br /> <br /> ----<br /> <br /> <br /> <br /> ==DNA binding &amp; active site==<br /> <br /> '''Bound nucleic acids:''' 22-nt template strand + 14-nt primer strand in the structure; incoming dTTP and a catalytic Mg²⁺ are observed.<br /> <br /> '''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.<br /> <br /> '''Residues coordinating catalysis / substrate:''' conserved Asp residues D549 (motif A) and D753 (motif C) coordinate the catalytic metal; Y554 stacks the incoming ribose (steric gate against rNTPs); R634 and K661 stabilize triphosphate. These motifs closely mirror canonical B-family polymerases.<br /> ----<br /> <br /> <br /> <br /> ==Processivity mechanism — “forward sliding clamp”==<br /> <br /> '''Key observation:''' A22–E4 folds back and, together with F8 NTD/Exo, forms a closed ring/channel that encircles the single-stranded template.<br /> <br /> '''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.<br /> <br /> '''Supporting biochemistry:''' Primer-extension assays show F8 alone is distributive (incorporates &lt;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.<br /> ----<br /> <br /> <br /> <br /> ==Notable structural features==<br /> <br /> Fingers domain rotates (~17°) toward palm in replicating state — brings R634 / K661 closer to incoming dNTP triphosphate.<br /> <br /> Thumb wraps around duplex; DNA duplex remains B-form over the 14 base pairs modeled.<br /> <br /> A22 Mid domain resembles ligase O-adenylylation/OB modules but substitutions (hydrophobic/negative residues) likely prevent ATP binding — A22 is a degenerative ligase-like linker rather than an active ligase.<br /> <br /> 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.<br /> <br /> &lt;/StructureSection&gt;</div>

Silky Srivastava https://proteopedia.org/index.php?title=Monkeypox_DNA_Polymerase&diff=4396052 2025-11-30T00:05:46Z

<p>Silky Srivastava: </p> <hr /> <div>==Your Heading Here (maybe something like 'Structure')==<br /> &lt;StructureSection load='8hg1' size='350' side='right' caption='testing' scene=''&gt;<br /> <br /> ==Introduction==<br /> 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.<br /> ----<br /> <br /> <br /> <br /> ==Biological Function==<br /> 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.<br /> ----<br /> <br /> <br /> <br /> ==Overall Architecture==<br /> <br /> '''Stoichiometry:''' 1 &lt;scene name='33/330227/Dna_polymerase_f8/1'&gt;F8&lt;/scene&gt; : 1 &lt;scene name='33/330227/A22/1'&gt;A22&lt;/scene&gt; : 1 &lt;scene name='33/330227/E4/2'&gt;E4&lt;/scene&gt; + &lt;scene name='33/330227/Primer/2'&gt;primer&lt;/scene&gt;–&lt;scene name='33/330227/Template/1'&gt;template&lt;/scene&gt; DNA + incoming dTTP.<br /> <br /> '''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).<br /> <br /> '''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).<br /> <br /> '''E4 (uracil-DNA glycosylase homolog):''' ~218 residues, resembles VACV D4 and contacts F8 Exo directly.<br /> <br /> ----<br /> <br /> <br /> <br /> ==DNA binding &amp; active site==<br /> <br /> '''Bound nucleic acids:''' 22-nt template strand + 14-nt primer strand in the structure; incoming dTTP and a catalytic Mg²⁺ are observed.<br /> <br /> '''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.<br /> <br /> '''Residues coordinating catalysis / substrate:''' conserved Asp residues D549 (motif A) and D753 (motif C) coordinate the catalytic metal; Y554 stacks the incoming ribose (steric gate against rNTPs); R634 and K661 stabilize triphosphate. These motifs closely mirror canonical B-family polymerases.<br /> ----<br /> <br /> <br /> <br /> ==Processivity mechanism — “forward sliding clamp”==<br /> <br /> '''Key observation:''' A22–E4 folds back and, together with F8 NTD/Exo, forms a closed ring/channel that encircles the single-stranded template.<br /> <br /> '''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.<br /> <br /> '''Supporting biochemistry:''' Primer-extension assays show F8 alone is distributive (incorporates &lt;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.<br /> ----<br /> <br /> <br /> <br /> ==Notable structural features==<br /> <br /> Fingers domain rotates (~17°) toward palm in replicating state — brings R634 / K661 closer to incoming dNTP triphosphate.<br /> <br /> Thumb wraps around duplex; DNA duplex remains B-form over the 14 base pairs modeled.<br /> <br /> A22 Mid domain resembles ligase O-adenylylation/OB modules but substitutions (hydrophobic/negative residues) likely prevent ATP binding — A22 is a degenerative ligase-like linker rather than an active ligase.<br /> <br /> 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.<br /> <br /> &lt;/StructureSection&gt;</div>

