Proteopedia - User contributions [en]

User:Jason Garcia/Sandbox1

2026-04-25T14:59:57Z

Jason Garcia:

=NpmA: Methlytransferase in Escherichia Coli=
<StructureSection load='3p2i' size='340' side='right' caption='SAM Dependent Methyltransferase NpmA=''>
This is a default text for your page '''Jason Garcia/Sandbox1'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
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.

== Introduction ==
Functioning as a plasmid-mediated methyltransferase, NpmA was discovered in Japan, 2003, and confers a high level of [https://en.wikipedia.org/wiki/Aminoglycoside aminoglycoside] antibiotic resistance against most antibiotics in-class. NpmA uses an S-adenosyl-methionine (SAM) as a methyl group cofactor to remove a methyl group from SAM, converting it to S-adenosyl-homocysteine (SAH), and add it to the 30S ribosome unit. This addition prevents the binding of aminoglycosides and blocks their ability to shut down the ribosome and RNA transcription. <ref name="Wachino">PMID:17875999</ref>.

=== Mechanism ===
[[Image:NpmA_Mechanism1.png|400px|right|thumb|Figure 1: NpmA Mechanism]]
Figure 1 depicts the proposed biochemical mechanism of action of NpmA and SAM. N1 of A1408 attacks the methyl group of SAM, converting it to SAH. The most likely candidate for an enzymatic base in the reaction is D35 based off of the crystal structure and its proximity to the reaction site.
=== Active Site ===

[[Image:NpmA_Active_Site_Image.png|200 px|right|thumb|Figure 2: NpmA Active Site Interactions]]

=== RNA Stabilization ===
Near the active site of NpmA, there are some regions that help in RNA stabilization. One of these regions involved <scene name='11/1107912/Trp/1'>W107 and W197</scene>
, which uses aromatic stacking with the tryptophan's' indole groups to stablize the A1408 of the RNA. Another region that assists in RNA stabilization.

== Disease ==
Development of antibiotic resistance via NpmA forces the use of other antibiotics, as non-aminoglycosides are still effective in treatment. Future research could explore the possibilities of the development of an aminoglycoside to attack the 50S ribosomal subunit, a change in structure to bypass the additional blocking methyl group, the development of an NpmA "breaker" to destroy the protein, or a CRISPER-Cas9 gene attack to remove the gene that encodes for NpmA.

== Relevance ==
The propagation of NpmA develops antibiotic resistance through its spread via plasmid-mediation, further highlighting itself as a target for understanding and combating antibiotic resistance.

This is a sample scene created with SAT to <scene name='10/1070530/1stp_coloerd/1'>color</scene> by Group, and another to make <scene name='10/1070530/1stp_transparency/1'>a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>
<scene name='11/1107912/Trp/1'>W107 and W197</scene>
== Student Contributors ==
Jason Garcia
Ashton Lake
Hayden Teague

User:Jason Garcia/Sandbox1

2026-04-24T17:30:13Z

Jason Garcia:

=NpmA: Methlytransferase in Escherichia Coli=
<StructureSection load='3p2i' size='340' side='right' caption='SAM Dependent Methyltransferase NpmA=''>
This is a default text for your page '''Jason Garcia/Sandbox1'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
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.

== Introduction ==
Functioning as a plasmid-mediated methyltransferase, NpmA was discovered in Japan, 2003, and confers a high level of [https://en.wikipedia.org/wiki/Aminoglycoside aminoglycoside] antibiotic resistance against most antibiotics in-class. NpmA uses an S-adenosyl-methionine (SAM) as a methyl group cofactor to remove a methyl group from SAM, converting it to S-adenosyl-homocysteine (SAH), and add it to the 30S ribosome unit. This addition prevents the binding of aminoglycosides and blocks their ability to shut down the ribosome and RNA transcription.

