Proteopedia - User contributions [en]

User:Ross Tsevis/Sandbox 1

2026-05-03T21:08:02Z

Ross Tsevis:

=APH(3')-IIIa: An Aminoglycoside Resistance Enzyme=
<StructureSection load='1L8T' size='350' side='right' caption='APH(3')-IIIa, PDB ID: 1L8T' scene='aphscene1'>

==Introduction==
APH(3')-IIIa is an aminoglycoside phosphotransferase enzyme that contributes to bacterial antibiotic resistance. This enzyme helps bacteria survive aminoglycoside antibiotics by phosphorylating the aminoglycoside, which reduces the drug's ability to bind to the bacterial ribosome. Because aminoglycosides are important antibiotics, understanding the structure and function of APH(3')-IIIa is useful for studying how resistance enzymes recognize and modify different drugs.<ref name='StructureRef'>PMID:12006485 </ref>

[[Image:proteoimage.png|400 px|right|thumb|Figure 1. Overall structure of APH(3')-IIIa.]]

==Function==
The main function of APH(3')-IIIa is to inactivate aminoglycoside antibiotics. It does this by transferring a phosphate group from ATP to the antibiotic. Once the antibiotic is phosphorylated, it can no longer bind effectively to the bacterial ribosome, allowing the bacteria to resist the effects of the drug.

==Structure==
APH(3')-IIIa contains structural features that are similar to other kinase-like enzymes. These features allow the enzyme to bind ATP and position the aminoglycoside substrate near the active site. The overall fold of the enzyme helps create a binding pocket where the antibiotic can interact with key residues.

===Active Site===
The active site of APH(3')-IIIa is important because this is where phosphate transfer occurs. Several residues near the active site help bind the substrate and orient it correctly for phosphorylation. In the interactive structure, selected residues are shown.

<scene name='11/1108566/Aphres/1'>APH(3')-IIIa Residues 180-200</scene>

==Biological Importance==
APH(3')-IIIa is biologically important because it is part of the larger problem of antibiotic resistance. By modifying aminoglycoside antibiotics, the enzyme lowers the effectiveness of these drugs. Studying this protein can help researchers better understand resistance mechanisms and potentially design inhibitors that restore antibiotic activity.

</StructureSection>
== References ==
<references/>
<ref name="Fong">PMID:12006485</ref>

==Student Contributors==
Ross Tsevis

User:Ross Tsevis/Sandbox 1

2026-05-03T21:03:34Z

Ross Tsevis:

=APH(3')-IIIa: An Aminoglycoside Resistance Enzyme=
<StructureSection load='1L8T' size='350' side='right' caption='APH(3')-IIIa, PDB ID: 1L8T' scene='aphscene1'>

==Introduction==
APH(3')-IIIa is an aminoglycoside phosphotransferase enzyme that contributes to bacterial antibiotic resistance. This enzyme helps bacteria survive aminoglycoside antibiotics by phosphorylating the aminoglycoside, which reduces the drug's ability to bind its normal target in the bacterial ribosome. Because aminoglycosides are important antibiotics, understanding the structure and function of APH(3')-IIIa is useful for studying how resistance enzymes recognize and modify different drugs.<ref name='StructureRef'>PMID:12006485 </ref>
APH(3')-IIIa is structurally important because it uses a kinase-like fold to bind nucleotide and antibiotic substrates. The three-dimensional structure helps show how specific residues near the active site position the antibiotic for phosphorylation.

[[Image:proteoimage.png|400 px|right|thumb|Figure 1. Overall structure of APH(3')-IIIa.]]

==Function==
The main function of APH(3')-IIIa is to inactivate aminoglycoside antibiotics. It does this by transferring a phosphate group from ATP to the antibiotic. Once the antibiotic is phosphorylated, it can no longer bind effectively to the bacterial ribosome, allowing the bacteria to resist the effects of the drug.

==Structure==
APH(3')-IIIa contains structural features that are similar to other kinase-like enzymes. These features allow the enzyme to bind ATP and position the aminoglycoside substrate near the active site. The overall fold of the enzyme helps create a binding pocket where the antibiotic can interact with key residues.

