Sandbox GGC10

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==Fungal tRNA ligase==
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=Sodium-Potassium Pump=
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<StructureSection load='6N0T' size='340' side='right' caption='Fungal tRNA ligase' scene=''>
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<StructureSection load='3B8E' size='340' side='right' caption='Na+/K+ Pump Protein' scene=''>
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Fungal tRNA ligase is an enzyme that attaches the appropriate amino acid onto its tRNA. It is done through esterfication or it is precursor to one of its compatible amino acid tRNAs to form an aminoacyl-tRNA.
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The Sodium Potassium Pump is important to the physiology of our bodies because it can be found in all human cells. This in turn helps maintain optimal ion balance. Hence, this is why our body uses one-fourth of its energy to power the pump and keep it regulating.
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== Function ==
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The primary function of this protein serves as the catalytic component of the active enzymes, which catalyzes the hydrolysis of the ATP coupled with the exchange of sodium and potassium across the plasma membrane. Additionally, this action potential assists in creating an electrochemical gradient of sodium and potassium ions by delivering the energy for the active transport of numerous nutrients.<ref>PMID:30725773</ref> Therefore, the NA+/K+ pump functions by having to transport sodium and potassium ions across the cell membrane in a 3 to 2 ratio (3 Na+ out and 2 K+ in). By doing this, the membrane potential increases its stability and therefore is essential in human cells as it constantly maintains an optimal ion balance.<ref>PMID:27490484</ref> In addition, the sodium-potassium pump functions in many systems. A high level of expression can be found in the kidneys as they are responsible for expressing 50 million pumps per cell to filter waste products in the blood, maintain optimal pH's, regulate electrolyte levels, and reabsorb glucose and amino acids. Another important place this ATPase activity can be seen is in the brain as the neurons need this pump to reverse postsynaptic sodium flux to activate action potentials.<ref>PMID:25566080</ref>
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== Background Information ==
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== Disease ==
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Transfer ribonucleic acid is a protein molecule that are between 70-90 nucleotides long. It is a type of RNA that helps translate messenger RNA sequences into the form of nonfunctional and functional proteins.
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If the Sodium Potassium Pump stops working or is inhibited, the sodium concentration will add up within the cell, and the intracellular potassium levels will fall. This has been shown to cause reduced intelligence, loss of Magnesium in urine, and epileptic seizures. This happens due to a mutation in the Alpha 1 form of the Sodium Potassium Pump. It is shown that the mutated protein is found both in the kidneys and the brain. Epileptic seizures occur because the kidneys, instead of absorbing the Magnesium, will secrete it in the urine caused by the convolutions of the protein itself.<ref>PMID:25907445</ref> This has been shown to lead to mental retardation in some cases. Additionally, the overarching picture of the sodium-potassium pump deficiency can cause severe damages. In short, the nervous and the muscular system will shut down so quickly; one would experience paralysis, interruption of heartbeat and respiration, and cessation of all brain and nerve activity. This would cause the nervous system to be non-functional and ultimately result in death.<ref>PMID:1665097</ref>
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TRNAs which are ribonucleic acids and are capable of forming bonds with mRNA (hydrogen bonds) and amino acids (ester linkages). The ester linkage with the amino acid is one of the most important parts of the tRNA due to the anticodon and the 3’ hydroxyl group. These bonding help to bring amino acids and mRNAs together in the process known as translation. During translation, tRNA functions at specific sites in the ribosome. At this time tRNAs read the messages received from nucleic acid and translate them into proteins known as amino acids These amino acids are made by individual codons.
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TRNA base pairs with three nucleotides on a mRNA chain. These three nucleotides are known as codons. In this process there is a corresponding strand or sequence that has an anticodon. When the anticodon and the codon is paired, this helps bring specificity to the process of translation.
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TRNAs can be classified based on the amino acids they carry and grouped based on their anticodon. There are about 20 different known tRNAs. There are 64 possible codons that can be translated by tRNA and give us the 20 amino acids and the 3 codes for stopping translation.
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Another important structure on the tRNA is the arms. There is a T-arm and D-arm. The D and T arms and the anticodon loop is the regions on the protein that looks like a cloverleaf. When folded into its tertiary structure and in a L-shape, the acceptor stem and the t-arm form a helix that extends while the anticodon and the D-arm forms another helix. These helices are perpendicular to each other allowing the D-arm and the T-arm are close to each other, but the anticodon loop and the acceptor arms are on opposite sides of the molecule.
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== Relevance ==
