Proteopedia - User contributions [en]

https://proteopedia.org/api.php?action=feedcontributions&feedformat=atom&user=Ashton+Lake Proteopedia - User contributions [en] 2026-09-21T03:32:13Z User contributions MediaWiki 1.43.8 https://proteopedia.org/index.php?title=User:Ashton_Lake/Sandbox_1&diff=4441531 User:Ashton Lake/Sandbox 1 2026-04-22T18:26:59Z

<p>Ashton Lake: </p> <hr /> <div>=NpmA: A Methyltransferase in E. Coli=<br /> <StructureSection load='3p2i' size='340' side='right' caption='SAM Dependent Methyltransferase NpmA' scene=''><br /> <br /> == Introduction ==<br /> NpmA is a plasmid-mediated methyltransferase that was discovered in Japan, 2003, and confers a high level of aminoglycoside antibiotic resistance against most antibiotics in- class. It is active as a <scene name='11/1107911/Intro/1'>monomer</scene> in solution but is known to dimerize as well. NpmA uses an S-adenosyl-methionine (SAM) as cofactor to remove a methyl group from SAM, converting it to S-adenosyl-homocysteine (SAH), and add it to the 30S ribosome unit on adenosine 1408. This addition prevents the binding of [https://www.ncbi.nlm.nih.gov/books/NBK541105/ aminoglycosides] and blocks their ability to shut down the ribosome and RNA transcription.<ref name=”Nilhofer Husain”>PMID=21062819</ref><br /> == RNA Stabilization ==<br /> Around the active site for NpmA, there are certain regions that help in stabilizing the RNA. One such region involves <scene name='11/1107911/Trp_res/1'>W107 and W197</scene>, which uses aromatic stacking with the tryptophans' indole groups to stabilize A1408 of the RNA. Another region that assists in RNA stabilization is <scene name='11/1107911/Spacefill_rna/1'>F62-F82</scene>. This region utilizes four positive lysine residues to hold onto the negative charge of the RNA.<ref name=”Husain”>PMID=27845431</ref><br /> <br /> == Co-Factor Stabilization ==<br /> === S-Adenosylmethionine ===<br /> SAM binding pocket uses hydrogen bonding interactions between residues <scene name='11/1107911/Sam_bonds/1'>N38, D55, A87, E88, T109, L104, and S195</scene>. Alanine and lysine use backbone residues for hydrogen bonding.<ref name=”Nilhofer Husain”>PMID=21062819</ref><br /> [[Image:SAMbonds.png|400 px|right|thumb|Figure 1: Active Site SAM Hydrogen Bonding]]<br /> === S-Adenosylhomocysteine ===<br /> SAH binding pocket utilizes hydrogen bonding with key residues such as <scene name='11/1107911/Sah/1'>D30, D55, A87, E88, L104, and T109.</scene> The alanine and lysine residues participate in hydrogen bonding with their backbone atoms.<ref name=”Nilhofer Husain”>PMID=21062819</ref><br /> [[Image:SAH_Stabilization.png|400 px|right|thumb|Figure 2: Active Site SAH Hydrogen Bonding]]<br /> == Similar Proteins ==<br /> Many proteins that have similar sequences and functions to NpmA differ in where the key residues occur. For example, <scene name='11/1107911/Kamb/1'>KamB</scene> is another SAM-dependent methyltransferase that methylates A1408 on the 30s subunit.<ref name=”Kawai”>PMID=34310216</ref> KamB does have the RNA stabilizing tryptophan residues, but they are <scene name='11/1107911/W105193/1'>W105 and W193</scene> which indicates that there are two residues that are likely missing from KamB that are in NpmA. This is common across many similar proteins to NpmA.<br /> == Student Contributors ==<br /> *Ashton Lake<br /> *Jason Garcia<br /> *Hayden Teague<br /> <br /> </StructureSection><br /> == References ==<br /> <references/><br /> <ref name=”Nilofer Husain”>PMID=21062819</ref>Nilofer Husain, Sonja Obranić, Lukasz Koscinski, J. Seetharaman, Fedora Babić, Janusz M. Bujnicki, Gordana Maravić-Vlahoviček, J. Sivaraman, Structural basis for the methylation of A1408 in 16S rRNA by a panaminoglycoside resistance methyltransferase NpmA from a clinical isolate and analysis of the NpmA interactions with the 30S ribosomal subunit, Nucleic Acids Research, Volume 39, Issue 5, 1 March 2011, Pages 1903–1918, https://doi.org/10.1093/nar/gkq1033.<br /> <br /> <ref name=”Husain”>PMID=27845431</ref>Husain, N., Tulsian, N., Chien, W. et al. Ligand-mediated changes in conformational dynamics of NpmA: implications for ribosomal interactions. Sci Rep 6, 37061 (2016). https://doi.org/10.1038/srep37061.<br /> <br /> <ref name=”Kawai”>PMID=34310216</ref>Kawai A, Suzuki M, Tsukamoto K, Minato Y, Doi Y,, 2021. Functional and Structural Characterization of Acquired 16S rRNA Methyltransferase NpmB1 Conferring Pan-Aminoglycoside Resistance. Antimicrob Agents Chemother 65:10.1128/aac.01009-21.</div>

Ashton Lake https://proteopedia.org/index.php?title=User:Ashton_Lake/Sandbox_1&diff=4441530 User:Ashton Lake/Sandbox 1 2026-04-22T18:26:33Z

<p>Ashton Lake: </p> <hr /> <div>=NpmA: A Methyltransferase in E. Coli=<br /> <StructureSection load='3p2i' size='340' side='right' caption='SAM Dependent Methyltransferase NpmA' scene=''><br /> <br /> == Introduction ==<br /> NpmA is a plasmid-mediated methyltransferase that was discovered in Japan, 2003, and confers a high level of aminoglycoside antibiotic resistance against most antibiotics in- class. It is active as a <scene name='11/1107911/Intro/1'>monomer</scene> in solution but is known to dimerize as well. NpmA uses an S-adenosyl-methionine (SAM) as cofactor to remove a methyl group from SAM, converting it to S-adenosyl-homocysteine (SAH), and add it to the 30S ribosome unit on adenosine 1408. This addition prevents the binding of [https://www.ncbi.nlm.nih.gov/books/NBK541105/ aminoglycosides] and blocks their ability to shut down the ribosome and RNA transcription.<ref name=”Husain”>PMID=21062819</ref><br /> == RNA Stabilization ==<br /> Around the active site for NpmA, there are certain regions that help in stabilizing the RNA. One such region involves <scene name='11/1107911/Trp_res/1'>W107 and W197</scene>, which uses aromatic stacking with the tryptophans' indole groups to stabilize A1408 of the RNA. Another region that assists in RNA stabilization is <scene name='11/1107911/Spacefill_rna/1'>F62-F82</scene>. This region utilizes four positive lysine residues to hold onto the negative charge of the RNA.<ref name=”Husain”>PMID=27845431</ref><br /> <br /> == Co-Factor Stabilization ==<br /> === S-Adenosylmethionine ===<br /> SAM binding pocket uses hydrogen bonding interactions between residues <scene name='11/1107911/Sam_bonds/1'>N38, D55, A87, E88, T109, L104, and S195</scene>. Alanine and lysine use backbone residues for hydrogen bonding.<ref name=”Husain”>PMID=21062819</ref><br /> [[Image:SAMbonds.png|400 px|right|thumb|Figure 1: Active Site SAM Hydrogen Bonding]]<br /> === S-Adenosylhomocysteine ===<br /> SAH binding pocket utilizes hydrogen bonding with key residues such as <scene name='11/1107911/Sah/1'>D30, D55, A87, E88, L104, and T109.</scene> The alanine and lysine residues participate in hydrogen bonding with their backbone atoms.<ref name=”Husain”>PMID=21062819</ref><br /> [[Image:SAH_Stabilization.png|400 px|right|thumb|Figure 2: Active Site SAH Hydrogen Bonding]]<br /> == Similar Proteins ==<br /> Many proteins that have similar sequences and functions to NpmA differ in where the key residues occur. For example, <scene name='11/1107911/Kamb/1'>KamB</scene> is another SAM-dependent methyltransferase that methylates A1408 on the 30s subunit.<ref name=”Kawai”>PMID=34310216</ref> KamB does have the RNA stabilizing tryptophan residues, but they are <scene name='11/1107911/W105193/1'>W105 and W193</scene> which indicates that there are two residues that are likely missing from KamB that are in NpmA. This is common across many similar proteins to NpmA.<br /> == Student Contributors ==<br /> *Ashton Lake<br /> *Jason Garcia<br /> *Hayden Teague<br /> <br /> </StructureSection><br /> == References ==<br /> <references/><br /> <ref name=”Nilofer Husain”>PMID=21062819</ref>Nilofer Husain, Sonja Obranić, Lukasz Koscinski, J. Seetharaman, Fedora Babić, Janusz M. Bujnicki, Gordana Maravić-Vlahoviček, J. Sivaraman, Structural basis for the methylation of A1408 in 16S rRNA by a panaminoglycoside resistance methyltransferase NpmA from a clinical isolate and analysis of the NpmA interactions with the 30S ribosomal subunit, Nucleic Acids Research, Volume 39, Issue 5, 1 March 2011, Pages 1903–1918, https://doi.org/10.1093/nar/gkq1033.<br /> <br /> <ref name=”Husain”>PMID=27845431</ref>Husain, N., Tulsian, N., Chien, W. et al. Ligand-mediated changes in conformational dynamics of NpmA: implications for ribosomal interactions. Sci Rep 6, 37061 (2016). https://doi.org/10.1038/srep37061.<br /> <br /> <ref name=”Kawai”>PMID=34310216</ref>Kawai A, Suzuki M, Tsukamoto K, Minato Y, Doi Y,, 2021. Functional and Structural Characterization of Acquired 16S rRNA Methyltransferase NpmB1 Conferring Pan-Aminoglycoside Resistance. Antimicrob Agents Chemother 65:10.1128/aac.01009-21.</div>

Ashton Lake https://proteopedia.org/index.php?title=User:Ashton_Lake/Sandbox_1&diff=4441529 User:Ashton Lake/Sandbox 1 2026-04-22T18:25:55Z

<p>Ashton Lake: </p> <hr /> <div>=NpmA: A Methyltransferase in E. Coli=<br /> <StructureSection load='3p2i' size='340' side='right' caption='SAM Dependent Methyltransferase NpmA' scene=''><br /> <br /> == Introduction ==<br /> NpmA is a plasmid-mediated methyltransferase that was discovered in Japan, 2003, and confers a high level of aminoglycoside antibiotic resistance against most antibiotics in- class. It is active as a <scene name='11/1107911/Intro/1'>monomer</scene> in solution but is known to dimerize as well. NpmA uses an S-adenosyl-methionine (SAM) as cofactor to remove a methyl group from SAM, converting it to S-adenosyl-homocysteine (SAH), and add it to the 30S ribosome unit on adenosine 1408. This addition prevents the binding of [https://www.ncbi.nlm.nih.gov/books/NBK541105/ aminoglycosides] and blocks their ability to shut down the ribosome and RNA transcription.<ref name=”Husain”>PMID=21062819</ref><br /> == RNA Stabilization ==<br /> Around the active site for NpmA, there are certain regions that help in stabilizing the RNA. One such region involves <scene name='11/1107911/Trp_res/1'>W107 and W197</scene>, which uses aromatic stacking with the tryptophans' indole groups to stabilize A1408 of the RNA. Another region that assists in RNA stabilization is <scene name='11/1107911/Spacefill_rna/1'>F62-F82</scene>. This region utilizes four positive lysine residues to hold onto the negative charge of the RNA.<ref name=”Husain”>PMID=27845431</ref><br /> <br /> == Co-Factor Stabilization ==<br /> === S-Adenosylmethionine ===<br /> SAM binding pocket uses hydrogen bonding interactions between residues <scene name='11/1107911/Sam_bonds/1'>N38, D55, A87, E88, T109, L104, and S195</scene>. Alanine and lysine use backbone residues for hydrogen bonding.<ref name=”Husain”>PMID=21062819</ref><br /> [[Image:SAMbonds.png|400 px|right|thumb|Figure 1: Active Site SAM Hydrogen Bonding]]<br /> === S-Adenosylhomocysteine ===<br /> SAH binding pocket utilizes hydrogen bonding with key residues such as <scene name='11/1107911/Sah/1'>D30, D55, A87, E88, L104, and T109.</scene> The alanine and lysine residues participate in hydrogen bonding with their backbone atoms.<ref name=”Husain”>PMID=21062819</ref><br /> [[Image:SAH_Stabilization.png|400 px|right|thumb|Figure 2: Active Site SAH Hydrogen Bonding]]<br /> == Similar Proteins ==<br /> Many proteins that have similar sequences and functions to NpmA differ in where the key residues occur. For example, <scene name='11/1107911/Kamb/1'>KamB</scene> is another SAM-dependent methyltransferase that methylates A1408 on the 30s subunit.<ref name=”Kawai”>PMID=34310216</ref> KamB does have the RNA stabilizing tryptophan residues, but they are <scene name='11/1107911/W105193/1'>W105 and W193</scene> which indicates that there are two residues that are likely missing from KamB that are in NpmA. This is common across many similar proteins to NpmA.<br /> == Student Contributors ==<br /> *Ashton Lake<br /> *Jason Garcia<br /> *Hayden Teague<br /> <br /> </StructureSection><br /> == References ==<br /> <references/><br /> <ref name=”Husain”>PMID=21062819</ref>Nilofer Husain, Sonja Obranić, Lukasz Koscinski, J. Seetharaman, Fedora Babić, Janusz M. Bujnicki, Gordana Maravić-Vlahoviček, J. Sivaraman, Structural basis for the methylation of A1408 in 16S rRNA by a panaminoglycoside resistance methyltransferase NpmA from a clinical isolate and analysis of the NpmA interactions with the 30S ribosomal subunit, Nucleic Acids Research, Volume 39, Issue 5, 1 March 2011, Pages 1903–1918, https://doi.org/10.1093/nar/gkq1033.<br /> <br /> <ref name=”Husain”>PMID=27845431</ref>Husain, N., Tulsian, N., Chien, W. et al. Ligand-mediated changes in conformational dynamics of NpmA: implications for ribosomal interactions. Sci Rep 6, 37061 (2016). https://doi.org/10.1038/srep37061.<br /> <br /> <ref name=”Kawai”>PMID=34310216</ref>Kawai A, Suzuki M, Tsukamoto K, Minato Y, Doi Y,, 2021. Functional and Structural Characterization of Acquired 16S rRNA Methyltransferase NpmB1 Conferring Pan-Aminoglycoside Resistance. Antimicrob Agents Chemother 65:10.1128/aac.01009-21.</div>

Ashton Lake https://proteopedia.org/index.php?title=User:Ashton_Lake/Sandbox_1&diff=4441528 User:Ashton Lake/Sandbox 1 2026-04-22T18:25:09Z