===Active Site===
The active site of APH(3')-IIIa is important because this is where phosphate transfer occurs. Several residues near the active site help bind the substrate and orient it correctly for phosphorylation. In the interactive structure, selected active-site residues are shown differently from the rest of the protein so they are easier to identify.

<scene name='11/1108566/Aphres/1'>APH(3')-IIIa Residues 180-200</scene>

===Substrate Binding===
APH(3')-IIIa can recognize multiple aminoglycoside antibiotics. This broad substrate recognition helps explain why the enzyme can contribute to resistance against more than one aminoglycoside drug. The shape and chemical environment of the binding site allow the enzyme to interact with different but related antibiotic structures.

==Biological Importance==
APH(3')-IIIa is biologically important because it is part of the larger problem of antibiotic resistance. By modifying aminoglycoside antibiotics, the enzyme lowers the effectiveness of these drugs. Studying this protein can help researchers better understand resistance mechanisms and potentially design inhibitors that restore antibiotic activity.

</StructureSection>
== References ==
<references/>
<ref name="Fong">PMID:12006485</ref>

==Student Contributors==
Ross Tsevis

User:Ross Tsevis/Sandbox 1

2026-05-03T20:41:36Z

Ross Tsevis:

=APH(3')-IIIa: An Aminoglycoside Resistance Enzyme=
<StructureSection load='1L8T' size='350' side='right' caption='APH(3')-IIIa, PDB ID: 1L8T' scene='aphscene1'>

==Introduction==
APH(3')-IIIa is an aminoglycoside phosphotransferase enzyme that contributes to bacterial antibiotic resistance. This enzyme helps bacteria survive aminoglycoside antibiotics by phosphorylating the aminoglycoside, which reduces the drug's ability to bind its normal target in the bacterial ribosome. Because aminoglycosides are important antibiotics, understanding the structure and function of APH(3')-IIIa is useful for studying how resistance enzymes recognize and modify different drugs.<ref name='StructureRef'>PMID:12006485 </ref>
APH(3')-IIIa is structurally important because it uses a kinase-like fold to bind nucleotide and antibiotic substrates. The three-dimensional structure helps show how specific residues near the active site position the antibiotic for phosphorylation.

[[Image:proteoimage.png|400 px|right|thumb|Figure 1. Overall structure of APH(3')-IIIa.]]

==Function==
The main function of APH(3')-IIIa is to inactivate aminoglycoside antibiotics. It does this by transferring a phosphate group from ATP to the antibiotic. Once the antibiotic is phosphorylated, it can no longer bind effectively to the bacterial ribosome, allowing the bacteria to resist the effects of the drug.

==Structure==
APH(3')-IIIa contains structural features that are similar to other kinase-like enzymes. These features allow the enzyme to bind ATP and position the aminoglycoside substrate near the active site. The overall fold of the enzyme helps create a binding pocket where the antibiotic can interact with key residues.

===Active Site===
The active site of APH(3')-IIIa is important because this is where phosphate transfer occurs. Several residues near the active site help bind the substrate and orient it correctly for phosphorylation. In the interactive structure, selected active-site residues are shown differently from the rest of the protein so they are easier to identify.

APH(3')-IIIa Residues 180-200

===Substrate Binding===
APH(3')-IIIa can recognize multiple aminoglycoside antibiotics. This broad substrate recognition helps explain why the enzyme can contribute to resistance against more than one aminoglycoside drug. The shape and chemical environment of the binding site allow the enzyme to interact with different but related antibiotic structures.

==Biological Importance==
APH(3')-IIIa is biologically important because it is part of the larger problem of antibiotic resistance. By modifying aminoglycoside antibiotics, the enzyme lowers the effectiveness of these drugs. Studying this protein can help researchers better understand resistance mechanisms and potentially design inhibitors that restore antibiotic activity.