=== Mechanism ===
[[Image:NpmA_Mechanism1.png|400px|right|thumb|Figure 1: NpmA Mechanism]]
Figure 1 depicts the proposed biochemical mechanism of action of NpmA and SAM. N1 of A1408 attacks the methyl group of SAM, converting it to SAH. The most likely candidate for an enzymatic base in the reaction is D35 based off of the crystal structure and its proximity to the reaction site.
=== Active Site ===

[[Image:NpmA_Active_Site_Image.png|200 px|right|thumb|Figure 2: NpmA Active Site Interactions]]

=== RNA Stabilization ===
Near the active site of NpmA, there are some regions that help in RNA stabilization. One of these regions involved <scene name='11/1107912/Trp/1'>W107 and W197</scene>
, which uses aromatic stacking with the tryptophan's' indole groups to stablize the A1408 of the RNA. Another region that assists in RNA stabilization.

== Disease ==
Development of antibiotic resistance via NpmA forces the use of other antibiotics, as non-aminoglycosides are still effective in treatment. Future research could explore the possibilities of the development of an aminoglycoside to attack the 50S ribosomal subunit, a change in structure to bypass the additional blocking methyl group, the development of an NpmA "breaker" to destroy the protein, or a CRISPER-Cas9 gene attack to remove the gene that encodes for NpmA.

== Relevance ==
The propagation of NpmA develops antibiotic resistance through its spread via plasmid-mediation, further highlighting itself as a target for understanding and combating antibiotic resistance.

This is a sample scene created with SAT to <scene name='10/1070530/1stp_coloerd/1'>color</scene> by Group, and another to make <scene name='10/1070530/1stp_transparency/1'>a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>
<scene name='11/1107912/Trp/1'>W107 and W197</scene>
== Student Contributors ==
Jason Garcia
Ashton Lake
Hayden Teague

User:Jason Garcia/Sandbox1

2026-04-22T19:56:30Z

Jason Garcia:

=NpmA: Methlytransferase in Escherichia Coli=
<StructureSection load='3p2i' size='340' side='right' caption='SAM Dependent Methyltransferase NpmA=''>
This is a default text for your page '''Jason Garcia/Sandbox1'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
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.

== Introduction ==
Functioning as a plasmid-mediated methyltransferase, NpmA was discovered in Japan, 2003, and confers a high level of [https://en.wikipedia.org/wiki/Aminoglycoside aminoglycoside] antibiotic resistance against most antibiotics in-class. NpmA uses an S-adenosyl-methionine (SAM) as a methyl group cofactor to remove a methyl group from SAM, converting it to S-adenosyl-homocysteine (SAH), and add it to the 30S ribosome unit. This addition prevents the binding of aminoglycosides and blocks their ability to shut down the ribosome and RNA transcription.

=== Mechanism ===
[[Image:NpmA_Mechanism1.png|400px|right|thumb|Figure 1: NpmA Mechanism]]
Figure 1 depicts the proposed biochemical mechanism of action of NpmA and SAM. N1 of A1408 attacks the methyl group of SAM, converting it to SAH. The most likely candidate for an enzymatic base in the reaction is D35 based off of the crystal structure and its proximity to the reaction site.
=== Active Site ===

[[Image:NpmA_Active_Site_Image.png|200 px|right|thumb|Figure 2: NpmA Active Site Interactions]]

=== RNA Stabilization ===
Near the active site of NpmA, there are some regions that help in RNA stabilization. One of these regions involved W107 and W197, which uses aromatic stacking with the tryptophan's' indole groups to stablize the A1408 of the RNA. Another region that assists in RNA stabilization.

== Disease ==
Development of antibiotic resistance via NpmA forces the use of other antibiotics, as non-aminoglycosides are still effective in treatment. Future research could explore the possibilities of the development of an aminoglycoside to attack the 50S ribosomal subunit, a change in structure to bypass the additional blocking methyl group, the development of an NpmA "breaker" to destroy the protein, or a CRISPER-Cas9 gene attack to remove the gene that encodes for NpmA.

== Relevance ==
The propagation of NpmA develops antibiotic resistance through its spread via plasmid-mediation, further highlighting itself as a target for understanding and combating antibiotic resistance.