<p>Ashton Lake: </p> <hr /> <div>=NpmA: A Methyltransferase in E. Coli=<br /> <StructureSection load='3p2i' size='340' side='right' caption='SAM Dependent Methyltransferase NpmA' scene=''><br /> <br /> == Introduction ==<br /> NpmA is a plasmid-mediated methyltransferase that was discovered in Japan, 2003, and confers a high level of aminoglycoside antibiotic resistance against most antibiotics in- class. It is active as a <scene name='11/1107911/Intro/1'>monomer</scene> in solution but is known to dimerize as well. NpmA uses an S-adenosyl-methionine (SAM) as cofactor to remove a methyl group from SAM, converting it to S-adenosyl-homocysteine (SAH), and add it to the 30S ribosome unit on adenosine 1408. This addition prevents the binding of [https://www.ncbi.nlm.nih.gov/books/NBK541105/ aminoglycosides] and blocks their ability to shut down the ribosome and RNA transcription.<ref name=”Husain 2011”>PMID=21062819</ref><br /> == RNA Stabilization ==<br /> Around the active site for NpmA, there are certain regions that help in stabilizing the RNA. One such region involves <scene name='11/1107911/Trp_res/1'>W107 and W197</scene>, which uses aromatic stacking with the tryptophans' indole groups to stabilize A1408 of the RNA. Another region that assists in RNA stabilization is <scene name='11/1107911/Spacefill_rna/1'>F62-F82</scene>. This region utilizes four positive lysine residues to hold onto the negative charge of the RNA.<ref name=”Husain 2016”>PMID=27845431</ref><br /> <br /> == Co-Factor Stabilization ==<br /> === S-Adenosylmethionine ===<br /> SAM binding pocket uses hydrogen bonding interactions between residues <scene name='11/1107911/Sam_bonds/1'>N38, D55, A87, E88, T109, L104, and S195</scene>. Alanine and lysine use backbone residues for hydrogen bonding.<ref name=”Husain 2011”>PMID=21062819</ref><br /> [[Image:SAMbonds.png|400 px|right|thumb|Figure 1: Active Site SAM Hydrogen Bonding]]<br /> === S-Adenosylhomocysteine ===<br /> SAH binding pocket utilizes hydrogen bonding with key residues such as <scene name='11/1107911/Sah/1'>D30, D55, A87, E88, L104, and T109.</scene> The alanine and lysine residues participate in hydrogen bonding with their backbone atoms.<ref name=”Husain 2011”>PMID=21062819</ref><br /> [[Image:SAH_Stabilization.png|400 px|right|thumb|Figure 2: Active Site SAH Hydrogen Bonding]]<br /> == Similar Proteins ==<br /> Many proteins that have similar sequences and functions to NpmA differ in where the key residues occur. For example, <scene name='11/1107911/Kamb/1'>KamB</scene> is another SAM-dependent methyltransferase that methylates A1408 on the 30s subunit.<ref name=”Kawai”>PMID=34310216</ref> KamB does have the RNA stabilizing tryptophan residues, but they are <scene name='11/1107911/W105193/1'>W105 and W193</scene> which indicates that there are two residues that are likely missing from KamB that are in NpmA. This is common across many similar proteins to NpmA.<br /> == Student Contributors ==<br /> *Ashton Lake<br /> *Jason Garcia<br /> *Hayden Teague<br /> <br /> </StructureSection><br /> == References ==<br /> <references/><br /> <ref name=”Husain, Obranić, et al.”>PMID=21062819</ref>Nilofer Husain, Sonja Obranić, Lukasz Koscinski, J. Seetharaman, Fedora Babić, Janusz M. Bujnicki, Gordana Maravić-Vlahoviček, J. Sivaraman, Structural basis for the methylation of A1408 in 16S rRNA by a panaminoglycoside resistance methyltransferase NpmA from a clinical isolate and analysis of the NpmA interactions with the 30S ribosomal subunit, Nucleic Acids Research, Volume 39, Issue 5, 1 March 2011, Pages 1903–1918, https://doi.org/10.1093/nar/gkq1033.<br /> <br /> <ref name=”Husain, Tilsian, Chien, et al.”>PMID=27845431</ref>Husain, N., Tulsian, N., Chien, W. et al. Ligand-mediated changes in conformational dynamics of NpmA: implications for ribosomal interactions. Sci Rep 6, 37061 (2016). https://doi.org/10.1038/srep37061.<br /> <br /> <ref name=”Kawai”>PMID=34310216</ref>Kawai A, Suzuki M, Tsukamoto K, Minato Y, Doi Y,, 2021. Functional and Structural Characterization of Acquired 16S rRNA Methyltransferase NpmB1 Conferring Pan-Aminoglycoside Resistance. Antimicrob Agents Chemother 65:10.1128/aac.01009-21.</div>

Ashton Lake https://proteopedia.org/index.php?title=User:Ashton_Lake/Sandbox_1&diff=4441527 User:Ashton Lake/Sandbox 1 2026-04-22T18:23:33Z

<p>Ashton Lake: </p> <hr /> <div>=NpmA: A Methyltransferase in E. Coli=<br /> <StructureSection load='3p2i' size='340' side='right' caption='SAM Dependent Methyltransferase NpmA' scene=''><br /> <br /> == Introduction ==<br /> NpmA is a plasmid-mediated methyltransferase that was discovered in Japan, 2003, and confers a high level of aminoglycoside antibiotic resistance against most antibiotics in- class. It is active as a <scene name='11/1107911/Intro/1'>monomer</scene> in solution but is known to dimerize as well. NpmA uses an S-adenosyl-methionine (SAM) as cofactor to remove a methyl group from SAM, converting it to S-adenosyl-homocysteine (SAH), and add it to the 30S ribosome unit on adenosine 1408. This addition prevents the binding of [https://www.ncbi.nlm.nih.gov/books/NBK541105/ aminoglycosides] and blocks their ability to shut down the ribosome and RNA transcription.<ref name=”Husain 2011”>PMID=21062819</ref><br /> == RNA Stabilization ==<br /> Around the active site for NpmA, there are certain regions that help in stabilizing the RNA. One such region involves <scene name='11/1107911/Trp_res/1'>W107 and W197</scene>, which uses aromatic stacking with the tryptophans' indole groups to stabilize A1408 of the RNA. Another region that assists in RNA stabilization is <scene name='11/1107911/Spacefill_rna/1'>F62-F82</scene>. This region utilizes four positive lysine residues to hold onto the negative charge of the RNA.<ref name=”Husain 2016”>PMID=27845431</ref><br /> <br /> == Co-Factor Stabilization ==<br /> === S-Adenosylmethionine ===<br /> SAM binding pocket uses hydrogen bonding interactions between residues <scene name='11/1107911/Sam_bonds/1'>N38, D55, A87, E88, T109, L104, and S195</scene>. Alanine and lysine use backbone residues for hydrogen bonding.<ref name=”Husain 2011”>PMID=21062819</ref><br /> [[Image:SAMbonds.png|400 px|right|thumb|Figure 1: Active Site SAM Hydrogen Bonding]]<br /> === S-Adenosylhomocysteine ===<br /> SAH binding pocket utilizes hydrogen bonding with key residues such as <scene name='11/1107911/Sah/1'>D30, D55, A87, E88, L104, and T109.</scene> The alanine and lysine residues participate in hydrogen bonding with their backbone atoms.<ref name=”Husain 2011”>PMID=21062819</ref><br /> [[Image:SAH_Stabilization.png|400 px|right|thumb|Figure 2: Active Site SAH Hydrogen Bonding]]<br /> == Similar Proteins ==<br /> Many proteins that have similar sequences and functions to NpmA differ in where the key residues occur. For example, <scene name='11/1107911/Kamb/1'>KamB</scene> is another SAM-dependent methyltransferase that methylates A1408 on the 30s subunit.<ref name=”Kawai”>PMID=34310216</ref> KamB does have the RNA stabilizing tryptophan residues, but they are <scene name='11/1107911/W105193/1'>W105 and W193</scene> which indicates that there are two residues that are likely missing from KamB that are in NpmA. This is common across many similar proteins to NpmA.<br /> == Student Contributors ==<br /> *Ashton Lake<br /> *Jason Garcia<br /> *Hayden Teague<br /> <br /> </StructureSection><br /> == References ==<br /> <references/><br /> <ref name=”Husain 2011”>PMID=21062819</ref>Nilofer Husain, Sonja Obranić, Lukasz Koscinski, J. Seetharaman, Fedora Babić, Janusz M. Bujnicki, Gordana Maravić-Vlahoviček, J. Sivaraman, Structural basis for the methylation of A1408 in 16S rRNA by a panaminoglycoside resistance methyltransferase NpmA from a clinical isolate and analysis of the NpmA interactions with the 30S ribosomal subunit, Nucleic Acids Research, Volume 39, Issue 5, 1 March 2011, Pages 1903–1918, https://doi.org/10.1093/nar/gkq1033.<br /> <br /> <ref name=”Husain 2016”>PMID=27845431</ref>Husain, N., Tulsian, N., Chien, W. et al. Ligand-mediated changes in conformational dynamics of NpmA: implications for ribosomal interactions. Sci Rep 6, 37061 (2016). https://doi.org/10.1038/srep37061.<br /> <br /> <ref name=”Kawai”>PMID=34310216</ref>Kawai A, Suzuki M, Tsukamoto K, Minato Y, Doi Y,, 2021. Functional and Structural Characterization of Acquired 16S rRNA Methyltransferase NpmB1 Conferring Pan-Aminoglycoside Resistance. Antimicrob Agents Chemother 65:10.1128/aac.01009-21.</div>

Ashton Lake https://proteopedia.org/index.php?title=User:Ashton_Lake/Sandbox_1&diff=4441526 User:Ashton Lake/Sandbox 1 2026-04-22T18:22:18Z

<p>Ashton Lake: </p> <hr /> <div>=NpmA: A Methyltransferase in E. Coli=<br /> <StructureSection load='3p2i' size='340' side='right' caption='SAM Dependent Methyltransferase NpmA' scene=''><br /> <br /> == Introduction ==<br /> NpmA is a plasmid-mediated methyltransferase that was discovered in Japan, 2003, and confers a high level of aminoglycoside antibiotic resistance against most antibiotics in- class. It is active as a <scene name='11/1107911/Intro/1'>monomer</scene> in solution but is known to dimerize as well. NpmA uses an S-adenosyl-methionine (SAM) as cofactor to remove a methyl group from SAM, converting it to S-adenosyl-homocysteine (SAH), and add it to the 30S ribosome unit on adenosine 1408. This addition prevents the binding of [https://www.ncbi.nlm.nih.gov/books/NBK541105/ aminoglycosides] and blocks their ability to shut down the ribosome and RNA transcription.<ref name=”Husain 2011”>PMID=21062819<br /> == RNA Stabilization ==<br /> Around the active site for NpmA, there are certain regions that help in stabilizing the RNA. One such region involves <scene name='11/1107911/Trp_res/1'>W107 and W197</scene>, which uses aromatic stacking with the tryptophans' indole groups to stabilize A1408 of the RNA. Another region that assists in RNA stabilization is <scene name='11/1107911/Spacefill_rna/1'>F62-F82</scene>. This region utilizes four positive lysine residues to hold onto the negative charge of the RNA.<ref name=”Husain 2016”><br /> <br /> == Co-Factor Stabilization ==<br /> === S-Adenosylmethionine ===<br /> SAM binding pocket uses hydrogen bonding interactions between residues <scene name='11/1107911/Sam_bonds/1'>N38, D55, A87, E88, T109, L104, and S195</scene>. Alanine and lysine use backbone residues for hydrogen bonding.<ref name=”Husain 2011”>PMID=21062819<br /> [[Image:SAMbonds.png|400 px|right|thumb|Figure 1: Active Site SAM Hydrogen Bonding]]<br /> === S-Adenosylhomocysteine ===<br /> SAH binding pocket utilizes hydrogen bonding with key residues such as <scene name='11/1107911/Sah/1'>D30, D55, A87, E88, L104, and T109.</scene> The alanine and lysine residues participate in hydrogen bonding with their backbone atoms.<ref name=”Husain 2011”>PMID=21062819<br /> [[Image:SAH_Stabilization.png|400 px|right|thumb|Figure 2: Active Site SAH Hydrogen Bonding]]<br /> == Similar Proteins ==<br /> Many proteins that have similar sequences and functions to NpmA differ in where the key residues occur. For example, <scene name='11/1107911/Kamb/1'>KamB</scene> is another SAM-dependent methyltransferase that methylates A1408 on the 30s subunit.<ref name=”Kawai”> KamB does have the RNA stabilizing tryptophan residues, but they are <scene name='11/1107911/W105193/1'>W105 and W193</scene> which indicates that there are two residues that are likely missing from KamB that are in NpmA. This is common across many similar proteins to NpmA.<br /> == Student Contributors ==<br /> *Ashton Lake<br /> *Jason Garcia<br /> *Hayden Teague<br /> <br /> </StructureSection><br /> == References ==<br /> <references/><br /> <ref name=”Husain 2011”>PMID=21062819</ref>Nilofer Husain, Sonja Obranić, Lukasz Koscinski, J. Seetharaman, Fedora Babić, Janusz M. Bujnicki, Gordana Maravić-Vlahoviček, J. Sivaraman, Structural basis for the methylation of A1408 in 16S rRNA by a panaminoglycoside resistance methyltransferase NpmA from a clinical isolate and analysis of the NpmA interactions with the 30S ribosomal subunit, Nucleic Acids Research, Volume 39, Issue 5, 1 March 2011, Pages 1903–1918, https://doi.org/10.1093/nar/gkq1033.<br /> <br /> <ref name=”Husain 2016”>PMID=27845431</ref>Husain, N., Tulsian, N., Chien, W. et al. Ligand-mediated changes in conformational dynamics of NpmA: implications for ribosomal interactions. Sci Rep 6, 37061 (2016). https://doi.org/10.1038/srep37061.<br /> <br /> <ref name=”Kawai”>PMID=34310216</ref>Kawai A, Suzuki M, Tsukamoto K, Minato Y, Doi Y,, 2021. Functional and Structural Characterization of Acquired 16S rRNA Methyltransferase NpmB1 Conferring Pan-Aminoglycoside Resistance. Antimicrob Agents Chemother 65:10.1128/aac.01009-21.</div>

Ashton Lake https://proteopedia.org/index.php?title=User:Ashton_Lake/Sandbox_1&diff=4441525 User:Ashton Lake/Sandbox 1 2026-04-22T18:21:36Z

<p>Ashton Lake: </p> <hr /> <div>=NpmA: A Methyltransferase in E. Coli=<br /> <StructureSection load='3p2i' size='340' side='right' caption='SAM Dependent Methyltransferase NpmA' scene=''><br /> <br /> == Introduction ==<br /> NpmA is a plasmid-mediated methyltransferase that was discovered in Japan, 2003, and confers a high level of aminoglycoside antibiotic resistance against most antibiotics in- class. It is active as a <scene name='11/1107911/Intro/1'>monomer</scene> in solution but is known to dimerize as well. NpmA uses an S-adenosyl-methionine (SAM) as cofactor to remove a methyl group from SAM, converting it to S-adenosyl-homocysteine (SAH), and add it to the 30S ribosome unit on adenosine 1408. This addition prevents the binding of [https://www.ncbi.nlm.nih.gov/books/NBK541105/ aminoglycosides] and blocks their ability to shut down the ribosome and RNA transcription.<ref name=”Husain 2011”><br /> == RNA Stabilization ==<br /> Around the active site for NpmA, there are certain regions that help in stabilizing the RNA. One such region involves <scene name='11/1107911/Trp_res/1'>W107 and W197</scene>, which uses aromatic stacking with the tryptophans' indole groups to stabilize A1408 of the RNA. Another region that assists in RNA stabilization is <scene name='11/1107911/Spacefill_rna/1'>F62-F82</scene>. This region utilizes four positive lysine residues to hold onto the negative charge of the RNA.<ref name=”Husain 2016”><br /> <br /> == Co-Factor Stabilization ==<br /> === S-Adenosylmethionine ===<br /> SAM binding pocket uses hydrogen bonding interactions between residues <scene name='11/1107911/Sam_bonds/1'>N38, D55, A87, E88, T109, L104, and S195</scene>. Alanine and lysine use backbone residues for hydrogen bonding.<ref name=”Husain 2011”><br /> [[Image:SAMbonds.png|400 px|right|thumb|Figure 1: Active Site SAM Hydrogen Bonding]]<br /> === S-Adenosylhomocysteine ===<br /> SAH binding pocket utilizes hydrogen bonding with key residues such as <scene name='11/1107911/Sah/1'>D30, D55, A87, E88, L104, and T109.</scene> The alanine and lysine residues participate in hydrogen bonding with their backbone atoms.<ref name=”Husain 2011”><br /> [[Image:SAH_Stabilization.png|400 px|right|thumb|Figure 2: Active Site SAH Hydrogen Bonding]]<br /> == Similar Proteins ==<br /> Many proteins that have similar sequences and functions to NpmA differ in where the key residues occur. For example, <scene name='11/1107911/Kamb/1'>KamB</scene> is another SAM-dependent methyltransferase that methylates A1408 on the 30s subunit.<ref name=”Kawai”> KamB does have the RNA stabilizing tryptophan residues, but they are <scene name='11/1107911/W105193/1'>W105 and W193</scene> which indicates that there are two residues that are likely missing from KamB that are in NpmA. This is common across many similar proteins to NpmA.<br /> == Student Contributors ==<br /> *Ashton Lake<br /> *Jason Garcia<br /> *Hayden Teague<br /> <br /> </StructureSection><br /> == References ==<br /> <references/><br /> <ref name=”Husain 2011”>PMID=21062819</ref>Nilofer Husain, Sonja Obranić, Lukasz Koscinski, J. Seetharaman, Fedora Babić, Janusz M. Bujnicki, Gordana Maravić-Vlahoviček, J. Sivaraman, Structural basis for the methylation of A1408 in 16S rRNA by a panaminoglycoside resistance methyltransferase NpmA from a clinical isolate and analysis of the NpmA interactions with the 30S ribosomal subunit, Nucleic Acids Research, Volume 39, Issue 5, 1 March 2011, Pages 1903–1918, https://doi.org/10.1093/nar/gkq1033.<br /> <br /> <ref name=”Husain 2016”>PMID=27845431</ref>Husain, N., Tulsian, N., Chien, W. et al. Ligand-mediated changes in conformational dynamics of NpmA: implications for ribosomal interactions. Sci Rep 6, 37061 (2016). https://doi.org/10.1038/srep37061.<br /> <br /> <ref name=”Kawai”>PMID=34310216</ref>Kawai A, Suzuki M, Tsukamoto K, Minato Y, Doi Y,, 2021. Functional and Structural Characterization of Acquired 16S rRNA Methyltransferase NpmB1 Conferring Pan-Aminoglycoside Resistance. Antimicrob Agents Chemother 65:10.1128/aac.01009-21.</div>