Silky Srivastava https://proteopedia.org/index.php?title=Monkeypox_DNA_Polymerase&diff=4396051 2025-11-30T00:01:47Z

<p>Silky Srivastava: </p> <hr /> <div>==Your Heading Here (maybe something like 'Structure')==<br /> &lt;StructureSection load='8hg1' size='350' side='right' caption='testing' scene=''&gt;<br /> <br /> ==Introduction==<br /> 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.<br /> ----<br /> <br /> <br /> <br /> ==Biological Function==<br /> 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.<br /> ----<br /> <br /> <br /> <br /> ==Overall Architecture==<br /> <br /> '''Stoichiometry:''' 1 &lt;scene name='33/330227/Dna_polymerase_f8/1'&gt;F8&lt;/scene&gt; : 1 &lt;scene name='33/330227/A22/1'&gt;A22&lt;/scene&gt; : 1 &lt;scene name='33/330227/E4/2'&gt;E4&lt;/scene&gt; + &lt;scene name='33/330227/Primer/1'&gt;primer&lt;/scene&gt;–&lt;scene name='33/330227/Template/1'&gt;template&lt;/scene&gt; DNA + incoming dTTP.<br /> <br /> '''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).<br /> <br /> '''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).<br /> <br /> '''E4 (uracil-DNA glycosylase homolog):''' ~218 residues, resembles VACV D4 and contacts F8 Exo directly.<br /> <br /> ----<br /> <br /> <br /> <br /> ==DNA binding &amp; active site==<br /> <br /> '''Bound nucleic acids:''' 22-nt template strand + 14-nt primer strand in the structure; incoming dTTP and a catalytic Mg²⁺ are observed.<br /> <br /> '''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.<br /> <br /> '''Residues coordinating catalysis / substrate:''' conserved Asp residues D549 (motif A) and D753 (motif C) coordinate the catalytic metal; Y554 stacks the incoming ribose (steric gate against rNTPs); R634 and K661 stabilize triphosphate. These motifs closely mirror canonical B-family polymerases.<br /> ----<br /> <br /> <br /> <br /> ==Processivity mechanism — “forward sliding clamp”==<br /> <br /> '''Key observation:''' A22–E4 folds back and, together with F8 NTD/Exo, forms a closed ring/channel that encircles the single-stranded template.<br /> <br /> '''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.<br /> <br /> '''Supporting biochemistry:''' Primer-extension assays show F8 alone is distributive (incorporates &lt;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.<br /> ----<br /> <br /> <br /> <br /> ==Notable structural features==<br /> <br /> Fingers domain rotates (~17°) toward palm in replicating state — brings R634 / K661 closer to incoming dNTP triphosphate.<br /> <br /> Thumb wraps around duplex; DNA duplex remains B-form over the 14 base pairs modeled.<br /> <br /> A22 Mid domain resembles ligase O-adenylylation/OB modules but substitutions (hydrophobic/negative residues) likely prevent ATP binding — A22 is a degenerative ligase-like linker rather than an active ligase.<br /> <br /> 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.<br /> <br /> &lt;/StructureSection&gt;</div>