This is a sample scene created with SAT to <scene name='10/1070530/1stp_coloerd/1'>color</scene> by Group, and another to make <scene name='10/1070530/1stp_transparency/1'>a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

== Student Contributors ==
Jason Garcia
Ashton Lake
Hayden Teague

User:Jason Garcia/Sandbox1

2026-04-21T13:39:44Z

Jason Garcia:

=NpmA: Methlytransferase in Escherichia Coli=
<StructureSection load='3p2i' size='340' side='right' caption='SAM Dependent Methyltransferase NpmA=''>
This is a default text for your page '''Jason Garcia/Sandbox1'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
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.

== Introduction ==

Functioning as a plasmid-mediated methyltransferase, NpmA was discovered in Japan, 2003, and confers a high level of [https://en.wikipedia.org/wiki/Aminoglycoside aminoglycoside] antibiotic resistance against most antibiotics in-class. NpmA uses an S-adenosyl-methionine (SAM) as a methyl group cofactor to remove a methyl group from SAM, converting it to S-adenosyl-homocysteine (SAH), and add it to the 30S ribosome unit. This addition prevents the binding of aminoglycosides and blocks their ability to shut down the ribosome and RNA transcription.

== Function ==

=== Mechanism ===

[[Image:NpmA_Mechanism1.png|400px|right|thumb|Figure 1: NpmA Mechanism]]
Figure 1 depicts the proposed biochemical mechanism of action of NpmA and SAM. N1 of A1408 attacks the methyl group of SAM, converting it to SAH. The most likely candidate for an enzymatic base in the reaction is D35 based off of the crystal structure and its proximity to the reaction site.
=== Active Site ===

[[Image:NpmA_Active_Site_Image.png|200 px|right|thumb|Figure 2: NpmA Active Site Interactions]]

=== Structural Highlights ===

== Disease ==
Development of antibiotic resistance via NpmA forces the use of other antibiotics, as non-aminoglycosides are still effective in treatment. Future research could explore the possibilities of the development of an aminoglycoside to attack the 50S ribosomal subunit, a change in structure to bypass the additional blocking methyl group, the development of an NpmA "breaker" to destroy the protein, or a CRISPER-Cas9 gene attack to remove the gene that encodes for NpmA.

== Relevance ==

The propagation of NpmA develops antibiotic resistance through its spread via plasmid-mediation, further highlighting itself as a target for understanding and combating antibiotic resistance.

This is a sample scene created with SAT to <scene name='10/1070530/1stp_coloerd/1'>color</scene> by Group, and another to make <scene name='10/1070530/1stp_transparency/1'>a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

== Student Contributors ==

User:Jason Garcia/Sandbox1

2026-04-21T13:35:51Z

Jason Garcia:

=NpmA: Methlytransferase in Escherichia Coli=
<StructureSection load='3p2i' size='340' side='right' caption='SAM Dependent Methyltransferase NpmA=''>
This is a default text for your page '''Jason Garcia/Sandbox1'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
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.

== Introduction ==

Functioning as a plasmid-mediated methyltransferase, NpmA was discovered in Japan, 2003, and confers a high level of [https://en.wikipedia.org/wiki/Aminoglycoside aminoglycoside] antibiotic resistance against most antibiotics in-class. NpmA uses an S-adenosyl-methionine (SAM) as a methyl group cofactor to remove a methyl group from SAM, converting it to S-adenosyl-homocysteine (SAH), and add it to the 30S ribosome unit. This addition prevents the binding of aminoglycosides and blocks their ability to shut down the ribosome and RNA transcription.

== Function ==

=== Mechanism ===

[[Image:NpmA_Mechanism1.png|400px|right|thumb|Figure 1: NpmA Mechanism]]

=== Active Site ===

[[Image:NpmA_Active_Site_Image.png|400 px|right|thumb|Figure 2: NpmA Active Site Interactions]]

=== Structural Highlights ===

== Disease ==
Development of antibiotic resistance via NpmA forces the use of other antibiotics, as non-aminoglycosides are still effective in treatment. Future research could explore the possibilities of the development of an aminoglycoside to attack the 50S ribosomal subunit, a change in structure to bypass the additional blocking methyl group, the development of an NpmA "breaker" to destroy the protein, or a CRISPER-Cas9 gene attack to remove the gene that encodes for NpmA.