Ashton Lake https://proteopedia.org/index.php?title=User:Ashton_Lake/Sandbox_1&diff=4441524 User:Ashton Lake/Sandbox 1 2026-04-22T18:20:04Z

<p>Ashton Lake: </p> <hr /> <div>=NpmA: A Methyltransferase in E. Coli=<br /> <StructureSection load='3p2i' size='340' side='right' caption='SAM Dependent Methyltransferase NpmA' scene=''><br /> <br /> == Introduction ==<br /> NpmA is a plasmid-mediated methyltransferase that was discovered in Japan, 2003, and confers a high level of aminoglycoside antibiotic resistance against most antibiotics in- class. It is active as a <scene name='11/1107911/Intro/1'>monomer</scene> in solution but is known to dimerize as well. NpmA uses an S-adenosyl-methionine (SAM) as cofactor to remove a methyl group from SAM, converting it to S-adenosyl-homocysteine (SAH), and add it to the 30S ribosome unit on adenosine 1408. This addition prevents the binding of [https://www.ncbi.nlm.nih.gov/books/NBK541105/ aminoglycosides] and blocks their ability to shut down the ribosome and RNA transcription.<br /> == RNA Stabilization ==<br /> Around the active site for NpmA, there are certain regions that help in stabilizing the RNA. One such region involves <scene name='11/1107911/Trp_res/1'>W107 and W197</scene>, which uses aromatic stacking with the tryptophans' indole groups to stabilize A1408 of the RNA. Another region that assists in RNA stabilization is <scene name='11/1107911/Spacefill_rna/1'>F62-F82</scene>. This region utilizes four positive lysine residues to hold onto the negative charge of the RNA.<br /> <br /> == Co-Factor Stabilization ==<br /> === S-Adenosylmethionine ===<br /> SAM binding pocket uses hydrogen bonding interactions between residues <scene name='11/1107911/Sam_bonds/1'>N38, D55, A87, E88, T109, L104, and S195</scene>. Alanine and lysine use backbone residues for hydrogen bonding.<br /> [[Image:SAMbonds.png|400 px|right|thumb|Figure 1: Active Site SAM Hydrogen Bonding]]<br /> === S-Adenosylhomocysteine ===<br /> SAH binding pocket utilizes hydrogen bonding with key residues such as <scene name='11/1107911/Sah/1'>D30, D55, A87, E88, L104, and T109.</scene> The alanine and lysine residues participate in hydrogen bonding with their backbone atoms.<br /> [[Image:SAH_Stabilization.png|400 px|right|thumb|Figure 2: Active Site SAH Hydrogen Bonding]]<br /> == Similar Proteins ==<br /> Many proteins that have similar sequences and functions to NpmA differ in where the key residues occur. For example, <scene name='11/1107911/Kamb/1'>KamB</scene> is another SAM-dependent methyltransferase that methylates A1408 on the 30s subunit. KamB does have the RNA stabilizing tryptophan residues, but they are <scene name='11/1107911/W105193/1'>W105 and W193</scene> which indicates that there are two residues that are likely missing from KamB that are in NpmA. This is common across many similar proteins to NpmA.<br /> == Student Contributors ==<br /> *Ashton Lake<br /> *Jason Garcia<br /> *Hayden Teague<br /> <br /> </StructureSection><br /> == References ==<br /> <references/><br /> <ref name=”Husain 2011”>PMID=21062819</ref>Nilofer Husain, Sonja Obranić, Lukasz Koscinski, J. Seetharaman, Fedora Babić, Janusz M. Bujnicki, Gordana Maravić-Vlahoviček, J. Sivaraman, Structural basis for the methylation of A1408 in 16S rRNA by a panaminoglycoside resistance methyltransferase NpmA from a clinical isolate and analysis of the NpmA interactions with the 30S ribosomal subunit, Nucleic Acids Research, Volume 39, Issue 5, 1 March 2011, Pages 1903–1918, https://doi.org/10.1093/nar/gkq1033.<br /> <br /> <ref name=”Husain 2016”>PMID=27845431</ref>Husain, N., Tulsian, N., Chien, W. et al. Ligand-mediated changes in conformational dynamics of NpmA: implications for ribosomal interactions. Sci Rep 6, 37061 (2016). https://doi.org/10.1038/srep37061.<br /> <br /> <ref name=”Kawai”>PMID=34310216</ref>Kawai A, Suzuki M, Tsukamoto K, Minato Y, Doi Y,, 2021. Functional and Structural Characterization of Acquired 16S rRNA Methyltransferase NpmB1 Conferring Pan-Aminoglycoside Resistance. Antimicrob Agents Chemother 65:10.1128/aac.01009-21.</div>

Ashton Lake https://proteopedia.org/index.php?title=User:Ashton_Lake/Sandbox_1&diff=4441523 User:Ashton Lake/Sandbox 1 2026-04-22T18:19:29Z

<p>Ashton Lake: </p> <hr /> <div>=NpmA: A Methyltransferase in E. Coli=<br /> <StructureSection load='3p2i' size='340' side='right' caption='SAM Dependent Methyltransferase NpmA' scene=''><br /> <br /> == Introduction ==<br /> NpmA is a plasmid-mediated methyltransferase that was discovered in Japan, 2003, and confers a high level of aminoglycoside antibiotic resistance against most antibiotics in- class. It is active as a <scene name='11/1107911/Intro/1'>monomer</scene> in solution but is known to dimerize as well. NpmA uses an S-adenosyl-methionine (SAM) as cofactor to remove a methyl group from SAM, converting it to S-adenosyl-homocysteine (SAH), and add it to the 30S ribosome unit on adenosine 1408. This addition prevents the binding of [https://www.ncbi.nlm.nih.gov/books/NBK541105/ aminoglycosides] and blocks their ability to shut down the ribosome and RNA transcription.<br /> == RNA Stabilization ==<br /> Around the active site for NpmA, there are certain regions that help in stabilizing the RNA. One such region involves <scene name='11/1107911/Trp_res/1'>W107 and W197</scene>, which uses aromatic stacking with the tryptophans' indole groups to stabilize A1408 of the RNA. Another region that assists in RNA stabilization is <scene name='11/1107911/Spacefill_rna/1'>F62-F82</scene>. This region utilizes four positive lysine residues to hold onto the negative charge of the RNA.<br /> <br /> == Co-Factor Stabilization ==<br /> === S-Adenosylmethionine ===<br /> SAM binding pocket uses hydrogen bonding interactions between residues <scene name='11/1107911/Sam_bonds/1'>N38, D55, A87, E88, T109, L104, and S195</scene>. Alanine and lysine use backbone residues for hydrogen bonding.<br /> [[Image:SAMbonds.png|400 px|right|thumb|Figure 1: Active Site SAM Hydrogen Bonding]]<br /> === S-Adenosylhomocysteine ===<br /> SAH binding pocket utilizes hydrogen bonding with key residues such as <scene name='11/1107911/Sah/1'>D30, D55, A87, E88, L104, and T109.</scene> The alanine and lysine residues participate in hydrogen bonding with their backbone atoms.<br /> [[Image:SAH_Stabilization.png|400 px|right|thumb|Figure 2: Active Site SAH Hydrogen Bonding]]<br /> == Similar Proteins ==<br /> Many proteins that have similar sequences and functions to NpmA differ in where the key residues occur. For example, <scene name='11/1107911/Kamb/1'>KamB</scene> is another SAM-dependent methyltransferase that methylates A1408 on the 30s subunit. KamB does have the RNA stabilizing tryptophan residues, but they are <scene name='11/1107911/W105193/1'>W105 and W193</scene> which indicates that there are two residues that are likely missing from KamB that are in NpmA. This is common across many similar proteins to NpmA.<br /> == Student Contributors ==<br /> *Ashton Lake<br /> *Jason Garcia<br /> *Hayden Teague<br /> <br /> </StructureSection><br /> == References ==<br /> <references/><br /> <ref name=”Husain 2010”>PMID=21062819</ref>Nilofer Husain, Sonja Obranić, Lukasz Koscinski, J. Seetharaman, Fedora Babić, Janusz M. Bujnicki, Gordana Maravić-Vlahoviček, J. Sivaraman, Structural basis for the methylation of A1408 in 16S rRNA by a panaminoglycoside resistance methyltransferase NpmA from a clinical isolate and analysis of the NpmA interactions with the 30S ribosomal subunit, Nucleic Acids Research, Volume 39, Issue 5, 1 March 2011, Pages 1903–1918, https://doi.org/10.1093/nar/gkq1033.<br /> <br /> <ref name=”Husain 2016”>PMID=27845431</ref>Husain, N., Tulsian, N., Chien, W. et al. Ligand-mediated changes in conformational dynamics of NpmA: implications for ribosomal interactions. Sci Rep 6, 37061 (2016). https://doi.org/10.1038/srep37061<br /> <br /> <ref name=”Kawai”>PMID=34310216</ref>Kawai A, Suzuki M, Tsukamoto K, Minato Y, Doi Y,, 2021. Functional and Structural Characterization of Acquired 16S rRNA Methyltransferase NpmB1 Conferring Pan-Aminoglycoside Resistance. Antimicrob Agents Chemother 65:10.1128/aac.01009-21.</div>

Ashton Lake https://proteopedia.org/index.php?title=User:Ashton_Lake/Sandbox_1&diff=4441522 User:Ashton Lake/Sandbox 1 2026-04-22T17:49:30Z

<p>Ashton Lake: </p> <hr /> <div>=NpmA: A Methyltransferase in E. Coli=<br /> <StructureSection load='3p2i' size='340' side='right' caption='SAM Dependent Methyltransferase NpmA' scene=''><br /> <br /> == Introduction ==<br /> NpmA is a plasmid-mediated methyltransferase that was discovered in Japan, 2003, and confers a high level of aminoglycoside antibiotic resistance against most antibiotics in- class. It is active as a <scene name='11/1107911/Intro/1'>monomer</scene> in solution but is known to dimerize as well. NpmA uses an S-adenosyl-methionine (SAM) as cofactor to remove a methyl group from SAM, converting it to S-adenosyl-homocysteine (SAH), and add it to the 30S ribosome unit on adenosine 1408. This addition prevents the binding of [https://www.ncbi.nlm.nih.gov/books/NBK541105/ aminoglycosides] and blocks their ability to shut down the ribosome and RNA transcription.<br /> == RNA Stabilization ==<br /> Around the active site for NpmA, there are certain regions that help in stabilizing the RNA. One such region involves <scene name='11/1107911/Trp_res/1'>W107 and W197</scene>, which uses aromatic stacking with the tryptophans' indole groups to stabilize A1408 of the RNA. Another region that assists in RNA stabilization is <scene name='11/1107911/Spacefill_rna/1'>F62-F82</scene>. This region utilizes four positive lysine residues to hold onto the negative charge of the RNA.<br /> <br /> == Co-Factor Stabilization ==<br /> === S-Adenosylmethionine ===<br /> SAM binding pocket uses hydrogen bonding interactions between residues <scene name='11/1107911/Sam_bonds/1'>N38, D55, A87, E88, T109, L104, and S195</scene>. Alanine and lysine use backbone residues for hydrogen bonding.<br /> [[Image:SAMbonds.png|400 px|right|thumb|Figure 1: Active Site SAM Hydrogen Bonding]]<br /> === S-Adenosylhomocysteine ===<br /> SAH binding pocket utilizes hydrogen bonding with key residues such as <scene name='11/1107911/Sah/1'>D30, D55, A87, E88, L104, and T109.</scene> The alanine and lysine residues participate in hydrogen bonding with their backbone atoms.<br /> [[Image:SAH_Stabilization.png|400 px|right|thumb|Figure 2: Active Site SAH Hydrogen Bonding]]<br /> == Similar Proteins ==<br /> Many proteins that have similar sequences and functions to NpmA differ in where the key residues occur. For example, <scene name='11/1107911/Kamb/1'>KamB</scene> is another SAM-dependent methyltransferase that methylates A1408 on the 30s subunit. KamB does have the RNA stabilizing tryptophan residues, but they are <scene name='11/1107911/W105193/1'>W105 and W193</scene> which indicates that there are two residues that are likely missing from KamB that are in NpmA. This is common across many similar proteins to NpmA.<br /> == Student Contributors ==<br /> *Ashton Lake<br /> *Jason Garcia<br /> *Hayden Teague<br /> <br /> </StructureSection><br /> == References ==<br /> <references/><br /> <ref name=”Husain 2010”>PMID=21062819</ref>Nilofer Husain, Sonja Obranić, Lukasz Koscinski, J. Seetharaman, Fedora Babić, Janusz M. Bujnicki, Gordana Maravić-Vlahoviček, J. Sivaraman, Structural basis for the methylation of A1408 in 16S rRNA by a panaminoglycoside resistance methyltransferase NpmA from a clinical isolate and analysis of the NpmA interactions with the 30S ribosomal subunit, Nucleic Acids Research, Volume 39, Issue 5, 1 March 2011, Pages 1903–1918, https://doi.org/10.1093/nar/gkq1033.<br /> <br /> <ref name=”Husain 2016”>PMID=27845431</ref>Husain, N., Tulsian, N., Chien, W. et al. Ligand-mediated changes in conformational dynamics of NpmA: implications for ribosomal interactions. Sci Rep 6, 37061 (2016). https://doi.org/10.1038/srep37061</div>

Ashton Lake https://proteopedia.org/index.php?title=User:Ashton_Lake/Sandbox_1&diff=4441521 User:Ashton Lake/Sandbox 1 2026-04-22T17:49:04Z

<p>Ashton Lake: </p> <hr /> <div>=NpmA: A Methyltransferase in E. Coli=<br /> <StructureSection load='3p2i' size='340' side='right' caption='SAM Dependent Methyltransferase NpmA' scene=''><br /> <br /> == Introduction ==<br /> NpmA is a plasmid-mediated methyltransferase that was discovered in Japan, 2003, and confers a high level of aminoglycoside antibiotic resistance against most antibiotics in- class. It is active as a <scene name='11/1107911/Intro/1'>monomer</scene> in solution but is known to dimerize as well. NpmA uses an S-adenosyl-methionine (SAM) as cofactor to remove a methyl group from SAM, converting it to S-adenosyl-homocysteine (SAH), and add it to the 30S ribosome unit on adenosine 1408. This addition prevents the binding of [https://www.ncbi.nlm.nih.gov/books/NBK541105/ aminoglycosides] and blocks their ability to shut down the ribosome and RNA transcription.<br /> == RNA Stabilization ==<br /> Around the active site for NpmA, there are certain regions that help in stabilizing the RNA. One such region involves <scene name='11/1107911/Trp_res/1'>W107 and W197</scene>, which uses aromatic stacking with the tryptophans' indole groups to stabilize A1408 of the RNA. Another region that assists in RNA stabilization is <scene name='11/1107911/Spacefill_rna/1'>F62-F82</scene>. This region utilizes four positive lysine residues to hold onto the negative charge of the RNA.<br /> <br /> == Co-Factor Stabilization ==<br /> === S-Adenosylmethionine ===<br /> SAM binding pocket uses hydrogen bonding interactions between residues <scene name='11/1107911/Sam_bonds/1'>N38, D55, A87, E88, T109, L104, and S195</scene>. Alanine and lysine use backbone residues for hydrogen bonding.<br /> [[Image:SAMbonds.png|400 px|right|thumb|Figure 1: Active Site SAM Hydrogen Bonding]]<br /> === S-Adenosylhomocysteine ===<br /> SAH binding pocket utilizes hydrogen bonding with key residues such as <scene name='11/1107911/Sah/1'>D30, D55, A87, E88, L104, and T109.</scene> The alanine and lysine residues participate in hydrogen bonding with their backbone atoms.<br /> [[Image:SAH_Stabilization.png|400 px|right|thumb|Figure 2: Active Site SAH Hydrogen Bonding]]<br /> == Similar Proteins ==<br /> Many proteins that have similar sequences and functions to NpmA differ in where the key residues occur. For example, <scene name='11/1107911/Kamb/1'>KamB</scene> is another SAM-dependent methyltransferase that methylates A1408 on the 30s subunit. KamB does have the RNA stabilizing tryptophan residues, but they are <scene name='11/1107911/W105193/1'>W105 and W193</scene> which indicates that there are two residues that are likely missing from KamB that are in NpmA. This is common across many similar proteins to NpmA.<br /> == Student Contributors ==<br /> *Ashton Lake<br /> *Jason Garcia<br /> *Hayden Teague<br /> <br /> </StructureSection><br /> == References ==<br /> <references/><br /> <ref name=”Husain”>PMID=21062819</ref>Nilofer Husain, Sonja Obranić, Lukasz Koscinski, J. Seetharaman, Fedora Babić, Janusz M. Bujnicki, Gordana Maravić-Vlahoviček, J. Sivaraman, Structural basis for the methylation of A1408 in 16S rRNA by a panaminoglycoside resistance methyltransferase NpmA from a clinical isolate and analysis of the NpmA interactions with the 30S ribosomal subunit, Nucleic Acids Research, Volume 39, Issue 5, 1 March 2011, Pages 1903–1918, https://doi.org/10.1093/nar/gkq1033.<br /> <br /> <ref name=”Husain 2016”>PMID=27845431</ref>Husain, N., Tulsian, N., Chien, W. et al. Ligand-mediated changes in conformational dynamics of NpmA: implications for ribosomal interactions. Sci Rep 6, 37061 (2016). https://doi.org/10.1038/srep37061</div>