Silky Srivastava https://proteopedia.org/index.php?title=Monkeypox_DNA_Polymerase&diff=4396050 2025-11-29T23:59:38Z

<p>Silky Srivastava: </p> <hr /> <div>==Your Heading Here (maybe something like 'Structure')==<br /> &lt;StructureSection load='8hg1' size='350' side='right' caption='testing' scene=''&gt;<br /> <br /> ==Introduction==<br /> 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.<br /> ----<br /> <br /> <br /> <br /> ==Biological Function==<br /> 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.<br /> ----<br /> <br /> <br /> <br /> ==Overall Architecture==<br /> <br /> '''Stoichiometry:''' 1 &lt;scene name='33/330227/Dna_polymerase_f8/1'&gt;F8&lt;/scene&gt; : 1 &lt;scene name='33/330227/A22/1'&gt;A22&lt;/scene&gt; : 1 &lt;scene name='33/330227/E4/2'&gt;E4&lt;/scene&gt; + &lt;scene name='33/330227/Primer/1'&gt;primer&lt;/scene&gt;–template DNA + incoming dTTP.<br /> <br /> '''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).<br /> <br /> '''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).<br /> <br /> '''E4 (uracil-DNA glycosylase homolog):''' ~218 residues, resembles VACV D4 and contacts F8 Exo directly.<br /> <br /> ----<br /> <br /> <br /> <br /> ==DNA binding &amp; active site==<br /> <br /> '''Bound nucleic acids:''' 22-nt template strand + 14-nt primer strand in the structure; incoming dTTP and a catalytic Mg²⁺ are observed.<br /> <br /> '''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.<br /> <br /> '''Residues coordinating catalysis / substrate:''' conserved Asp residues D549 (motif A) and D753 (motif C) coordinate the catalytic metal; Y554 stacks the incoming ribose (steric gate against rNTPs); R634 and K661 stabilize triphosphate. These motifs closely mirror canonical B-family polymerases.<br /> ----<br /> <br /> <br /> <br /> ==Processivity mechanism — “forward sliding clamp”==<br /> <br /> '''Key observation:''' A22–E4 folds back and, together with F8 NTD/Exo, forms a closed ring/channel that encircles the single-stranded template.<br /> <br /> '''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.<br /> <br /> '''Supporting biochemistry:''' Primer-extension assays show F8 alone is distributive (incorporates &lt;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.<br /> ----<br /> <br /> <br /> <br /> ==Notable structural features==<br /> <br /> Fingers domain rotates (~17°) toward palm in replicating state — brings R634 / K661 closer to incoming dNTP triphosphate.<br /> <br /> Thumb wraps around duplex; DNA duplex remains B-form over the 14 base pairs modeled.<br /> <br /> A22 Mid domain resembles ligase O-adenylylation/OB modules but substitutions (hydrophobic/negative residues) likely prevent ATP binding — A22 is a degenerative ligase-like linker rather than an active ligase.<br /> <br /> 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.<br /> <br /> &lt;/StructureSection&gt;</div>

Silky Srivastava https://proteopedia.org/index.php?title=Monkeypox_DNA_Polymerase&diff=4396049 2025-11-29T23:57:29Z