</StructureSection>
== References ==
<references/>
<ref name="Fong">PMID:12006485</ref>

==Student Contributors==
Ross Tsevis

User:Ross Tsevis/Sandbox 1

2026-05-03T20:36:54Z

Ross Tsevis:

=APH(3')-IIIa: An Aminoglycoside Resistance Enzyme=
<StructureSection load='1L8T' size='350' side='right' caption='APH(3')-IIIa, PDB ID: 1L8T' scene='aphscene1'>

==Introduction==
APH(3')-IIIa is an aminoglycoside phosphotransferase enzyme that contributes to bacterial antibiotic resistance. This enzyme helps bacteria survive aminoglycoside antibiotics by phosphorylating the aminoglycoside, which reduces the drug's ability to bind its normal target in the bacterial ribosome. Because aminoglycosides are important antibiotics, understanding the structure and function of APH(3')-IIIa is useful for studying how resistance enzymes recognize and modify different drugs.<ref name='StructureRef'>PMID:12006485 </ref>
APH(3')-IIIa is structurally important because it uses a kinase-like fold to bind nucleotide and antibiotic substrates. The three-dimensional structure helps show how specific residues near the active site position the antibiotic for phosphorylation.

[[Image:proteoimage.png|400 px|right|thumb|Figure 1. Overall structure of APH(3')-IIIa.]]

==Function==
The main function of APH(3')-IIIa is to inactivate aminoglycoside antibiotics. It does this by transferring a phosphate group from ATP to the antibiotic. Once the antibiotic is phosphorylated, it can no longer bind effectively to the bacterial ribosome, allowing the bacteria to resist the effects of the drug.

==Structure==
APH(3')-IIIa contains structural features that are similar to other kinase-like enzymes. These features allow the enzyme to bind ATP and position the aminoglycoside substrate near the active site. The overall fold of the enzyme helps create a binding pocket where the antibiotic can interact with key residues.

===Active Site===
The active site of APH(3')-IIIa is important because this is where phosphate transfer occurs. Several residues near the active site help bind the substrate and orient it correctly for phosphorylation. In the interactive structure, selected active-site residues are shown differently from the rest of the protein so they are easier to identify.

===Substrate Binding===
APH(3')-IIIa can recognize multiple aminoglycoside antibiotics. This broad substrate recognition helps explain why the enzyme can contribute to resistance against more than one aminoglycoside drug. The shape and chemical environment of the binding site allow the enzyme to interact with different but related antibiotic structures.

==Biological Importance==
APH(3')-IIIa is biologically important because it is part of the larger problem of antibiotic resistance. By modifying aminoglycoside antibiotics, the enzyme lowers the effectiveness of these drugs. Studying this protein can help researchers better understand resistance mechanisms and potentially design inhibitors that restore antibiotic activity.

</StructureSection>
== References ==
<references/>
<ref name="Fong">PMID:12006485</ref>

==Student Contributors==
Ross Tsevis

User:Ross Tsevis/Sandbox 1

2026-05-03T19:56:16Z

Ross Tsevis:

=APH(3')-IIIa: An Aminoglycoside Resistance Enzyme=
<StructureSection load='1L8T' size='350' side='right' caption='APH(3')-IIIa, PDB ID: 1L8T' scene='aphscene1'>

==Introduction==
==Structure==

APH(3')-IIIa has a three-dimensional structure that helps explain how it binds aminoglycoside antibiotics and contributes to antibiotic resistance.

[[Image:proteoimage.png|400 px|right|thumb|Figure 1. Overall structure of APH(3')-IIIa.]]
== 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/>

==Student Contributors==
Ross Tsevis

User:Ross Tsevis/Sandbox 1

2026-05-01T21:06:38Z

Ross Tsevis:

=APH(3')-IIIa: An Aminoglycoside Resistance Enzyme=
<StructureSection load='1L8T' size='350' side='right' caption='APH(3')-IIIa, PDB ID: 1L8T' scene='YOUR SAVED SCENE NAME'>

==Introduction==
==Structure==

APH(3')-IIIa has a three-dimensional structure that helps explain how it binds aminoglycoside antibiotics and contributes to antibiotic resistance.