== Relevance ==

The propagation of NpmA develops antibiotic resistance through its spread via plasmid-mediation, further highlighting itself as a target for understanding and combating antibiotic resistance.

This is a sample scene created with SAT to <scene name='10/1070530/1stp_coloerd/1'>color</scene> by Group, and another to make <scene name='10/1070530/1stp_transparency/1'>a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

== Student Contributors ==

User:Jason Garcia/Sandbox1

2026-04-21T13:31:36Z

Jason Garcia:

File:NpmA Mechanism1.png

2026-04-21T13:31:22Z

Jason Garcia:

User:Jason Garcia/Sandbox1

2026-04-21T13:30:05Z

Jason Garcia:

File:NpmA Mechanism.png

2026-04-21T13:29:27Z

Jason Garcia:

File:Image 2026-04-21 092454201.png

2026-04-21T13:24:59Z

Jason Garcia:

User:Jason Garcia/Sandbox1

2026-04-21T13:20:07Z

Jason Garcia:

User:Jason Garcia/Sandbox1

2026-04-21T13:13:12Z

Jason Garcia:

User:Jason Garcia/Sandbox1

2026-04-21T13:11:20Z

Jason Garcia:

File:NpmA Active Site Image.png

2026-04-21T13:10:44Z

Jason Garcia: Active site of NpmA methyltransferase protein

== Summary ==
Active site of NpmA methyltransferase protein

User:Jason Garcia/Sandbox1

2026-04-21T13:05:08Z

Jason Garcia:

User:Jason Garcia/Sandbox1

2026-04-21T13:04:17Z

Jason Garcia:

=NpmA: Methlytransferase in Escherichia Coli=
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Jason Garcia/Sandbox1'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
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.

== Introduction ==

== Function ==

=== Mechanism ===

=== Active Site ===

=== Structural Highlights ===

== Disease ==

== Relevance ==

This is a sample scene created with SAT to <scene name='10/1070530/1stp_coloerd/1'>color</scene> by Group, and another to make <scene name='10/1070530/1stp_transparency/1'>a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

== Student Contributors ==

User:Jason Garcia/Sandbox1

2026-04-21T12:59:41Z

Jason Garcia:

=NpmA=
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Jason Garcia/Sandbox1'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
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.

== Function ==

== Mechanism ==

== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name='10/1070530/1stp_coloerd/1'>color</scene> by Group, and another to make <scene name='10/1070530/1stp_transparency/1'>a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

User:Jason Garcia/Sandbox1

2026-04-21T12:58:24Z

Jason Garcia:

=NpmA=
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Jason Garcia/Sandbox1'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
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.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name='10/1070530/1stp_coloerd/1'>color</scene> by Group, and another to make <scene name='10/1070530/1stp_transparency/1'>a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

User:Jason Garcia/Sandbox1

2026-04-21T12:56:36Z

Jason Garcia: Created page with "==Your Heading Here (maybe something like 'Structure')== <StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''> This is a default text for your page '''Jason Garcia/Sandbox1'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs. 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:2..."

==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Jason Garcia/Sandbox1'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
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.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name='10/1070530/1stp_coloerd/1'>color</scene> by Group, and another to make <scene name='10/1070530/1stp_transparency/1'>a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

User:Jason Garcia

2026-04-21T12:56:00Z

Jason Garcia:

* Full Real Name: Jason Garcia

* Position: Student

* Institution (NO ABBREVIATIONS): Butler University

* City, State/Province: Indianapolis, Indiana

* Country: United States of America

* Field of Expertise or Study: Biochemistry

* ORCID ID:
*[[User:Jason Garcia/Sandbox1]]
(ORCID, the Open Researcher and Contributor ID, is a free, unique, persistent identifier https://orcid.org)