<p>Silky Srivastava: </p> <hr /> <div>==Your Heading Here (maybe something like 'Structure')==<br /> &lt;StructureSection load='8hg1' size='350' side='right' caption='testing' scene=''&gt;<br /> <br /> ==Introduction==<br /> 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.<br /> ----<br /> <br /> <br /> <br /> ==Biological Function==<br /> 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.<br /> ----<br /> <br /> <br /> <br /> ==Overall Architecture==<br /> <br /> '''Stoichiometry:''' 1 &lt;scene name='33/330227/Dna_polymerase_f8/1'&gt;F8&lt;/scene&gt; : 1 &lt;scene name='33/330227/A22/1'&gt;A22&lt;/scene&gt; : 1 &lt;scene name='33/330227/E4/2'&gt;E4&lt;/scene&gt; + primer–template DNA + incoming dTTP.<br /> <br /> '''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).<br /> <br /> '''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).<br /> <br /> '''E4 (uracil-DNA glycosylase homolog):''' ~218 residues, resembles VACV D4 and contacts F8 Exo directly.<br /> <br /> ----<br /> <br /> <br /> <br /> ==DNA binding &amp; active site==<br /> <br /> '''Bound nucleic acids:''' 22-nt template strand + 14-nt primer strand in the structure; incoming dTTP and a catalytic Mg²⁺ are observed.<br /> <br /> '''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.<br /> <br /> '''Residues coordinating catalysis / substrate:''' conserved Asp residues D549 (motif A) and D753 (motif C) coordinate the catalytic metal; Y554 stacks the incoming ribose (steric gate against rNTPs); R634 and K661 stabilize triphosphate. These motifs closely mirror canonical B-family polymerases.<br /> ----<br /> <br /> <br /> <br /> ==Processivity mechanism — “forward sliding clamp”==<br /> <br /> '''Key observation:''' A22–E4 folds back and, together with F8 NTD/Exo, forms a closed ring/channel that encircles the single-stranded template.<br /> <br /> '''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.<br /> <br /> '''Supporting biochemistry:''' Primer-extension assays show F8 alone is distributive (incorporates &lt;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.<br /> ----<br /> <br /> <br /> <br /> ==Notable structural features==<br /> <br /> Fingers domain rotates (~17°) toward palm in replicating state — brings R634 / K661 closer to incoming dNTP triphosphate.<br /> <br /> Thumb wraps around duplex; DNA duplex remains B-form over the 14 base pairs modeled.<br /> <br /> A22 Mid domain resembles ligase O-adenylylation/OB modules but substitutions (hydrophobic/negative residues) likely prevent ATP binding — A22 is a degenerative ligase-like linker rather than an active ligase.<br /> <br /> 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.<br /> <br /> &lt;/StructureSection&gt;</div>

Silky Srivastava https://proteopedia.org/index.php?title=Monkeypox_DNA_Polymerase&diff=4396048 2025-11-29T23:56:02Z

<p>Silky Srivastava: </p> <hr /> <div>==Your Heading Here (maybe something like 'Structure')==<br /> &lt;StructureSection load='8hg1' size='350' side='right' caption='testing' scene=''&gt;<br /> <br /> ==Introduction==<br /> 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.<br /> ----<br /> <br /> <br /> <br /> ==Biological Function==<br /> 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.<br /> ----<br /> <br /> <br /> <br /> ==Overall Architecture==<br /> <br /> '''Stoichiometry:''' 1 &lt;scene name='33/330227/Dna_polymerase_f8/1'&gt;F8&lt;/scene&gt; : 1 &lt;scene name='33/330227/A22/1'&gt;A22&lt;/scene&gt; : 1 E4 + primer–template DNA + incoming dTTP.<br /> <br /> '''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).<br /> <br /> '''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).<br /> <br /> '''E4 (uracil-DNA glycosylase homolog):''' ~218 residues, resembles VACV D4 and contacts F8 Exo directly.<br /> <br /> ----<br /> <br /> <br /> <br /> ==DNA binding &amp; active site==<br /> <br /> '''Bound nucleic acids:''' 22-nt template strand + 14-nt primer strand in the structure; incoming dTTP and a catalytic Mg²⁺ are observed.<br /> <br /> '''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.<br /> <br /> '''Residues coordinating catalysis / substrate:''' conserved Asp residues D549 (motif A) and D753 (motif C) coordinate the catalytic metal; Y554 stacks the incoming ribose (steric gate against rNTPs); R634 and K661 stabilize triphosphate. These motifs closely mirror canonical B-family polymerases.<br /> ----<br /> <br /> <br /> <br /> ==Processivity mechanism — “forward sliding clamp”==<br /> <br /> '''Key observation:''' A22–E4 folds back and, together with F8 NTD/Exo, forms a closed ring/channel that encircles the single-stranded template.<br /> <br /> '''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.<br /> <br /> '''Supporting biochemistry:''' Primer-extension assays show F8 alone is distributive (incorporates &lt;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.<br /> ----<br /> <br /> <br /> <br /> ==Notable structural features==<br /> <br /> Fingers domain rotates (~17°) toward palm in replicating state — brings R634 / K661 closer to incoming dNTP triphosphate.<br /> <br /> Thumb wraps around duplex; DNA duplex remains B-form over the 14 base pairs modeled.<br /> <br /> A22 Mid domain resembles ligase O-adenylylation/OB modules but substitutions (hydrophobic/negative residues) likely prevent ATP binding — A22 is a degenerative ligase-like linker rather than an active ligase.<br /> <br /> 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.<br /> <br /> &lt;/StructureSection&gt;</div>