Ashton Lake https://proteopedia.org/index.php?title=User:Ashton_Lake/Sandbox_1&diff=4441520 User:Ashton Lake/Sandbox 1 2026-04-22T17:48:07Z

<p>Ashton Lake: </p> <hr /> <div>=NpmA: A Methyltransferase in E. Coli=<br /> <StructureSection load='3p2i' size='340' side='right' caption='SAM Dependent Methyltransferase NpmA' scene=''><br /> <br /> == Introduction ==<br /> NpmA is a plasmid-mediated methyltransferase that was discovered in Japan, 2003, and confers a high level of aminoglycoside antibiotic resistance against most antibiotics in- class. It is active as a <scene name='11/1107911/Intro/1'>monomer</scene> in solution but is known to dimerize as well. NpmA uses an S-adenosyl-methionine (SAM) as cofactor to remove a methyl group from SAM, converting it to S-adenosyl-homocysteine (SAH), and add it to the 30S ribosome unit on adenosine 1408. This addition prevents the binding of [https://www.ncbi.nlm.nih.gov/books/NBK541105/ aminoglycosides] and blocks their ability to shut down the ribosome and RNA transcription.<br /> == RNA Stabilization ==<br /> Around the active site for NpmA, there are certain regions that help in stabilizing the RNA. One such region involves <scene name='11/1107911/Trp_res/1'>W107 and W197</scene>, which uses aromatic stacking with the tryptophans' indole groups to stabilize A1408 of the RNA. Another region that assists in RNA stabilization is <scene name='11/1107911/Spacefill_rna/1'>F62-F82</scene>. This region utilizes four positive lysine residues to hold onto the negative charge of the RNA.<br /> <br /> == Co-Factor Stabilization ==<br /> === S-Adenosylmethionine ===<br /> SAM binding pocket uses hydrogen bonding interactions between residues <scene name='11/1107911/Sam_bonds/1'>N38, D55, A87, E88, T109, L104, and S195</scene>. Alanine and lysine use backbone residues for hydrogen bonding.<br /> [[Image:SAMbonds.png|400 px|right|thumb|Figure 1: Active Site SAM Hydrogen Bonding]]<br /> === S-Adenosylhomocysteine ===<br /> SAH binding pocket utilizes hydrogen bonding with key residues such as <scene name='11/1107911/Sah/1'>D30, D55, A87, E88, L104, and T109.</scene> The alanine and lysine residues participate in hydrogen bonding with their backbone atoms.<br /> [[Image:SAH_Stabilization.png|400 px|right|thumb|Figure 2: Active Site SAH Hydrogen Bonding]]<br /> == Similar Proteins ==<br /> Many proteins that have similar sequences and functions to NpmA differ in where the key residues occur. For example, <scene name='11/1107911/Kamb/1'>KamB</scene> is another SAM-dependent methyltransferase that methylates A1408 on the 30s subunit. KamB does have the RNA stabilizing tryptophan residues, but they are <scene name='11/1107911/W105193/1'>W105 and W193</scene> which indicates that there are two residues that are likely missing from KamB that are in NpmA. This is common across many similar proteins to NpmA.<br /> == Student Contributors ==<br /> *Ashton Lake<br /> *Jason Garcia<br /> *Hayden Teague<br /> <br /> </StructureSection><br /> == References ==<br /> <references/><br /> <ref name=”Husain”>PMID=21062819</ref>Nilofer Husain, Sonja Obranić, Lukasz Koscinski, J. Seetharaman, Fedora Babić, Janusz M. Bujnicki, Gordana Maravić-Vlahoviček, J. Sivaraman, Structural basis for the methylation of A1408 in 16S rRNA by a panaminoglycoside resistance methyltransferase NpmA from a clinical isolate and analysis of the NpmA interactions with the 30S ribosomal subunit, Nucleic Acids Research, Volume 39, Issue 5, 1 March 2011, Pages 1903–1918, https://doi.org/10.1093/nar/gkq1033.<br /> <br /> <ref name=”Husain”>PMID=27845431</ref>Husain, N., Tulsian, N., Chien, W. et al. Ligand-mediated changes in conformational dynamics of NpmA: implications for ribosomal interactions. Sci Rep 6, 37061 (2016). https://doi.org/10.1038/srep37061</div>

Ashton Lake https://proteopedia.org/index.php?title=User:Ashton_Lake/Sandbox_1&diff=4441519 User:Ashton Lake/Sandbox 1 2026-04-22T17:47:54Z

<p>Ashton Lake: </p> <hr /> <div>=NpmA: A Methyltransferase in E. Coli=<br /> <StructureSection load='3p2i' size='340' side='right' caption='SAM Dependent Methyltransferase NpmA' scene=''><br /> <br /> == Introduction ==<br /> NpmA is a plasmid-mediated methyltransferase that was discovered in Japan, 2003, and confers a high level of aminoglycoside antibiotic resistance against most antibiotics in- class. It is active as a <scene name='11/1107911/Intro/1'>monomer</scene> in solution but is known to dimerize as well. NpmA uses an S-adenosyl-methionine (SAM) as cofactor to remove a methyl group from SAM, converting it to S-adenosyl-homocysteine (SAH), and add it to the 30S ribosome unit on adenosine 1408. This addition prevents the binding of [https://www.ncbi.nlm.nih.gov/books/NBK541105/ aminoglycosides] and blocks their ability to shut down the ribosome and RNA transcription.<br /> == RNA Stabilization ==<br /> Around the active site for NpmA, there are certain regions that help in stabilizing the RNA. One such region involves <scene name='11/1107911/Trp_res/1'>W107 and W197</scene>, which uses aromatic stacking with the tryptophans' indole groups to stabilize A1408 of the RNA. Another region that assists in RNA stabilization is <scene name='11/1107911/Spacefill_rna/1'>F62-F82</scene>. This region utilizes four positive lysine residues to hold onto the negative charge of the RNA.<br /> <br /> == Co-Factor Stabilization ==<br /> === S-Adenosylmethionine ===<br /> SAM binding pocket uses hydrogen bonding interactions between residues <scene name='11/1107911/Sam_bonds/1'>N38, D55, A87, E88, T109, L104, and S195</scene>. Alanine and lysine use backbone residues for hydrogen bonding.<br /> [[Image:SAMbonds.png|400 px|right|thumb|Figure 1: Active Site SAM Hydrogen Bonding]]<br /> === S-Adenosylhomocysteine ===<br /> SAH binding pocket utilizes hydrogen bonding with key residues such as <scene name='11/1107911/Sah/1'>D30, D55, A87, E88, L104, and T109.</scene> The alanine and lysine residues participate in hydrogen bonding with their backbone atoms.<br /> [[Image:SAH_Stabilization.png|400 px|right|thumb|Figure 2: Active Site SAH Hydrogen Bonding]]<br /> == Similar Proteins ==<br /> Many proteins that have similar sequences and functions to NpmA differ in where the key residues occur. For example, <scene name='11/1107911/Kamb/1'>KamB</scene> is another SAM-dependent methyltransferase that methylates A1408 on the 30s subunit. KamB does have the RNA stabilizing tryptophan residues, but they are <scene name='11/1107911/W105193/1'>W105 and W193</scene> which indicates that there are two residues that are likely missing from KamB that are in NpmA. This is common across many similar proteins to NpmA.<br /> == Student Contributors ==<br /> *Ashton Lake<br /> *Jason Garcia<br /> *Hayden Teague<br /> <br /> </StructureSection><br /> == References ==<br /> <references/><br /> <ref name=”Husain”>PMID=21062819</ref>Nilofer Husain, Sonja Obranić, Lukasz Koscinski, J. Seetharaman, Fedora Babić, Janusz M. Bujnicki, Gordana Maravić-Vlahoviček, J. Sivaraman, Structural basis for the methylation of A1408 in 16S rRNA by a panaminoglycoside resistance methyltransferase NpmA from a clinical isolate and analysis of the NpmA interactions with the 30S ribosomal subunit, Nucleic Acids Research, Volume 39, Issue 5, 1 March 2011, Pages 1903–1918, https://doi.org/10.1093/nar/gkq1033.<br /> <ref name=”Husain”>PMID=27845431</ref>Husain, N., Tulsian, N., Chien, W. et al. Ligand-mediated changes in conformational dynamics of NpmA: implications for ribosomal interactions. Sci Rep 6, 37061 (2016). https://doi.org/10.1038/srep37061</div>

Ashton Lake https://proteopedia.org/index.php?title=User:Ashton_Lake/Sandbox_1&diff=4441518 User:Ashton Lake/Sandbox 1 2026-04-22T17:45:06Z

<p>Ashton Lake: </p> <hr /> <div>=NpmA: A Methyltransferase in E. Coli=<br /> <StructureSection load='3p2i' size='340' side='right' caption='SAM Dependent Methyltransferase NpmA' scene=''><br /> <br /> == Introduction ==<br /> NpmA is a plasmid-mediated methyltransferase that was discovered in Japan, 2003, and confers a high level of aminoglycoside antibiotic resistance against most antibiotics in- class. It is active as a <scene name='11/1107911/Intro/1'>monomer</scene> in solution but is known to dimerize as well. NpmA uses an S-adenosyl-methionine (SAM) as cofactor to remove a methyl group from SAM, converting it to S-adenosyl-homocysteine (SAH), and add it to the 30S ribosome unit on adenosine 1408. This addition prevents the binding of [https://www.ncbi.nlm.nih.gov/books/NBK541105/ aminoglycosides] and blocks their ability to shut down the ribosome and RNA transcription.<br /> == RNA Stabilization ==<br /> Around the active site for NpmA, there are certain regions that help in stabilizing the RNA. One such region involves <scene name='11/1107911/Trp_res/1'>W107 and W197</scene>, which uses aromatic stacking with the tryptophans' indole groups to stabilize A1408 of the RNA. Another region that assists in RNA stabilization is <scene name='11/1107911/Spacefill_rna/1'>F62-F82</scene>. This region utilizes four positive lysine residues to hold onto the negative charge of the RNA.<br /> <br /> == Co-Factor Stabilization ==<br /> === S-Adenosylmethionine ===<br /> SAM binding pocket uses hydrogen bonding interactions between residues <scene name='11/1107911/Sam_bonds/1'>N38, D55, A87, E88, T109, L104, and S195</scene>. Alanine and lysine use backbone residues for hydrogen bonding.<br /> [[Image:SAMbonds.png|400 px|right|thumb|Figure 1: Active Site SAM Hydrogen Bonding]]<br /> === S-Adenosylhomocysteine ===<br /> SAH binding pocket utilizes hydrogen bonding with key residues such as <scene name='11/1107911/Sah/1'>D30, D55, A87, E88, L104, and T109.</scene> The alanine and lysine residues participate in hydrogen bonding with their backbone atoms.<br /> [[Image:SAH_Stabilization.png|400 px|right|thumb|Figure 2: Active Site SAH Hydrogen Bonding]]<br /> == Similar Proteins ==<br /> Many proteins that have similar sequences and functions to NpmA differ in where the key residues occur. For example, <scene name='11/1107911/Kamb/1'>KamB</scene> is another SAM-dependent methyltransferase that methylates A1408 on the 30s subunit. KamB does have the RNA stabilizing tryptophan residues, but they are <scene name='11/1107911/W105193/1'>W105 and W193</scene> which indicates that there are two residues that are likely missing from KamB that are in NpmA. This is common across many similar proteins to NpmA.<br /> == Student Contributors ==<br /> *Ashton Lake<br /> *Jason Garcia<br /> *Hayden Teague<br /> <br /> </StructureSection><br /> == References ==<br /> <references/><br /> <ref name=”Husain”>PMID=21062819</ref>Nilofer Husain, Sonja Obranić, Lukasz Koscinski, J. Seetharaman, Fedora Babić, Janusz M. Bujnicki, Gordana Maravić-Vlahoviček, J. Sivaraman, Structural basis for the methylation of A1408 in 16S rRNA by a panaminoglycoside resistance methyltransferase NpmA from a clinical isolate and analysis of the NpmA interactions with the 30S ribosomal subunit, Nucleic Acids Research, Volume 39, Issue 5, 1 March 2011, Pages 1903–1918, https://doi.org/10.1093/nar/gkq1033.</div>

Ashton Lake https://proteopedia.org/index.php?title=User:Ashton_Lake/Sandbox_1&diff=4441517 User:Ashton Lake/Sandbox 1 2026-04-22T17:43:44Z

<p>Ashton Lake: </p> <hr /> <div>=NpmA: A Methyltransferase in E. Coli=<br /> <StructureSection load='3p2i' size='340' side='right' caption='SAM Dependent Methyltransferase NpmA' scene=''><br /> <br /> == Introduction ==<br /> NpmA is a plasmid-mediated methyltransferase that was discovered in Japan, 2003, and confers a high level of aminoglycoside antibiotic resistance against most antibiotics in- class. It is active as a <scene name='11/1107911/Intro/1'>monomer</scene> in solution but is known to dimerize as well. NpmA uses an S-adenosyl-methionine (SAM) as cofactor to remove a methyl group from SAM, converting it to S-adenosyl-homocysteine (SAH), and add it to the 30S ribosome unit on adenosine 1408. This addition prevents the binding of [https://www.ncbi.nlm.nih.gov/books/NBK541105/ aminoglycosides] and blocks their ability to shut down the ribosome and RNA transcription.<br /> == RNA Stabilization ==<br /> Around the active site for NpmA, there are certain regions that help in stabilizing the RNA. One such region involves <scene name='11/1107911/Trp_res/1'>W107 and W197</scene>, which uses aromatic stacking with the tryptophans' indole groups to stabilize A1408 of the RNA. Another region that assists in RNA stabilization is <scene name='11/1107911/Spacefill_rna/1'>F62-F82</scene>. This region utilizes four positive lysine residues to hold onto the negative charge of the RNA.<br /> <br /> == Co-Factor Stabilization ==<br /> === S-Adenosylmethionine ===<br /> SAM binding pocket uses hydrogen bonding interactions between residues <scene name='11/1107911/Sam_bonds/1'>N38, D55, A87, E88, T109, L104, and S195</scene>. Alanine and lysine use backbone residues for hydrogen bonding.<br /> [[Image:SAMbonds.png|400 px|right|thumb|Figure 1: Active Site SAM Hydrogen Bonding]]<br /> === S-Adenosylhomocysteine ===<br /> SAH binding pocket utilizes hydrogen bonding with key residues such as <scene name='11/1107911/Sah/1'>D30, D55, A87, E88, L104, and T109.</scene> The alanine and lysine residues participate in hydrogen bonding with their backbone atoms.<br /> [[Image:SAH_Stabilization.png|400 px|right|thumb|Figure 2: Active Site SAH Hydrogen Bonding]]<br /> == Similar Proteins ==<br /> Many proteins that have similar sequences and functions to NpmA differ in where the key residues occur. For example, <scene name='11/1107911/Kamb/1'>KamB</scene> is another SAM-dependent methyltransferase that methylates A1408 on the 30s subunit. KamB does have the RNA stabilizing tryptophan residues, but they are <scene name='11/1107911/W105193/1'>W105 and W193</scene> which indicates that there are two residues that are likely missing from KamB that are in NpmA. This is common across many similar proteins to NpmA.<br /> == Student Contributors ==<br /> *Ashton Lake<br /> *Jason Garcia<br /> *Hayden Teague<br /> <br /> </StructureSection><br /> == References ==<br /> <references/><br /> <ref name=”Husain”></ref>Nilofer Husain, Sonja Obranić, Lukasz Koscinski, J. Seetharaman, Fedora Babić, Janusz M. Bujnicki, Gordana Maravić-Vlahoviček, J. Sivaraman, Structural basis for the methylation of A1408 in 16S rRNA by a panaminoglycoside resistance methyltransferase NpmA from a clinical isolate and analysis of the NpmA interactions with the 30S ribosomal subunit, Nucleic Acids Research, Volume 39, Issue 5, 1 March 2011, Pages 1903–1918, https://doi.org/10.1093/nar/gkq1033.</div>

