Sandbox Reserved 1698
From Proteopedia
(Difference between revisions)
(New page: {{Sandbox_Reserved_BHall_F21}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --> ==Your Heading Here (maybe something like 'Structure')== <StructureSection load='1stp' size='340' side='right' cap...) |
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{{Sandbox_Reserved_BHall_F21}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --> | {{Sandbox_Reserved_BHall_F21}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --> | ||
| - | == | + | ==1INP == |
| - | <StructureSection load=' | + | <StructureSection load='7KIR' size='340' side='right' caption='1-Inositol polyphosphate' scene=''> |
| - | This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the < and > signs. | + | This is a default text for your page '''Sandbox 1677'''. 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. | 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 == | + | == Function of your protein == |
| + | The organism "Bos taurus". protein 1INP regulates inositol phosphate signaling other proteins within the family, also has roles in gluconeogenesis and nucleotide metabolism. The specific protein mentioned in the has a PDB ID of 1INP, however the protein that we will look at for ligand has PDB ID of 7KIR. This specific protein is an enzyme because its mention that it binds to substrate. It also mentions the speed of a reaction changes due to protein, and slowed down by inhibitors. | ||
| - | == | + | <scene name='89/892741/Cartoon_1inp/1'>Cartoon_1INP</scene> |
| + | == Biological relevance and broader implications == | ||
| + | |||
| + | The biological relevance is that many organisms have the same enzyme and they chose to use it from cows. | ||
| + | If they can see the importance of 7KIR in IP3 inhibition. | ||
| + | They can better understand the metabolic pathway. | ||
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| + | == Important amino acids== | ||
| + | This is diagram of the <scene name='89/892741/Electron_active_site/1'>active site</scene>in the 1INP. | ||
| + | <ref> PMID:33172890</ref> | ||
| + | Electron density attribute to substrate binding. Two calcium ions (CA1 and CA2). The three metal sites in the active site of 1INP show Mg2+, Ca2+. Mg2+ in metal site are seem in the ligand interactions in both 1INP. This magnesium ions stabilize the protein and ligand to be able to catalyze the substrate. | ||
| - | == Relevance == | ||
== Structural highlights == | == Structural highlights == | ||
| + | Our protein has secondary structure contains <scene name='89/892741/77_helix/1'>77% alpha</scene>, and <scene name='89/892741/Beta_sheets_33/2'>33% beta sheets | ||
| + | </scene> | ||
| + | Also contains <scene name='89/892741/Tertiary_structure/1'>tertiary structure</scene> which is formed by the hydrophobic and non polar | ||
| + | |||
| + | Not able to see the active site due too <scene name='89/892741/Space_filing/1'>space filling</scene> | ||
| + | == Other important features == | ||
| + | Other interesting features including the mutation of D54 which results in loss of INPPL activity with changing the substrate affinity, the D54 mutant is known to trap the substrate in INPP1. | ||
| + | |||
| + | Enough though the protein 1INP doesn't have ligand, but has similar protein known as 7KIR, which contains similar catalytic amino acid. The catalytic amino acids are glutamic acid and aspartic acid, the enzyme they studied had mutation at D5, this causes amino acid alanine to become aspartic acid. | ||
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| + | Included catalytic amino acids are Thr 312, Lys 270, Ser 268, Glu 269, Ser 157, Asp 156, Thr 158, Ala 291, Lys 294, and Thr 313. This all the protein contributed to hydrogen bonding to the ligand. | ||
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| + | "DPIDxT" six-amino acid motif anchor metal binding. sites likely involve catalysis | ||
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">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. | This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">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. | ||
Current revision
| This Sandbox is Reserved from 10/01/2021 through 01/01//2022 for use in Biochemistry taught by Bonnie Hall at Grand View University, Des Moines, USA. This reservation includes Sandbox Reserved 1690 through Sandbox Reserved 1699. |
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1INP
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References
- ↑ Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. and Sussman, J. L. (2013), JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem., 53:207-216. doi:http://dx.doi.org/10.1002/ijch.201300024
- ↑ Herraez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ. 2006 Jul;34(4):255-61. doi: 10.1002/bmb.2006.494034042644. PMID:21638687 doi:10.1002/bmb.2006.494034042644
- ↑ Dollins DE, Xiong JP, Endo-Streeter S, Anderson DE, Bansal VS, Ponder JW, Ren Y, York JD. A Structural Basis for Lithium and Substrate Binding of an Inositide Phosphatase. J Biol Chem. 2020 Nov 10. pii: RA120.014057. doi: 10.1074/jbc.RA120.014057. PMID:33172890 doi:http://dx.doi.org/10.1074/jbc.RA120.014057