Silky Srivastava https://proteopedia.org/index.php?title=Monkeypox_DNA_Polymerase&diff=4396047 2025-11-29T23:26:21Z

<p>Silky Srivastava: </p> <hr /> <div>==Your Heading Here (maybe something like 'Structure')==<br /> &lt;StructureSection load='8hg1' size='350' side='right' caption='testing' scene=''&gt;<br /> <br /> ==Introduction==<br /> 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.<br /> ----<br /> <br /> <br /> <br /> ==Biological Function==<br /> 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.<br /> ----<br /> <br /> <br /> <br /> ==Overall Architecture==<br /> <br /> '''Stoichiometry:''' 1 &lt;scene name='33/330227/Dna_polymerase_f8/1'&gt;F8&lt;/scene&gt; : 1 A22 : 1 E4 + primer–template DNA + incoming dTTP.<br /> <br /> '''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).<br /> <br /> '''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).<br /> <br /> '''E4 (uracil-DNA glycosylase homolog):''' ~218 residues, resembles VACV D4 and contacts F8 Exo directly.<br /> <br /> ----<br /> <br /> <br /> <br /> ==DNA binding &amp; active site==<br /> <br /> '''Bound nucleic acids:''' 22-nt template strand + 14-nt primer strand in the structure; incoming dTTP and a catalytic Mg²⁺ are observed.<br /> <br /> '''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.<br /> <br /> '''Residues coordinating catalysis / substrate:''' conserved Asp residues D549 (motif A) and D753 (motif C) coordinate the catalytic metal; Y554 stacks the incoming ribose (steric gate against rNTPs); R634 and K661 stabilize triphosphate. These motifs closely mirror canonical B-family polymerases.<br /> ----<br /> <br /> <br /> <br /> ==Processivity mechanism — “forward sliding clamp”==<br /> <br /> '''Key observation:''' A22–E4 folds back and, together with F8 NTD/Exo, forms a closed ring/channel that encircles the single-stranded template.<br /> <br /> '''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.<br /> <br /> '''Supporting biochemistry:''' Primer-extension assays show F8 alone is distributive (incorporates &lt;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.<br /> ----<br /> <br /> <br /> <br /> ==Notable structural features==<br /> <br /> Fingers domain rotates (~17°) toward palm in replicating state — brings R634 / K661 closer to incoming dNTP triphosphate.<br /> <br /> Thumb wraps around duplex; DNA duplex remains B-form over the 14 base pairs modeled.<br /> <br /> A22 Mid domain resembles ligase O-adenylylation/OB modules but substitutions (hydrophobic/negative residues) likely prevent ATP binding — A22 is a degenerative ligase-like linker rather than an active ligase.<br /> <br /> 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.<br /> <br /> &lt;/StructureSection&gt;</div>

Silky Srivastava https://proteopedia.org/index.php?title=Monkeypox_DNA_Polymerase&diff=4396043 2025-11-29T22:50:33Z