Ashton Lake https://proteopedia.org/index.php?title=User:Ashton_Lake/Sandbox_1&diff=4441516 User:Ashton Lake/Sandbox 1 2026-04-22T17:42:17Z

<p>Ashton Lake: </p> <hr /> <div>=NpmA: A Methyltransferase in E. Coli=<br /> <StructureSection load='3p2i' size='340' side='right' caption='SAM Dependent Methyltransferase NpmA' scene=''><br /> <br /> == Introduction ==<br /> NpmA is a plasmid-mediated methyltransferase that was discovered in Japan, 2003, and confers a high level of aminoglycoside antibiotic resistance against most antibiotics in- class. It is active as a <scene name='11/1107911/Intro/1'>monomer</scene> in solution but is known to dimerize as well. NpmA uses an S-adenosyl-methionine (SAM) as cofactor to remove a methyl group from SAM, converting it to S-adenosyl-homocysteine (SAH), and add it to the 30S ribosome unit on adenosine 1408. This addition prevents the binding of [https://www.ncbi.nlm.nih.gov/books/NBK541105/ aminoglycosides] and blocks their ability to shut down the ribosome and RNA transcription.<br /> == RNA Stabilization ==<br /> Around the active site for NpmA, there are certain regions that help in stabilizing the RNA. One such region involves <scene name='11/1107911/Trp_res/1'>W107 and W197</scene>, which uses aromatic stacking with the tryptophans' indole groups to stabilize A1408 of the RNA. Another region that assists in RNA stabilization is <scene name='11/1107911/Spacefill_rna/1'>F62-F82</scene>. This region utilizes four positive lysine residues to hold onto the negative charge of the RNA.<br /> <br /> == Co-Factor Stabilization ==<br /> === S-Adenosylmethionine ===<br /> SAM binding pocket uses hydrogen bonding interactions between residues <scene name='11/1107911/Sam_bonds/1'>N38, D55, A87, E88, T109, L104, and S195</scene>. Alanine and lysine use backbone residues for hydrogen bonding.<br /> [[Image:SAMbonds.png|400 px|right|thumb|Figure 1: Active Site SAM Hydrogen Bonding]]<br /> === S-Adenosylhomocysteine ===<br /> SAH binding pocket utilizes hydrogen bonding with key residues such as <scene name='11/1107911/Sah/1'>D30, D55, A87, E88, L104, and T109.</scene> The alanine and lysine residues participate in hydrogen bonding with their backbone atoms.<br /> [[Image:SAH_Stabilization.png|400 px|right|thumb|Figure 2: Active Site SAH Hydrogen Bonding]]<br /> == Similar Proteins ==<br /> Many proteins that have similar sequences and functions to NpmA differ in where the key residues occur. For example, <scene name='11/1107911/Kamb/1'>KamB</scene> is another SAM-dependent methyltransferase that methylates A1408 on the 30s subunit. KamB does have the RNA stabilizing tryptophan residues, but they are <scene name='11/1107911/W105193/1'>W105 and W193</scene> which indicates that there are two residues that are likely missing from KamB that are in NpmA. This is common across many similar proteins to NpmA.<br /> == Student Contributors ==<br /> *Ashton Lake<br /> *Jason Garcia<br /> *Hayden Teague<br /> <br /> </StructureSection><br /> == References ==<br /> <references/><br /> <ref name=”Ransey”>PMID:28504306</ref>Nilofer Husain, Sonja Obranić, Lukasz Koscinski, J. Seetharaman, Fedora Babić, Janusz M. Bujnicki, Gordana Maravić-Vlahoviček, J. Sivaraman, Structural basis for the methylation of A1408 in 16S rRNA by a panaminoglycoside resistance methyltransferase NpmA from a clinical isolate and analysis of the NpmA interactions with the 30S ribosomal subunit, Nucleic Acids Research, Volume 39, Issue 5, 1 March 2011, Pages 1903–1918, https://doi.org/10.1093/nar/gkq1033.</div>

Ashton Lake https://proteopedia.org/index.php?title=User:Ashton_Lake/Sandbox_1&diff=4441515 User:Ashton Lake/Sandbox 1 2026-04-22T17:37:25Z

<p>Ashton Lake: </p> <hr /> <div>=NpmA: A Methyltransferase in E. Coli=<br /> <StructureSection load='3p2i' size='340' side='right' caption='SAM Dependent Methyltransferase NpmA' scene=''><br /> <br /> == Introduction ==<br /> NpmA is a plasmid-mediated methyltransferase that was discovered in Japan, 2003, and confers a high level of aminoglycoside antibiotic resistance against most antibiotics in- class. It is active as a <scene name='11/1107911/Intro/1'>monomer</scene> in solution but is known to dimerize as well. NpmA uses an S-adenosyl-methionine (SAM) as cofactor to remove a methyl group from SAM, converting it to S-adenosyl-homocysteine (SAH), and add it to the 30S ribosome unit on adenosine 1408. This addition prevents the binding of [https://www.ncbi.nlm.nih.gov/books/NBK541105/ aminoglycosides] and blocks their ability to shut down the ribosome and RNA transcription.<br /> == RNA Stabilization ==<br /> Around the active site for NpmA, there are certain regions that help in stabilizing the RNA. One such region involves <scene name='11/1107911/Trp_res/1'>W107 and W197</scene>, which uses aromatic stacking with the tryptophans' indole groups to stabilize A1408 of the RNA. Another region that assists in RNA stabilization is <scene name='11/1107911/Spacefill_rna/1'>F62-F82</scene>. This region utilizes four positive lysine residues to hold onto the negative charge of the RNA.<br /> <br /> == Co-Factor Stabilization ==<br /> === S-Adenosylmethionine ===<br /> SAM binding pocket uses hydrogen bonding interactions between residues <scene name='11/1107911/Sam_bonds/1'>N38, D55, A87, E88, T109, L104, and S195</scene>. Alanine and lysine use backbone residues for hydrogen bonding.<br /> [[Image:SAMbonds.png|400 px|right|thumb|Figure 1: Active Site SAM Hydrogen Bonding]]<br /> === S-Adenosylhomocysteine ===<br /> SAH binding pocket utilizes hydrogen bonding with key residues such as <scene name='11/1107911/Sah/1'>D30, D55, A87, E88, L104, and T109.</scene> The alanine and lysine residues participate in hydrogen bonding with their backbone atoms.<br /> [[Image:SAH_Stabilization.png|400 px|right|thumb|Figure 2: Active Site SAH Hydrogen Bonding]]<br /> == Similar Proteins ==<br /> Many proteins that have similar sequences and functions to NpmA differ in where the key residues occur. For example, <scene name='11/1107911/Kamb/1'>KamB</scene> is another SAM-dependent methyltransferase that methylates A1408 on the 30s subunit. KamB does have the RNA stabilizing tryptophan residues, but they are <scene name='11/1107911/W105193/1'>W105 and W193</scene> which indicates that there are two residues that are likely missing from KamB that are in NpmA. This is common across many similar proteins to NpmA.<br /> == Student Contributors ==<br /> *Ashton Lake<br /> *Jason Garcia<br /> *Hayden Teague<br /> <br /> </StructureSection><br /> == References ==<br /> <references/><br /> <ref name=”Ransey”>PMID:28504306</ref>Ransey E, Paredes E, Dey SK, Das SR, Heroux A, Macbeth MR. Crystal structure of the Entamoeba histolytica RNA lariat debranching enzyme EhDbr1 reveals a catalytic Zn2+ /Mn2+ heterobinucleation. FEBS Lett. 2017 Jul;591(13):2003-2010. doi: 10.1002/1873-3468.12677. Epub 2017 Jun 14. PMID: 28504306; PMCID: PMC5733776.</div>

Ashton Lake https://proteopedia.org/index.php?title=User:Ashton_Lake/Sandbox_1&diff=4441514 User:Ashton Lake/Sandbox 1 2026-04-22T17:34:29Z

<p>Ashton Lake: </p> <hr /> <div>=NpmA: A Methyltransferase in E. Coli=<br /> <StructureSection load='3p2i' size='340' side='right' caption='SAM Dependent Methyltransferase NpmA' scene=''><br /> <br /> == Introduction ==<br /> NpmA is a plasmid-mediated methyltransferase that was discovered in Japan, 2003, and confers a high level of aminoglycoside antibiotic resistance against most antibiotics in- class. It is active as a <scene name='11/1107911/Intro/1'>monomer</scene> in solution but is known to dimerize as well. NpmA uses an S-adenosyl-methionine (SAM) as a methyl group cofactor to remove a CH3 group from SAM, converting it to S-adenosyl-homocysteine (SAH), and add it to the 30S ribosome unit on adenosine 1408. This addition prevents the binding of [https://www.ncbi.nlm.nih.gov/books/NBK541105/ aminoglycosides] and blocks their ability to shut down the ribosome and RNA transcription.<br /> == RNA Stabilization ==<br /> Around the active site for NpmA, there are certain regions that help in stabilizing the RNA. One such region involves <scene name='11/1107911/Trp_res/1'>W107 and W197</scene>, which uses aromatic stacking with the tryptophans' indole groups to stabilize A1408 of the RNA. Another region that assists in RNA stabilization is <scene name='11/1107911/Spacefill_rna/1'>F62-F82</scene>. This region utilizes four positive lysine residues to hold onto the negative charge of the RNA.<br /> <br /> == Co-Factor Stabilization ==<br /> === S-Adenosylmethionine ===<br /> SAM binding pocket uses hydrogen bonding interactions between residues <scene name='11/1107911/Sam_bonds/1'>N38, D55, A87, E88, T109, L104, and S195</scene>. Alanine and lysine use backbone residues for hydrogen bonding.<br /> [[Image:SAMbonds.png|400 px|right|thumb|Figure 1: Active Site SAM Hydrogen Bonding]]<br /> === S-Adenosylhomocysteine ===<br /> SAH binding pocket utilizes hydrogen bonding with key residues such as <scene name='11/1107911/Sah/1'>D30, D55, A87, E88, L104, and T109.</scene> The alanine and lysine residues participate in hydrogen bonding with their backbone atoms.<br /> [[Image:SAH_Stabilization.png|400 px|right|thumb|Figure 2: Active Site SAH Hydrogen Bonding]]<br /> == Similar Proteins ==<br /> Many proteins that have similar sequences and functions to NpmA differ in where the key residues occur. For example, <scene name='11/1107911/Kamb/1'>KamB</scene> is another SAM-dependent methyltransferase that methylates A1408 on the 30s subunit. KamB does have the RNA stabilizing tryptophan residues, but they are W105 and W193 which indicates that there are two residues that are likely missing from KamB that are in NpmA. This is common across many similar proteins to NpmA.<br /> == Student Contributors ==<br /> *Ashton Lake<br /> *Jason Garcia<br /> *Hayden Teague<br /> <br /> </StructureSection><br /> == References ==<br /> <references/><br /> <ref name=”Ransey”>PMID:28504306</ref>Ransey E, Paredes E, Dey SK, Das SR, Heroux A, Macbeth MR. Crystal structure of the Entamoeba histolytica RNA lariat debranching enzyme EhDbr1 reveals a catalytic Zn2+ /Mn2+ heterobinucleation. FEBS Lett. 2017 Jul;591(13):2003-2010. doi: 10.1002/1873-3468.12677. Epub 2017 Jun 14. PMID: 28504306; PMCID: PMC5733776.</div>

Ashton Lake https://proteopedia.org/index.php?title=User:Ashton_Lake/Sandbox_1&diff=4441513 User:Ashton Lake/Sandbox 1 2026-04-22T17:32:51Z

<p>Ashton Lake: </p> <hr /> <div>=NpmA: A Methyltransferase in E. Coli=<br /> <StructureSection load='3p2i' size='340' side='right' caption='SAM Dependent Methyltransferase NpmA' scene=''><br /> <br /> == Introduction ==<br /> NpmA is a plasmid-mediated methyltransferase that was discovered in Japan, 2003, and confers a high level of aminoglycoside antibiotic resistance against most antibiotics in- class. It is active as a <scene name='11/1107911/Intro/1'>monomer</scene> in solution but is known to dimerize as well. NpmA uses an S-adenosyl-methionine (SAM) as a methyl group cofactor to remove a CH3 group from SAM, converting it to S-adenosyl-homocysteine (SAH), and add it to the 30S ribosome unit on adenosine 1408. This addition prevents the binding of [https://www.ncbi.nlm.nih.gov/books/NBK541105/ aminoglycosides] and blocks their ability to shut down the ribosome and RNA transcription.<br /> == RNA Stabilization ==<br /> Around the active site for NpmA, there are certain regions that help in stabilizing the RNA. One such region involves <scene name='11/1107911/Trp_res/1'>W107 and W197</scene>, which uses aromatic stacking with the tryptophans' indole groups to stabilize A1408 of the RNA. Another region that assists in RNA stabilization is <scene name='11/1107911/Spacefill_rna/1'>F62-F82</scene>. This region utilizes four positive lysine residues to hold onto the negative charge of the RNA.<br /> <br /> == Co-Factor Stabilization ==<br /> === S-Adenosylmethionine ===<br /> SAM binding pocket uses hydrogen bonding interactions between residues <scene name='11/1107911/Sam_bonds/1'>N38, D55, A87, E88, T109, L104, and S195</scene>. Alanine and lysine use backbone residues for hydrogen bonding.<br /> [[Image:SAMbonds.png|400 px|right|thumb|Figure 1: Active Site SAM Hydrogen Bonding]]<br /> === S-Adenosylhomocysteine ===<br /> SAH binding pocket utilizes hydrogen bonding with key residues such as <scene name='11/1107911/Sah/1'>D30, D55, A87, E88, L104, and T109.</scene> The alanine and lysine residues participate in hydrogen bonding with their backbone atoms.<br /> [[Image:SAH_Stabilization.png|400 px|right|thumb|Figure 2: Active Site SAH Hydrogen Bonding]]<br /> == Similar Proteins ==<br /> Many proteins that have similar sequences and functions to NpmA differ in where the key residues occur. For example, KamB is another SAM-dependent methyltransferase that methylates A1408 on the 30s subunit. KamB does have the RNA stabilizing tryptophan residues, but they are W105 and W193 which indicates that there are two residues that are likely missing from KamB that are in NpmA. This is common across many similar proteins to NpmA.<br /> == Student Contributors ==<br /> *Ashton Lake<br /> *Jason Garcia<br /> *Hayden Teague<br /> <br /> </StructureSection><br /> == References ==<br /> <references/><br /> <ref name=”Ransey”>PMID:28504306</ref>Ransey E, Paredes E, Dey SK, Das SR, Heroux A, Macbeth MR. Crystal structure of the Entamoeba histolytica RNA lariat debranching enzyme EhDbr1 reveals a catalytic Zn2+ /Mn2+ heterobinucleation. FEBS Lett. 2017 Jul;591(13):2003-2010. doi: 10.1002/1873-3468.12677. Epub 2017 Jun 14. PMID: 28504306; PMCID: PMC5733776.</div>

Ashton Lake https://proteopedia.org/index.php?title=User:Ashton_Lake/Sandbox_1&diff=4441512 User:Ashton Lake/Sandbox 1 2026-04-22T17:26:06Z