[[Image:proteoimage.png|400 px|right|thumb|Figure 1. Overall structure of APH(3')-IIIa.]]
== 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/>

==Student Contributors==
Ross Tsevis

File:Proteoimage.png

2026-05-01T21:00:41Z

Ross Tsevis:

== Summary ==
APH(3')-IIIa shown with alpha helices (red), beta sheets (yellow), and Mg ions (green)

File:Proteoimage.png

2026-05-01T20:59:04Z

Ross Tsevis: APH(3')-IIIa

== Summary ==
APH(3')-IIIa

User:Ross Tsevis/Sandbox 1

2026-05-01T20:43:02Z

Ross Tsevis:

=APH(3')-IIIa: An Aminoglycoside Resistance Enzyme=
<StructureSection load='1L8T' size='350' side='right' caption='APH(3')-IIIa, PDB ID: 1L8T' scene='YOUR SAVED SCENE NAME'>

==Introduction==

== 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/>

==Student Contributors==
Ross Tsevis

User:Ross Tsevis/Sandbox 1

2026-05-01T20:23:50Z

Ross Tsevis:

== APH(3')-IIIa, ''Enterococcus faecalis''==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Ross Tsevis/Sandbox 1'''. 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 ==

== 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/>

==Student Contributors==
Ross Tsevis

User:Ross Tsevis/Sandbox 1

2026-05-01T20:21:12Z

Ross Tsevis:

== APH(3')-IIIa, ''Enterococcus faecalis''==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Ross Tsevis/Sandbox 1'''. 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 ==

== 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/>

==Student Contributors==
Ross Tsevis

Sandbox

2026-04-27T22:59:35Z

Ross Tsevis:

=== Cryo-EM Structure of the Human TRPV1 Ion Channel ===

<StructureSection
load='3j5p'
size='340'
side='right'
caption='Cryo-EM structure of the human TRPV1 ion channel in the apo state (Liao et al., 2013; ~3.5 Å resolution)'
scene=''>
</StructureSection>

Hello

=== Introduction ===

The transient receptor potential vanilloid 1 (TRPV1) ion channel is a heat- and ligand-gated cation channel essential for nociception, inflammatory pain, and thermal sensitivity. Activated by capsaicin, protons, noxious heat (>42°C), and lipid mediators, TRPV1 serves as a polymodal molecular sensor in the peripheral nervous system. Because of its central role in pain signaling, TRPV1 has been a major therapeutic target for developing next-generation analgesics. Understanding its three-dimensional structure is therefore crucial for elucidating its gating mechanism and ligand recognition.

=== Structural Highlights ===

Using single-particle cryo-electron microscopy, Liao, Cao, Julius, and Cheng (2013) determined the first near-atomic structures of TRPV1 in multiple functional states, including the apo (resting), capsaicin-bound, and toxin-bound conformations. TRPV1 assembles as a homotetramer, with each subunit containing six transmembrane helices (S1–S6), a re-entrant pore loop, and extensive cytosolic ankyrin repeat domains.

The vanilloid-binding pocket—formed between the S3–S4 helices and the S4–S5 linker—was resolved in detail, explaining how capsaicin stabilizes the open conformation by pulling on the S4–S5 linker and reshaping the S6 helices to widen the pore. Structures bound to the double-knot toxin (DkTx) reveal an even more dilated pore, representing a fully activated gating state. Comparisons across these states demonstrate the sequence of conformational rearrangements that underlie heat and ligand gating in TRPV1.

=== Significance ===

These cryo-EM structures provide a mechanistic blueprint for understanding how TRPV1 integrates thermal, chemical, and lipid-derived signals to regulate ion permeation. They reveal conserved gating transitions and define pharmacologically relevant ligand-binding pockets essential for rational drug design. The ability to visualize TRPV1 in distinct activation states enables development of selective analgesic modulators targeting neuropathic and inflammatory pain while minimizing adverse thermo-sensory effects.

=== References ===
* Liao M., Cao E., Julius D., Cheng Y. (2013). Structure of the TRPV1 ion channel determined by electron cryo-microscopy. *Nature*, 504, 107–112.

User:Ross Tsevis/Sandbox 1

2026-04-27T22:48:31Z

Ross Tsevis: 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 '''Ross Tsevis/Sandbox 1'''. 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 '''Ross Tsevis/Sandbox 1'''. 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:Ross Tsevis

2026-04-27T22:43:25Z

Ross Tsevis:

* Full Real Name: Ross Tsevis

* 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:

(ORCID, the Open Researcher and Contributor ID, is a free, unique, persistent identifier https://orcid.org)
*[[User:Ross Tsevis/Sandbox 1]]