<p>Silky Srivastava: </p> <hr /> <div>==Your Heading Here (maybe something like 'Structure')==<br /> &lt;StructureSection load='8hg1' size='350' side='right' caption='testing' scene=''&gt;<br /> <br /> ==Introduction==<br /> 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.<br /> ----<br /> <br /> <br /> <br /> ==Biological Function==<br /> 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.<br /> ----<br /> <br /> <br /> <br /> ==Overall Architecture==<br /> <br /> '''Stoichiometry:''' 1 F8 : 1 A22 : 1 E4 + primer–template DNA + incoming dTTP.<br /> <br /> '''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).<br /> <br /> '''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).<br /> <br /> '''E4 (uracil-DNA glycosylase homolog):''' ~218 residues, resembles VACV D4 and contacts F8 Exo directly.<br /> <br /> ----<br /> <br /> <br /> <br /> ==DNA binding &amp; active site==<br /> <br /> '''Bound nucleic acids:''' 22-nt template strand + 14-nt primer strand in the structure; incoming dTTP and a catalytic Mg²⁺ are observed.<br /> <br /> '''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.<br /> <br /> '''Residues coordinating catalysis / substrate:''' conserved Asp residues D549 (motif A) and D753 (motif C) coordinate the catalytic metal; Y554 stacks the incoming ribose (steric gate against rNTPs); R634 and K661 stabilize triphosphate. These motifs closely mirror canonical B-family polymerases.<br /> ----<br /> <br /> <br /> <br /> ==Processivity mechanism — “forward sliding clamp”==<br /> <br /> '''Key observation:''' A22–E4 folds back and, together with F8 NTD/Exo, forms a closed ring/channel that encircles the single-stranded template.<br /> <br /> '''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.<br /> <br /> '''Supporting biochemistry:''' Primer-extension assays show F8 alone is distributive (incorporates &lt;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.<br /> ----<br /> <br /> <br /> <br /> ==Notable structural features==<br /> <br /> Fingers domain rotates (~17°) toward palm in replicating state — brings R634 / K661 closer to incoming dNTP triphosphate.<br /> <br /> Thumb wraps around duplex; DNA duplex remains B-form over the 14 base pairs modeled.<br /> <br /> A22 Mid domain resembles ligase O-adenylylation/OB modules but substitutions (hydrophobic/negative residues) likely prevent ATP binding — A22 is a degenerative ligase-like linker rather than an active ligase.<br /> <br /> 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.<br /> <br /> &lt;/StructureSection&gt;</div>

Silky Srivastava https://proteopedia.org/index.php?title=File:8hg1.jpeg&diff=4396041 2025-11-29T22:24:03Z

<p>Silky Srivastava: </p> <hr /> <div></div>

Silky Srivastava https://proteopedia.org/index.php?title=Monkeypox_DNA_Polymerase&diff=4395988 2025-11-29T18:26:37Z

<p>Silky Srivastava: Removing all content from page</p> <hr /> <div></div>

Silky Srivastava https://proteopedia.org/index.php?title=Monkeypox_DNA_Polymerase&diff=4395987 2025-11-29T18:26:21Z

<p>Silky Srivastava: Replacing page with &#039;==Your Heading Here (maybe something like &#039;Structure&#039;)== &lt;StructureSection load=&#039;8hg1&#039; size=&#039;350&#039; side=&#039;right&#039; caption=&#039;Escherichia coli reca protein-bound DNA (PDB entry [[3re...&#039;</p> <hr /> <div>==Your Heading Here (maybe something like 'Structure')==<br /> &lt;StructureSection load='8hg1' size='350' side='right' caption='Escherichia coli reca protein-bound DNA (PDB entry [[3rec]])' scene=''&gt;<br /> <br /> Anything in this section will appear adjacent to the 3D structure and will be scrollable.<br /> <br /> &lt;/StructureSection&gt;</div>

Silky Srivastava