<p>Ashton Lake: </p> <hr /> <div>=NpmA: A Methyltransferase in E. Coli=<br /> <StructureSection load='3p2i' size='340' side='right' caption='SAM Dependent Methyltransferase NpmA' scene=''><br /> <br /> == Introduction ==<br /> NpmA is a plasmid-mediated methyltransferase that was discovered in Japan, 2003, and confers a high level of aminoglycoside antibiotic resistance against most antibiotics in- class. It is active as a <scene name='11/1107911/Intro/1'>monomer</scene> in solution but is known to dimerize as well. NpmA uses an S-adenosyl-methionine (SAM) as a methyl group cofactor to remove a CH3 group from SAM, converting it to S-adenosyl-homocysteine (SAH), and add it to the 30S ribosome unit on adenosine 1408. This addition prevents the binding of [https://www.ncbi.nlm.nih.gov/books/NBK541105/ aminoglycosides] and blocks their ability to shut down the ribosome and RNA transcription.<br /> == RNA Stabilization ==<br /> Around the active site for NpmA, there are certain regions that help in stabilizing the RNA. One such region involves <scene name='11/1107911/Trp_res/1'>W107 and W197</scene>, which uses aromatic stacking with the tryptophans' indole groups to stabilize A1408 of the RNA. Another region that assists in RNA stabilization is <scene name='11/1107911/Spacefill_rna/1'>F62-F82</scene>. This region utilizes four positive lysine residues to hold onto the negative charge of the RNA.<br /> <br /> == Co-Factor Stabilization ==<br /> === S-Adenosylmethionine ===<br /> SAM binding pocket uses hydrogen bonding interactions between residues <scene name='11/1107911/Sam_bonds/1'>N38, D55, A87, E88, T109, L104, and S195</scene>. Alanine and lysine use backbone residues for hydrogen bonding.<br /> [[Image:SAMbonds.png|400 px|right|thumb|Figure 1: Active Site SAM Hydrogen Bonding]]<br /> === S-Adenosylhomocysteine ===<br /> SAH binding pocket utilizes hydrogen bonding with key residues such as <scene name='11/1107911/Sah/1'>D30, D55, A87, E88, L104, and T109.</scene> The alanine and lysine residues participate in hydrogen bonding with their backbone atoms.<br /> [[Image:SAH_Stabilization.png|400 px|right|thumb|Figure 2: Active Site SAH Hydrogen Bonding]]<br /> == Similar Proteins ==<br /> == Student Contributors ==<br /> *Ashton Lake<br /> *Jason Garcia<br /> *Hayden Teague<br /> <br /> </StructureSection><br /> == References ==<br /> <references/><br /> <ref name=”Ransey”>PMID:28504306</ref>Ransey E, Paredes E, Dey SK, Das SR, Heroux A, Macbeth MR. Crystal structure of the Entamoeba histolytica RNA lariat debranching enzyme EhDbr1 reveals a catalytic Zn2+ /Mn2+ heterobinucleation. FEBS Lett. 2017 Jul;591(13):2003-2010. doi: 10.1002/1873-3468.12677. Epub 2017 Jun 14. PMID: 28504306; PMCID: PMC5733776.</div>

Ashton Lake https://proteopedia.org/index.php?title=User:Ashton_Lake/Sandbox_1&diff=4441511 User:Ashton Lake/Sandbox 1 2026-04-22T17:21:33Z

<p>Ashton Lake: </p> <hr /> <div>=NpmA: A Methyltransferase in E. Coli=<br /> <StructureSection load='3p2i' size='340' side='right' caption='SAM Dependent Methyltransferase NpmA' scene=''><br /> <br /> == Introduction ==<br /> NpmA is a plasmid-mediated methyltransferase that was discovered in Japan, 2003, and confers a high level of aminoglycoside antibiotic resistance against most antibiotics in- class. It is active as a <scene name='11/1107911/Intro/1'>monomer</scene> in solution but is known to dimerize as well. NpmA uses an S-adenosyl-methionine (SAM) as a methyl group cofactor to remove a CH3 group from SAM, converting it to S-adenosyl-homocysteine (SAH), and add it to the 30S ribosome unit on adenosine 1408. This addition prevents the binding of [https://www.ncbi.nlm.nih.gov/books/NBK541105/ aminoglycosides] and blocks their ability to shut down the ribosome and RNA transcription.<br /> == RNA Stabilization ==<br /> Around the active site for NpmA, there are certain regions that help in stabilizing the RNA. One such region involves <scene name='11/1107911/Trp_res/1'>W107 and W197</scene>, which uses aromatic stacking with the tryptophans' indole groups to stabilize A1408 of the RNA. Another region that assists in RNA stabilization is <scene name='11/1107911/Spacefill_rna/1'>F62-F82</scene>. This region utilizes four positive lysine residues to hold onto the negative charge of the RNA.<br /> <br /> == Co-Factor Stabilization ==<br /> === S-Adenosylmethionine ===<br /> SAM binding pocket uses hydrogen bonding interactions between residues N38, D55, A87, E88, T109, L104, and S195. Alanine and lysine use backbone residues for hydrogen bonding.<br /> [[Image:SAMbonds.png|400 px|right|thumb|Figure 1: Active Site SAM Hydrogen Bonding]]<br /> === S-Adenosylhomocysteine ===<br /> SAH binding pocket utilizes hydrogen bonding with key residues such as <scene name='11/1107911/Sah/1'>D30, D55, A87, E88, L104, and T109.</scene> The alanine and lysine residues participate in hydrogen bonding with their backbone atoms.<br /> [[Image:SAH_Stabilization.png|400 px|right|thumb|Figure 2: Active Site SAH Hydrogen Bonding]]<br /> == Similar Proteins ==<br /> == Student Contributors ==<br /> *Ashton Lake<br /> *Jason Garcia<br /> *Hayden Teague<br /> <br /> </StructureSection><br /> == References ==<br /> <references/><br /> <ref name=”Ransey”>PMID:28504306</ref>Ransey E, Paredes E, Dey SK, Das SR, Heroux A, Macbeth MR. Crystal structure of the Entamoeba histolytica RNA lariat debranching enzyme EhDbr1 reveals a catalytic Zn2+ /Mn2+ heterobinucleation. FEBS Lett. 2017 Jul;591(13):2003-2010. doi: 10.1002/1873-3468.12677. Epub 2017 Jun 14. PMID: 28504306; PMCID: PMC5733776.</div>

Ashton Lake https://proteopedia.org/index.php?title=User:Ashton_Lake/Sandbox_1&diff=4441510 User:Ashton Lake/Sandbox 1 2026-04-22T17:16:32Z

<p>Ashton Lake: </p> <hr /> <div>=NpmA: A Methyltransferase in E. Coli=<br /> <StructureSection load='3p2i' size='340' side='right' caption='SAM Dependent Methyltransferase NpmA' scene=''><br /> <br /> == Introduction ==<br /> NpmA is a plasmid-mediated methyltransferase that was discovered in Japan, 2003, and confers a high level of aminoglycoside antibiotic resistance against most antibiotics in- class. It is active as a <scene name='11/1107911/Intro/1'>monomer</scene> in solution but is known to dimerize as well. NpmA uses an S-adenosyl-methionine (SAM) as a methyl group cofactor to remove a CH3 group from SAM, converting it to S-adenosyl-homocysteine (SAH), and add it to the 30S ribosome unit on adenosine 1408. This addition prevents the binding of [https://www.ncbi.nlm.nih.gov/books/NBK541105/ aminoglycosides] and blocks their ability to shut down the ribosome and RNA transcription.<br /> == RNA Stabilization ==<br /> Around the active site for NpmA, there are certain regions that help in stabilizing the RNA. One such region involves <scene name='11/1107911/Trp_res/1'>W107 and W197</scene>, which uses aromatic stacking with the tryptophans' indole groups to stabilize A1408 of the RNA. Another region that assists in RNA stabilization is <scene name='11/1107911/Spacefill_rna/1'>F62-F82</scene>. This region utilizes four positive lysine residues to hold onto the negative charge of the RNA.<br /> <br /> == Co-Factor Stabilization ==<br /> === S-Adenosylmethionine ===<br /> [[Image:SAMbonds.png|400 px|right|thumb|Figure 1: Active Site SAM Hydrogen Bonding]]<br /> === S-Adenosylhomocysteine ===<br /> SAH binding pocket utilizes hydrogen bonding with key residues such as <scene name='11/1107911/Sah/1'>D30, D55, A87, E88, L104, and T109.</scene> The alanine and lysine residues participate in hydrogen bonding with their backbone atoms.<br /> [[Image:SAH_Stabilization.png|400 px|right|thumb|Figure 2: Active Site SAH Hydrogen Bonding]]<br /> == Similar Proteins ==<br /> == Student Contributors ==<br /> *Ashton Lake<br /> *Jason Garcia<br /> *Hayden Teague<br /> <br /> </StructureSection><br /> == References ==<br /> <references/><br /> <ref name=”Ransey”>PMID:28504306</ref>Ransey E, Paredes E, Dey SK, Das SR, Heroux A, Macbeth MR. Crystal structure of the Entamoeba histolytica RNA lariat debranching enzyme EhDbr1 reveals a catalytic Zn2+ /Mn2+ heterobinucleation. FEBS Lett. 2017 Jul;591(13):2003-2010. doi: 10.1002/1873-3468.12677. Epub 2017 Jun 14. PMID: 28504306; PMCID: PMC5733776.</div>

Ashton Lake https://proteopedia.org/index.php?title=File:SAMbonds.png&diff=4441509 File:SAMbonds.png 2026-04-22T17:15:42Z

<p>Ashton Lake: </p> <hr /> <div></div>

Ashton Lake https://proteopedia.org/index.php?title=User:Ashton_Lake/Sandbox_1&diff=4439418 User:Ashton Lake/Sandbox 1 2026-04-22T01:44:51Z

<p>Ashton Lake: </p> <hr /> <div>=NpmA: A Methyltransferase in E. Coli=<br /> <StructureSection load='3p2i' size='340' side='right' caption='SAM Dependent Methyltransferase NpmA' scene=''><br /> <br /> == Introduction ==<br /> NpmA is a plasmid-mediated methyltransferase that was discovered in Japan, 2003, and confers a high level of aminoglycoside antibiotic resistance against most antibiotics in- class. It is active as a <scene name='11/1107911/Intro/1'>monomer</scene> in solution but is known to dimerize as well. NpmA uses an S-adenosyl-methionine (SAM) as a methyl group cofactor to remove a CH3 group from SAM, converting it to S-adenosyl-homocysteine (SAH), and add it to the 30S ribosome unit on adenosine 1408. This addition prevents the binding of [https://www.ncbi.nlm.nih.gov/books/NBK541105/ aminoglycosides] and blocks their ability to shut down the ribosome and RNA transcription.<br /> == RNA Stabilization ==<br /> Around the active site for NpmA, there are certain regions that help in stabilizing the RNA. One such region involves <scene name='11/1107911/Trp_res/1'>W107 and W197</scene>, which uses aromatic stacking with the tryptophans' indole groups to stabilize A1408 of the RNA. Another region that assists in RNA stabilization is <scene name='11/1107911/Spacefill_rna/1'>F62-F82</scene>. This region utilizes four positive lysine residues to hold onto the negative charge of the RNA.<br /> <br /> == Co-Factor Stabilization ==<br /> === S-Adenosylmethionine ===<br /> === S-Adenosylhomocysteine ===<br /> SAH binding pocket utilizes hydrogen bonding with key residues such as <scene name='11/1107911/Sah/1'>D30, D55, A87, E88, L104, and T109.</scene> The alanine and lysine residues participate in hydrogen bonding with their backbone atoms.<br /> [[Image:SAH_Stabilization.png|400 px|right|thumb|Figure 1: Active Site SAH Hydrogen Bonding]]<br /> == Similar Proteins ==<br /> == Student Contributors ==<br /> *Ashton Lake<br /> *Jason Garcia<br /> *Hayden Teague<br /> <br /> </StructureSection><br /> == References ==<br /> <references/><br /> <ref name=”Ransey”>PMID:28504306</ref>Ransey E, Paredes E, Dey SK, Das SR, Heroux A, Macbeth MR. Crystal structure of the Entamoeba histolytica RNA lariat debranching enzyme EhDbr1 reveals a catalytic Zn2+ /Mn2+ heterobinucleation. FEBS Lett. 2017 Jul;591(13):2003-2010. doi: 10.1002/1873-3468.12677. Epub 2017 Jun 14. PMID: 28504306; PMCID: PMC5733776.</div>

Ashton Lake https://proteopedia.org/index.php?title=User:Ashton_Lake/Sandbox_1&diff=4439417 User:Ashton Lake/Sandbox 1 2026-04-22T01:29:15Z

<p>Ashton Lake: </p> <hr /> <div>=NpmA: A Methyltransferase in E. Coli=<br /> <StructureSection load='3p2i' size='340' side='right' caption='SAM Dependent Methyltransferase NpmA' scene=''><br /> <br /> == Introduction ==<br /> NpmA is a plasmid-mediated methyltransferase that was discovered in Japan, 2003, and confers a high level of aminoglycoside antibiotic resistance against most antibiotics in- class. It is active as a <scene name='11/1107911/Intro/1'>monomer</scene> in solution but is known to dimerize as well. NpmA uses an S-adenosyl-methionine (SAM) as a methyl group cofactor to remove a CH3 group from SAM, converting it to S-adenosyl-homocysteine (SAH), and add it to the 30S ribosome unit on adenosine 1408. This addition prevents the binding of [https://www.ncbi.nlm.nih.gov/books/NBK541105/ aminoglycosides] and blocks their ability to shut down the ribosome and RNA transcription.<br /> == RNA Stabilization ==<br /> Around the active site for NpmA, there are certain regions that help in stabilizing the RNA. One such region involves <scene name='11/1107911/Trp_res/1'>W107 and W197</scene>, which uses aromatic stacking with the tryptophans' indole groups to stabilize A1408 of the RNA. Another region that assists in RNA stabilization is <scene name='11/1107911/Spacefill_rna/1'>F62-F82</scene>. This region utilizes four positive lysine residues to hold onto the negative charge of the RNA.<br /> <br /> == Co-Factor Stabilization ==<br /> === S-Adenosylmethionine ===<br /> === S-Adenosylhomocysteine ===<br /> [[Image:SAH_Stabilization.png|400 px|right|thumb|Figure 1: Active Site SAH Hydrogen Bonding]]<br /> == Similar Proteins ==<br /> == Student Contributors ==<br /> *Ashton Lake<br /> *Jason Garcia<br /> *Hayden Teague<br /> <br /> </StructureSection><br /> == References ==<br /> <references/><br /> <ref name=”Ransey”>PMID:28504306</ref>Ransey E, Paredes E, Dey SK, Das SR, Heroux A, Macbeth MR. Crystal structure of the Entamoeba histolytica RNA lariat debranching enzyme EhDbr1 reveals a catalytic Zn2+ /Mn2+ heterobinucleation. FEBS Lett. 2017 Jul;591(13):2003-2010. doi: 10.1002/1873-3468.12677. Epub 2017 Jun 14. PMID: 28504306; PMCID: PMC5733776.</div>

Ashton Lake https://proteopedia.org/index.php?title=User:Ashton_Lake/Sandbox_1&diff=4439416 User:Ashton Lake/Sandbox 1 2026-04-22T01:16:44Z

<p>Ashton Lake: </p> <hr /> <div>=NpmA: A Methyltransferase in E. Coli=<br /> <StructureSection load='3p2i' size='340' side='right' caption='SAM Dependent Methyltransferase NpmA' scene=''><br /> <br /> == Introduction ==<br /> NpmA is a plasmid-mediated methyltransferase that was discovered in Japan, 2003, and confers a high level of aminoglycoside antibiotic resistance against most antibiotics in- class. It is active as a <scene name='11/1107911/Intro/1'>monomer</scene> in solution but is known to dimerize as well. NpmA uses an S-adenosyl-methionine (SAM) as a methyl group cofactor to remove a CH3 group from SAM, converting it to S-adenosyl-homocysteine (SAH), and add it to the 30S ribosome unit on adenosine 1408. This addition prevents the binding of [https://www.ncbi.nlm.nih.gov/books/NBK541105/ aminoglycosides] and blocks their ability to shut down the ribosome and RNA transcription.<br /> == RNA Stabilization ==<br /> Around the active site for NpmA, there are certain regions that help in stabilizing the RNA. One such region involves <scene name='11/1107911/Trp_res/1'>W107 and W197</scene>, which uses aromatic stacking with the tryptophans' indole groups to stabilize A1408 of the RNA.<br /> <scene name='11/1107911/Spacefill_rna/1'>RNA stabilizing region: F62-F82</scene><br /> == Co-Factor Stabilization ==<br /> === S-Adenosylmethionine ===<br /> === S-Adenosylhomocysteine ===<br /> [[Image:SAH_Stabilization.png|400 px|right|thumb|Figure 1: Active Site SAH Hydrogen Bonding]]<br /> == Similar Proteins ==<br /> == Student Contributors ==<br /> *Ashton Lake<br /> *Jason Garcia<br /> *Hayden Teague<br /> <br /> </StructureSection><br /> == References ==<br /> <references/><br /> <ref name=”Ransey”>PMID:28504306</ref>Ransey E, Paredes E, Dey SK, Das SR, Heroux A, Macbeth MR. Crystal structure of the Entamoeba histolytica RNA lariat debranching enzyme EhDbr1 reveals a catalytic Zn2+ /Mn2+ heterobinucleation. FEBS Lett. 2017 Jul;591(13):2003-2010. doi: 10.1002/1873-3468.12677. Epub 2017 Jun 14. PMID: 28504306; PMCID: PMC5733776.</div>

Ashton Lake https://proteopedia.org/index.php?title=User:Ashton_Lake/Sandbox_1&diff=4439415 User:Ashton Lake/Sandbox 1 2026-04-22T01:04:17Z

<p>Ashton Lake: </p> <hr /> <div>=NpmA: A Methyltransferase in E. Coli=<br /> <StructureSection load='3p2i' size='340' side='right' caption='SAM Dependent Methyltransferase NpmA' scene=''><br /> <br /> == Introduction ==<br /> NpmA is a plasmid-mediated methyltransferase that was discovered in Japan, 2003, and confers a high level of aminoglycoside antibiotic resistance against most antibiotics in- class. It is active as a <scene name='11/1107911/Intro/1'>monomer</scene> in solution but is known to dimerize as well. NpmA uses an S-adenosyl-methionine (SAM) as a methyl group cofactor to remove a CH3 group from SAM, converting it to S-adenosyl-homocysteine (SAH), and add it to the 30S ribosome unit on adenosine 1408. This addition prevents the binding of [https://www.ncbi.nlm.nih.gov/books/NBK541105/ aminoglycosides] and blocks their ability to shut down the ribosome and RNA transcription.<br /> == RNA Stabilization ==<br /> Around the active site for NpmA, there are certain regions that help in stabilizing the RNA. One such region involves <scene name='11/1107911/Trp_res/1'>W107 and W197</scene> <br /> <scene name='11/1107911/Spacefill_rna/1'>RNA stabilizing region: F62-F82</scene><br /> == Co-Factor Stabilization ==<br /> === S-Adenosylmethionine ===<br /> === S-Adenosylhomocysteine ===<br /> [[Image:SAH_Stabilization.png|400 px|right|thumb|Figure 1: Active Site SAH Hydrogen Bonding]]<br /> == Similar Proteins ==<br /> == Student Contributors ==<br /> *Ashton Lake<br /> *Jason Garcia<br /> *Hayden Teague<br /> <br /> </StructureSection><br /> == References ==<br /> <references/><br /> <ref name=”Ransey”>PMID:28504306</ref>Ransey E, Paredes E, Dey SK, Das SR, Heroux A, Macbeth MR. Crystal structure of the Entamoeba histolytica RNA lariat debranching enzyme EhDbr1 reveals a catalytic Zn2+ /Mn2+ heterobinucleation. FEBS Lett. 2017 Jul;591(13):2003-2010. doi: 10.1002/1873-3468.12677. Epub 2017 Jun 14. PMID: 28504306; PMCID: PMC5733776.</div>

Ashton Lake https://proteopedia.org/index.php?title=User:Ashton_Lake/Sandbox_1&diff=4439414 User:Ashton Lake/Sandbox 1 2026-04-22T00:47:33Z

<p>Ashton Lake: </p> <hr /> <div>=NpmA: A Methyltransferase in E. Coli=<br /> <StructureSection load='3p2i' size='340' side='right' caption='SAM Dependent Methyltransferase NpmA' scene=''><br /> <br /> == Introduction ==<br /> NpmA is a plasmid-mediated methyltransferase that was discovered in Japan, 2003, and confers a high level of aminoglycoside antibiotic resistance against most antibiotics in- class. It is active as a <scene name='11/1107911/Intro/1'>monomer</scene> in solution but is known to dimerize as well. NpmA uses an S-adenosyl-methionine (SAM) as a methyl group cofactor to remove a CH3 group from SAM, converting it to S-adenosyl-homocysteine (SAH), and add it to the 30S ribosome unit on adenosine 1408. This addition prevents the binding of [https://www.ncbi.nlm.nih.gov/books/NBK541105/ aminoglycosides] and blocks their ability to shut down the ribosome and RNA transcription.<br /> == RNA Stabilization ==<br /> <scene name='11/1107911/Trp_res/1'>A1408 Stabilizing Trp Residues</scene><br /> <scene name='11/1107911/Spacefill_rna/1'>RNA stabilizing region: F62-F82</scene><br /> == Co-Factor Stabilization ==<br /> === S-Adenosylmethionine ===<br /> === S-Adenosylhomocysteine ===<br /> [[Image:SAH_Stabilization.png|400 px|right|thumb|Figure 1: Active Site SAH Hydrogen Bonding]]<br /> == Similar Proteins ==<br /> == Student Contributors ==<br /> *Ashton Lake<br /> *Jason Garcia<br /> *Hayden Teague<br /> <br /> </StructureSection><br /> == References ==<br /> <references/><br /> <ref name=”Ransey”>PMID:28504306</ref>Ransey E, Paredes E, Dey SK, Das SR, Heroux A, Macbeth MR. Crystal structure of the Entamoeba histolytica RNA lariat debranching enzyme EhDbr1 reveals a catalytic Zn2+ /Mn2+ heterobinucleation. FEBS Lett. 2017 Jul;591(13):2003-2010. doi: 10.1002/1873-3468.12677. Epub 2017 Jun 14. PMID: 28504306; PMCID: PMC5733776.</div>

Ashton Lake https://proteopedia.org/index.php?title=User:Ashton_Lake/Sandbox_1&diff=4439373 User:Ashton Lake/Sandbox 1 2026-04-21T16:03:24Z

<p>Ashton Lake: </p> <hr /> <div>=NpmA: A Methyltransferase in E. Coli=<br /> <StructureSection load='3p2i' size='340' side='right' caption='SAM Dependent Methyltransferase NpmA' scene=''><br /> <br /> == Introduction ==<br /> <scene name='11/1107911/Intro/1'>NpmA Monomer</scene><br /> [https://www.ncbi.nlm.nih.gov/books/NBK541105/ Aminoglycoside Information]<br /> == RNA Stabilization ==<br /> <scene name='11/1107911/Trp_res/1'>A1408 Stabilizing Trp Residues</scene><br /> <scene name='11/1107911/Spacefill_rna/1'>RNA stabilizing region: F62-F82</scene><br /> == Co-Factor Stabilization ==<br /> === S-Adenosylmethionine ===<br /> === S-Adenosylhomocysteine ===<br /> [[Image:SAH_Stabilization.png|400 px|right|thumb|Figure 1: Active Site SAH Hydrogen Bonding]]<br /> == Similar Proteins ==<br /> == Student Contributors ==<br /> *Ashton Lake<br /> *Jason Garcia<br /> *Hayden Teague<br /> <br /> </StructureSection><br /> == References ==<br /> <references/><br /> <ref name=”Ransey”>PMID:28504306</ref>Ransey E, Paredes E, Dey SK, Das SR, Heroux A, Macbeth MR. Crystal structure of the Entamoeba histolytica RNA lariat debranching enzyme EhDbr1 reveals a catalytic Zn2+ /Mn2+ heterobinucleation. FEBS Lett. 2017 Jul;591(13):2003-2010. doi: 10.1002/1873-3468.12677. Epub 2017 Jun 14. PMID: 28504306; PMCID: PMC5733776.</div>

Ashton Lake https://proteopedia.org/index.php?title=User:Ashton_Lake/Sandbox_1&diff=4439372 User:Ashton Lake/Sandbox 1 2026-04-21T16:03:04Z

<p>Ashton Lake: </p> <hr /> <div>=NpmA: A Methyltransferase in E. Coli=<br /> <StructureSection load='3p2i' size='340' side='right' caption='SAM Dependent Methyltransferase NpmA' scene=''><br /> <br /> == Introduction ==<br /> <scene name='11/1107911/Intro/1'>NpmA Monomer</scene><br /> [https://www.ncbi.nlm.nih.gov/books/NBK541105/ Aminoglycoside Information]<br /> == RNA Stabilization ==<br /> <scene name='11/1107911/Trp_res/1'>A1408 Stabilizing Trp Residues</scene><br /> <scene name='11/1107911/Spacefill_rna/1'>RNA stabilizing region: F62-F82</scene><br /> == Co-Factor Stabilization ==<br /> === S-Adenosylmethionine ===<br /> === S-Adenosylhomocysteine ===<br /> [[Image:SAH_Stabilization.png|400 px|right|thumb|Figure 1: Active Site SAH Hydrogen Bonding]]<br /> == Similar Proteins ==<br /> == Student Contributors ==<br /> *Ashton Lake<br /> *Jason Garcia<br /> *Hayden Teague<br /> <br /> </StructureSection><br /> == References ==<br /> <references/><br /> Ransey E, Paredes E, Dey SK, Das SR, Heroux A, Macbeth MR. Crystal structure of the Entamoeba histolytica RNA lariat debranching enzyme EhDbr1 reveals a catalytic Zn2+ /Mn2+ heterobinucleation. FEBS Lett. 2017 Jul;591(13):2003-2010. doi: 10.1002/1873-3468.12677. Epub 2017 Jun 14. PMID: 28504306; PMCID: PMC5733776.</div>

Ashton Lake https://proteopedia.org/index.php?title=User:Ashton_Lake/Sandbox_1&diff=4439371 User:Ashton Lake/Sandbox 1 2026-04-21T16:02:42Z

<p>Ashton Lake: </p> <hr /> <div>=NpmA: A Methyltransferase in E. Coli=<br /> <StructureSection load='3p2i' size='340' side='right' caption='SAM Dependent Methyltransferase NpmA' scene=''><br /> <br /> == Introduction ==<br /> <scene name='11/1107911/Intro/1'>NpmA Monomer</scene><br /> [https://www.ncbi.nlm.nih.gov/books/NBK541105/ Aminoglycoside Information]<br /> == RNA Stabilization ==<br /> <scene name='11/1107911/Trp_res/1'>A1408 Stabilizing Trp Residues</scene><br /> <scene name='11/1107911/Spacefill_rna/1'>RNA stabilizing region: F62-F82</scene><br /> == Co-Factor Stabilization ==<br /> === S-Adenosylmethionine ===<br /> === S-Adenosylhomocysteine ===<br /> [[Image:SAH_Stabilization.png|400 px|right|thumb|Figure 1: Active Site SAH Hydrogen Bonding]]<br /> == Similar Proteins ==<br /> == Student Contributors ==<br /> *Ashton Lake<br /> *Jason Garcia<br /> *Hayden Teague<br /> <br /> </StructureSection><br /> == References ==<br /> <references/><br /> <ref name=”Ransey”>PMID:28504306</ref></div>

Ashton Lake https://proteopedia.org/index.php?title=User:Ashton_Lake/Sandbox_1&diff=4439370 User:Ashton Lake/Sandbox 1 2026-04-21T16:02:29Z

<p>Ashton Lake: </p> <hr /> <div>=NpmA: A Methyltransferase in E. Coli=<br /> <StructureSection load='3p2i' size='340' side='right' caption='SAM Dependent Methyltransferase NpmA' scene=''><br /> <br /> == Introduction ==<br /> <scene name='11/1107911/Intro/1'>NpmA Monomer</scene><br /> [https://www.ncbi.nlm.nih.gov/books/NBK541105/ Aminoglycoside Information]<br /> == RNA Stabilization ==<br /> <scene name='11/1107911/Trp_res/1'>A1408 Stabilizing Trp Residues</scene><br /> <scene name='11/1107911/Spacefill_rna/1'>RNA stabilizing region: F62-F82</scene><br /> == Co-Factor Stabilization ==<br /> === S-Adenosylmethionine ===<br /> === S-Adenosylhomocysteine ===<br /> [[Image:SAH_Stabilization.png|400 px|right|thumb|Figure 1: Active Site SAH Hydrogen Bonding]]<br /> == Similar Proteins ==<br /> == Student Contributors ==<br /> *Ashton Lake<br /> *Jason Garcia<br /> *Hayden Teague<br /> <br /> </StructureSection><br /> == References ==<br /> <references/><br /> <ref name=”Ransey”>PMID:28504306</ref</div>

Ashton Lake https://proteopedia.org/index.php?title=User:Ashton_Lake/Sandbox_1&diff=4439369 User:Ashton Lake/Sandbox 1 2026-04-21T15:56:48Z

<p>Ashton Lake: </p> <hr /> <div>=NpmA: A Methyltransferase in E. Coli=<br /> <StructureSection load='3p2i' size='340' side='right' caption='SAM Dependent Methyltransferase NpmA' scene=''><br /> <br /> == Introduction ==<br /> <scene name='11/1107911/Intro/1'>NpmA Monomer</scene><br /> [https://www.ncbi.nlm.nih.gov/books/NBK541105/ Aminoglycoside Information]<br /> == RNA Stabilization ==<br /> <scene name='11/1107911/Trp_res/1'>A1408 Stabilizing Trp Residues</scene><br /> <scene name='11/1107911/Spacefill_rna/1'>RNA stabilizing region: F62-F82</scene><br /> == Co-Factor Stabilization ==<br /> === S-Adenosylmethionine ===<br /> === S-Adenosylhomocysteine ===<br /> [[Image:SAH_Stabilization.png|400 px|right|thumb|Figure 1: Active Site SAH Hydrogen Bonding]]<br /> == Similar Proteins ==<br /> == Student Contributors ==<br /> *Ashton Lake<br /> *Jason Garcia<br /> *Hayden Teague<br /> <br /> </StructureSection><br /> == References ==<br /> <references/></div>

Ashton Lake https://proteopedia.org/index.php?title=User:Ashton_Lake/Sandbox_1&diff=4439368 User:Ashton Lake/Sandbox 1 2026-04-21T15:51:22Z

<p>Ashton Lake: </p> <hr /> <div>=NpmA: A Methyltransferase in E. Coli=<br /> <StructureSection load='3p2i' size='340' side='right' caption='SAM Dependent Methyltransferase NpmA' scene=''><br /> <br /> == Introduction ==<br /> <scene name='11/1107911/Intro/1'>NpmA Monomer</scene><br /> [https://www.ncbi.nlm.nih.gov/books/NBK541105/ Aminoglycoside Information]<br /> == RNA Stabilization ==<br /> <scene name='11/1107911/Trp_res/1'>A1408 Stabilizing Trp Residues</scene><br /> <scene name='11/1107911/Spacefill_rna/1'>RNA stabilizing region: F62-F82</scene><br /> == Co-Factor Stabilization ==<br /> === S-Adenosylmethionine ===<br /> === S-Adenosylhomocysteine ===<br /> [[Image:SAH_Stabilization.png|400 px|right|thumb|Figure 1: Active Site SAH Hydrogen Bonding]]<br /> == Similar Proteins ==<br /> == References ==<br /> <references/><br /> == Student Contributors ==<br /> *Ashton Lake<br /> *Jason Garcia<br /> *Hayden Teague<br /> <br /> </StructureSection></div>

Ashton Lake https://proteopedia.org/index.php?title=User:Ashton_Lake/Sandbox_1&diff=4439367 User:Ashton Lake/Sandbox 1 2026-04-21T15:43:54Z

<p>Ashton Lake: </p> <hr /> <div>=NpmA: A Methyltransferase in E. Coli=<br /> <StructureSection load='3p2i' size='340' side='right' caption='SAM Dependent Methyltransferase NpmA' scene=''><br /> <br /> == Introduction ==<br /> <scene name='11/1107911/Intro/1'>NpmA Monomer</scene><br /> [https://www.ncbi.nlm.nih.gov/books/NBK541105/ Aminoglycoside Information]<br /> == RNA Stabilization ==<br /> <scene name='11/1107911/Spacefill_rna/1'>RNA stabilizing region: F62-F82</scene><br /> == Co-Factor Stabilization ==<br /> === S-Adenosylmethionine ===<br /> === S-Adenosylhomocysteine ===<br /> [[Image:SAH_Stabilization.png|400 px|right|thumb|Figure 1: Active Site SAH Hydrogen Bonding]]<br /> == Similar Proteins ==<br /> == References ==<br /> <references/><br /> == Student Contributors ==<br /> *Ashton Lake<br /> *Jason Garcia<br /> *Hayden Teague<br /> <br /> </StructureSection></div>

Ashton Lake https://proteopedia.org/index.php?title=User:Ashton_Lake/Sandbox_1&diff=4439366 User:Ashton Lake/Sandbox 1 2026-04-21T15:42:41Z

<p>Ashton Lake: </p> <hr /> <div>=NpmA: A Methyltransferase in E. Coli=<br /> <StructureSection load='3p2i' size='340' side='right' caption='SAM Dependent Methyltransferase NpmA' scene=''><br /> <br /> == Introduction ==<br /> [https://www.ncbi.nlm.nih.gov/books/NBK541105/ Aminoglycoside Information]<br /> == RNA Stabilization ==<br /> <scene name='11/1107911/Spacefill_rna/1'>RNA stabilizing region: F62-F82</scene><br /> == Co-Factor Stabilization ==<br /> === S-Adenosylmethionine ===<br /> === S-Adenosylhomocysteine ===<br /> [[Image:SAH_Stabilization.png|400 px|right|thumb|Figure 1: Active Site SAH Hydrogen Bonding]]<br /> == Similar Proteins ==<br /> == References ==<br /> <references/><br /> == Student Contributors ==<br /> *Ashton Lake<br /> *Jason Garcia<br /> *Hayden Teague<br /> <br /> </StructureSection></div>

Ashton Lake https://proteopedia.org/index.php?title=User:Ashton_Lake/Sandbox_1&diff=4439365 User:Ashton Lake/Sandbox 1 2026-04-21T15:42:21Z

<p>Ashton Lake: </p> <hr /> <div>=NpmA: A Methyltransferase in E. Coli=<br /> <StructureSection load='3p2i' size='340' side='right' caption='SAM Dependent Methyltransferase NpmA' scene=''<br /> <br /> == Introduction ==<br /> [https://www.ncbi.nlm.nih.gov/books/NBK541105/ Aminoglycoside Information]<br /> == RNA Stabilization ==<br /> <scene name='11/1107911/Spacefill_rna/1'>RNA stabilizing region: F62-F82</scene><br /> == Co-Factor Stabilization ==<br /> === S-Adenosylmethionine ===<br /> === S-Adenosylhomocysteine ===<br /> [[Image:SAH_Stabilization.png|400 px|right|thumb|Figure 1: Active Site SAH Hydrogen Bonding]]<br /> == Similar Proteins ==<br /> == References ==<br /> <references/><br /> == Student Contributors ==<br /> *Ashton Lake<br /> *Jason Garcia<br /> *Hayden Teague<br /> <br /> </StructureSection></div>

Ashton Lake https://proteopedia.org/index.php?title=User:Ashton_Lake/Sandbox_1&diff=4439364 User:Ashton Lake/Sandbox 1 2026-04-21T15:42:10Z

<p>Ashton Lake: </p> <hr /> <div>=NpmA: A Methyltransferase in E. Coli=<br /> <StructureSection load='3p2i' size='340' side='right' caption='SAM Dependent Methyltransferase NpmA' scene='<scene name='11/1107911/Intro/1'></scene>'<br /> <br /> == Introduction ==<br /> [https://www.ncbi.nlm.nih.gov/books/NBK541105/ Aminoglycoside Information]<br /> == RNA Stabilization ==<br /> <scene name='11/1107911/Spacefill_rna/1'>RNA stabilizing region: F62-F82</scene><br /> == Co-Factor Stabilization ==<br /> === S-Adenosylmethionine ===<br /> === S-Adenosylhomocysteine ===<br /> [[Image:SAH_Stabilization.png|400 px|right|thumb|Figure 1: Active Site SAH Hydrogen Bonding]]<br /> == Similar Proteins ==<br /> == References ==<br /> <references/><br /> == Student Contributors ==<br /> *Ashton Lake<br /> *Jason Garcia<br /> *Hayden Teague<br /> <br /> </StructureSection></div>

Ashton Lake https://proteopedia.org/index.php?title=User:Ashton_Lake/Sandbox_1&diff=4439363 User:Ashton Lake/Sandbox 1 2026-04-21T15:41:14Z

<p>Ashton Lake: </p> <hr /> <div>=NpmA: A Methyltransferase in E. Coli=<br /> <StructureSection load='3p2i' size='340' side='right' caption='SAM Dependent Methyltransferase NpmA' scene='<scene name='11/1107911/Intro/1'></scene>'><br /> <br /> == Introduction ==<br /> [https://www.ncbi.nlm.nih.gov/books/NBK541105/ Aminoglycoside Information]<br /> == RNA Stabilization ==<br /> <scene name='11/1107911/Spacefill_rna/1'>RNA stabilizing region: F62-F82</scene><br /> == Co-Factor Stabilization ==<br /> === S-Adenosylmethionine ===<br /> === S-Adenosylhomocysteine ===<br /> [[Image:SAH_Stabilization.png|400 px|right|thumb|Figure 1: Active Site SAH Hydrogen Bonding]]<br /> == Similar Proteins ==<br /> == References ==<br /> <references/><br /> == Student Contributors ==<br /> *Ashton Lake<br /> *Jason Garcia<br /> *Hayden Teague<br /> <br /> </StructureSection></div>

Ashton Lake https://proteopedia.org/index.php?title=User:Ashton_Lake/Sandbox_1&diff=4439362 User:Ashton Lake/Sandbox 1 2026-04-21T15:37:28Z

<p>Ashton Lake: </p> <hr /> <div>=NpmA: A Methyltransferase in E. Coli=<br /> <StructureSection load='3p2i' size='340' side='right' caption='SAM Dependent Methyltransferase NpmA' scene='Intro'><br /> <br /> == Introduction ==<br /> [https://www.ncbi.nlm.nih.gov/books/NBK541105/ Aminoglycoside Information]<br /> == RNA Stabilization ==<br /> <scene name='11/1107911/Spacefill_rna/1'>RNA stabilizing region: F62-F82</scene><br /> == Co-Factor Stabilization ==<br /> === S-Adenosylmethionine ===<br /> === S-Adenosylhomocysteine ===<br /> [[Image:SAH_Stabilization.png|400 px|right|thumb|Figure 1: Active Site SAH Hydrogen Bonding]]<br /> == Similar Proteins ==<br /> == References ==<br /> <references/><br /> == Student Contributors ==<br /> *Ashton Lake<br /> *Jason Garcia<br /> *Hayden Teague<br /> <br /> </StructureSection></div>

Ashton Lake https://proteopedia.org/index.php?title=User:Ashton_Lake/Sandbox_1&diff=4439361 User:Ashton Lake/Sandbox 1 2026-04-21T15:37:16Z

<p>Ashton Lake: </p> <hr /> <div>=NpmA: A Methyltransferase in E. Coli=<br /> <StructureSection load='3p2i' size='340' side='right' caption='SAM Dependent Methyltransferase NpmA' scene=''><br /> <br /> == Introduction ==<br /> [https://www.ncbi.nlm.nih.gov/books/NBK541105/ Aminoglycoside Information]<br /> == RNA Stabilization ==<br /> <scene name='11/1107911/Spacefill_rna/1'>RNA stabilizing region: F62-F82</scene><br /> == Co-Factor Stabilization ==<br /> === S-Adenosylmethionine ===<br /> === S-Adenosylhomocysteine ===<br /> [[Image:SAH_Stabilization.png|400 px|right|thumb|Figure 1: Active Site SAH Hydrogen Bonding]]<br /> == Similar Proteins ==<br /> == References ==<br /> <references/><br /> == Student Contributors ==<br /> *Ashton Lake<br /> *Jason Garcia<br /> *Hayden Teague<br /> <br /> </StructureSection></div>

Ashton Lake https://proteopedia.org/index.php?title=User:Ashton_Lake/Sandbox_1&diff=4439360 User:Ashton Lake/Sandbox 1 2026-04-21T15:34:47Z

<p>Ashton Lake: </p> <hr /> <div>=NpmA: A Methyltransferase in E. Coli=<br /> <StructureSection load='3p2i' size='340' side='right' color='violet' caption='SAM Dependent Methyltransferase NpmA' scene=''><br /> <br /> == Introduction ==<br /> [https://www.ncbi.nlm.nih.gov/books/NBK541105/ Aminoglycoside Information]<br /> == RNA Stabilization ==<br /> <scene name='11/1107911/Spacefill_rna/1'>RNA stabilizing region: F62-F82</scene><br /> == Co-Factor Stabilization ==<br /> === S-Adenosylmethionine ===<br /> === S-Adenosylhomocysteine ===<br /> [[Image:SAH_Stabilization.png|400 px|right|thumb|Figure 1: Active Site SAH Hydrogen Bonding]]<br /> == Similar Proteins ==<br /> == References ==<br /> <references/><br /> == Student Contributors ==<br /> *Ashton Lake<br /> *Jason Garcia<br /> *Hayden Teague<br /> <br /> </StructureSection></div>

Ashton Lake https://proteopedia.org/index.php?title=User:Ashton_Lake/Sandbox_1&diff=4439351 User:Ashton Lake/Sandbox 1 2026-04-21T14:20:25Z

<p>Ashton Lake: </p> <hr /> <div>=NpmA: A Methyltransferase in E. Coli=<br /> <StructureSection load='3p2i' size='340' side='right' caption='SAM Dependent Methyltransferase NpmA' scene=''><br /> <br /> == Introduction ==<br /> [https://www.ncbi.nlm.nih.gov/books/NBK541105/ Aminoglycoside Information]<br /> == RNA Stabilization ==<br /> <scene name='11/1107911/Spacefill_rna/1'>RNA stabilizing region: F62-F82</scene><br /> == Co-Factor Stabilization ==<br /> === S-Adenosylmethionine ===<br /> === S-Adenosylhomocysteine ===<br /> [[Image:SAH_Stabilization.png|400 px|right|thumb|Figure 1: Active Site SAH Hydrogen Bonding]]<br /> == Similar Proteins ==<br /> == References ==<br /> <references/><br /> == Student Contributors ==<br /> *Ashton Lake<br /> *Jason Garcia<br /> *Hayden Teague<br /> <br /> </StructureSection></div>

Ashton Lake https://proteopedia.org/index.php?title=User:Ashton_Lake/Sandbox_1&diff=4439349 User:Ashton Lake/Sandbox 1 2026-04-21T13:51:36Z

<p>Ashton Lake: </p> <hr /> <div>=NpmA: A Methyltransferase in E. Coli=<br /> <StructureSection load='3p2i' size='340' side='right' caption='SAM Dependent Methyltransferase NpmA' scene=''><br /> <br /> == Introduction ==<br /> [https://www.ncbi.nlm.nih.gov/books/NBK541105/ Aminoglycoside Information]<br /> == RNA Stabilization ==<br /> <scene name='11/1107911/Spacefill_rna/1'>Text To Be Displayed</scene><br /> == Co-Factor Stabilization ==<br /> === S-Adenosylmethionine ===<br /> === S-Adenosylhomocysteine ===<br /> [[Image:SAH_Stabilization.png|400 px|right|thumb|Figure 1: Active Site SAH Hydrogen Bonding]]<br /> == Similar Proteins ==<br /> == References ==<br /> <references/><br /> == Student Contributors ==<br /> *Ashton Lake<br /> *Jason Garcia<br /> *Hayden Teague<br /> <br /> </StructureSection></div>

Ashton Lake https://proteopedia.org/index.php?title=User:Ashton_Lake/Sandbox_1&diff=4439326 User:Ashton Lake/Sandbox 1 2026-04-21T13:30:46Z

<p>Ashton Lake: </p> <hr /> <div>=NpmA: A Methyltransferase in E. Coli=<br /> <StructureSection load='3p2i' size='340' side='right' caption='SAM Dependent Methyltransferase NpmA' scene=''><br /> <br /> == Introduction ==<br /> [https://www.ncbi.nlm.nih.gov/books/NBK541105/ Aminoglycoside Information]<br /> == RNA Stabilization ==<br /> <br /> == Co-Factor Stabilization ==<br /> === S-Adenosylmethionine ===<br /> === S-Adenosylhomocysteine ===<br /> [[Image:SAH_Stabilization.png|400 px|right|thumb|Figure 1: Active Site SAH Hydrogen Bonding]]<br /> == Similar Proteins ==<br /> == References ==<br /> <references/><br /> == Student Contributors ==<br /> *Ashton Lake<br /> *Jason Garcia<br /> *Hayden Teague<br /> <br /> </StructureSection></div>

Ashton Lake https://proteopedia.org/index.php?title=User:Ashton_Lake/Sandbox_1&diff=4439315 User:Ashton Lake/Sandbox 1 2026-04-21T13:16:01Z

<p>Ashton Lake: </p> <hr /> <div>=NpmA: A Methyltransferase in E. Coli=<br /> <StructureSection load='3p2i' size='340' side='right' caption='SAM Dependent Methyltransferase NpmA' scene=''><br /> <br /> == Introduction ==<br /> <br /> == RNA Stabilization ==<br /> <br /> == Co-Factor Stabilization ==<br /> === S-Adenosylmethionine ===<br /> === S-Adenosylhomocysteine ===<br /> [[Image:SAH_Stabilization.png|400 px|right|thumb|Figure 1: Active Site SAH Hydrogen Bonding]]<br /> == Similar Proteins ==<br /> == References ==<br /> <references/><br /> == Student Contributors ==<br /> *Ashton Lake<br /> *Jason Garcia<br /> *Hayden Teague<br /> <br /> </StructureSection></div>

Ashton Lake https://proteopedia.org/index.php?title=User:Ashton_Lake/Sandbox_1&diff=4439313 User:Ashton Lake/Sandbox 1 2026-04-21T13:15:29Z

<p>Ashton Lake: </p> <hr /> <div>=NpmA: A Methyltransferase in E. Coli=<br /> <StructureSection load='3p2i' size='340' side='right' caption='SAM Dependent Methyltransferase NpmA' scene=''><br /> This is a default text for your page '''Ashton Lake/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br /> <br /> == Introduction ==<br /> <br /> == RNA Stabilization ==<br /> <br /> == Co-Factor Stabilization ==<br /> === S-Adenosylmethionine ===<br /> === S-Adenosylhomocysteine ===<br /> [[Image:SAH_Stabilization.png|400 px|right|thumb|Figure 1: Active Site SAH Hydrogen Bonding]]<br /> == Similar Proteins ==<br /> == References ==<br /> <references/><br /> == Student Contributors ==<br /> *Ashton Lake<br /> *Jason Garcia<br /> *Hayden Teague<br /> <br /> </StructureSection></div>

Ashton Lake https://proteopedia.org/index.php?title=User:Ashton_Lake/Sandbox_1&diff=4439309 User:Ashton Lake/Sandbox 1 2026-04-21T13:12:59Z

<p>Ashton Lake: </p> <hr /> <div>=NpmA: A Methyltransferase in E. Coli=<br /> <StructureSection load='3p2i' size='340' side='right' caption='SAM Dependent Methyltransferase NpmA' scene=''><br /> This is a default text for your page '''Ashton Lake/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br /> <br /> == Introduction ==<br /> <br /> == RNA Stabilization ==<br /> <br /> == Co-Factor Stabilization ==<br /> === S-Adenosylmethionine ===<br /> === S-Adenosylhomocysteine ===<br /> [[Image:SAH_Stabilization.png]]<br /> == Similar Proteins ==<br /> == References ==<br /> <references/><br /> == Student Contributors ==<br /> *Ashton Lake<br /> *Jason Garcia<br /> *Hayden Teague<br /> <br /> </StructureSection></div>

Ashton Lake https://proteopedia.org/index.php?title=File:SAH_Stabilization.png&diff=4439304 File:SAH Stabilization.png 2026-04-21T13:10:39Z

<p>Ashton Lake: </p> <hr /> <div></div>

Ashton Lake https://proteopedia.org/index.php?title=User:Ashton_Lake/Sandbox_1&diff=4439296 User:Ashton Lake/Sandbox 1 2026-04-21T13:04:08Z

<p>Ashton Lake: </p> <hr /> <div>=NpmA: A Methyltransferase in E. Coli=<br /> <StructureSection load='3p2i' size='340' side='right' caption='SAM Dependent Methyltransferase NpmA' scene=''><br /> This is a default text for your page '''Ashton Lake/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br /> <br /> == Introduction ==<br /> <br /> == RNA Stabilization ==<br /> <br /> == Co-Factor Stabilization ==<br /> === S-Adenosylmethionine ===<br /> === S-Adenosylhomocysteine ===<br /> == Similar Proteins ==<br /> == References ==<br /> <references/><br /> == Student Contributors ==<br /> *Ashton Lake<br /> *Jason Garcia<br /> *Hayden Teague<br /> <br /> </StructureSection></div>

Ashton Lake