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The Sodium Potassium Pump is relevant because it creates an action potential throughout the cell membrane. This results in an imbalance of ions, which causes displacement between the outside and inside the cell. Physiologically speaking, this is why our nerve cells can propagate signals throughout the human body.<ref>PMID:9662481</ref> This protein is vital to our daily function as this Na+/K+ ATPase uses fifteen percent of our caloric intake in one day. The pump is also relevant to glucose absorption as that is crucial in human metabolism. This starts with Na+ ions being pumped out of cells in the small intestine into the blood with the help of the Sodium Potassium Pump. The Sodium-ion will later re-enter the small intestine cells via diffusion through a Sodium-Glucose Transporter Protein (SGLUT-1). This will cause the glucose concentration inside the cell to increase and form a gradient between inside the cell and the blood. This will assist glucose into the blood via facilitated diffusion.<ref>PMID:8794828</ref> Finally, both Na+ and K+ are found in the body as a form of electrolytes. Potassium assists in making various proteins, anabolism of carbohydrates in tissues, and helps support the electrical activity in the heart. Whereas sodium assists in maintaining healthy fluid balance, contractions of muscle, and conduction of nerve impulses. Avoiding this naturally occurring phenomenon can inhibit mental and physical growth.<ref>PMID:31082167</ref>
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== Referenced Paper Information ==
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== Structural highlights ==
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In the paper the study focused on the fungal ligase (Trl1) enzyme. This enzyme is important in the repairs of RNA breaks with 2’,3’-cyclic-〖PO〗_4 and 5’-OH ends that have been damaged during the splicing that takes place during the fungal unfolded protein response. These enzymes are made up of CPDs which are cyclic phosphodiesterase and KINs which are central GTP-dependent polynucleotide kinase. These proteins correct the damaged ends. This causes 3’-OH and, 2’-〖PO〗_4 and 5’-〖PO〗_4 to generate. These are required for sealing by a terminal ATP-dependent ligase domain. In this scene the <scene name='75/752264/Atp_binding_pocket/1'>ATP binding pocket with subunits labeled</scene> So, this paper focused on the crystallized Trl1-LIG domain from a fungus called Cheatomium thermophililium at two steps along the reaction pathway. These pathways are the covalent LIG-(lysyl-N)-AMP*〖Mn〗^(2+)intermediate <scene name='75/752264/Min_ion_labeled/1'>Min ion labeled</scene> and a LIG*ATP*(〖〖Mn〗^(2+))〗_2 Michaelis complex. The importance of these structures is due to the fact that they point out two-metal mechanism where a pentahydrated metal complex helps to stabilize the transition state of ATP α phosphate and the second metal bridges are β and γ phosphates <scene name='75/752264/Atp_binding_pocket_min_atp_2/1'>ATP and Min labeled and coloered</scene>. These helps orient the pyrophosphate leaving group. A memetic of RNA terminal 2’-PO4 is the LIG bound sulfate anion. Trl1-LIG instates fungal Trl1 as the original of the Rnl6 clade of ATP-dependent RNA ligase. This Trl-LIG has a special C-terminal that is distinctive C-terminal domain. Over all the study was to see how the Trl-LIG structure supports the large body of in vivo structure-function data for Saccharomyces cerevisiae Trl1.
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The Sodium Potassium Pump is a transmembrane protein that consists of the alpha, beta, and FXYD Subunits. The alpha subunit consists of <scene name='User:Faizal/sandbox_10/Alpha_subunit/1'>three functional domains:</scene> The actuator domain (A), the nucleotide-binding domain (N), and the phosphorylation domain (P). These domains function in the rate of ion transports and signaling. The Beta subunit consists of a few gatherings of <scene name='User:Faizal/sandbox_10/Beta_subunit_interactions/1'>aromatic residues</scene>. This is very crucial as this helps target the polypeptide to the membrane and overall improved stability.<ref>PMID:18695395</ref> Additionally, the Na+ K+ pump alternates between two conformations: E1 and E2. In the <scene name='Faizal/sandbox_10/E1_structure/6'>E1 State</scene>, the ATP will be cleaved and the gamma phosphate will be moved to ASP376. The phosphate group is shown by an MgF4 Analog. In the <scene name='User:Faizal/sandbox_10/E2_structure/2'>E2 state</scene>, the site of binding consists of THR779, SER782, ASN783, and ASP811. These function in creating a kink so that the K+ ion can bind to this site.<ref>PMID:3054114</ref>
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The goal of this experiment was to determine the structure of the RNA ligase (LIG) domain of a fungal Trl1. In the first reaction the LIG react with ATP to form a covalent LIG-(lysyl-N)-AMP intermediate. This causes a displacement to a pyrophosphate. In the second reaction LIG transfers AMP to 5’-〖PO〗^4 RNA terminus. This helps to form a RNA-adenylate intermediate (A_(5^' pp5') RNA). The third reaction is where the LIG directs the attack of an RNA 3’-OH an the AppRNA to form splice junction and displaces the AMP. This is a feature well defined of the Trl1-LIG.
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Studies help educate scientist on fungal tRNA splicing enzymology. It helps provide the structure of a catalytically active ligase domain of Trl1. Trl1-LIG <scene name='75/752264/Fungal_trna_ligase/3'></StructureSection></scene> imitates a new RNA clade.
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</StructureSection>
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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.
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<scene name='75/752264/Atp_binding_pocket/1'>ATP binding pocket with subunits labeled</scene>
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<scene name='75/752264/Atp_binding_pocket_min_and_atp/1'>ATP binding pocket with Min and ATP labeled</scene>
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<scene name='75/752264/Atp_binding_pocket_min_atp_2/1'>ATP and Min labeled and coloered</scene>
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<scene name='75/752264/Min_ion_labeled/1'>Min ion labeled</scene>
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== References ==
== References ==
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1) Shuman,S. and Lima,C.D. (2004) The polynucleotide ligase and RNA capping enzyme superfamily of covalent nucleotidyltransferases. Curr. Opin. Struct. Biol., 14, 757–764.
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<references/>
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2) Banerjee, A. Ghosh, S. Goldgur, Y. and Shuman, S. (2018) Structure and two-metal mechanism of fungal tRNA ligase. Nucleic Acid Research, 2019, Vol 47, No.3 doi:10.1093lnarlgky1275
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Current revision

Sodium-Potassium Pump

Na+/K+ Pump Protein

Drag the structure with the mouse to rotate

References

  1. Pirahanchi Y, Jessu R, Aeddula NR. Physiology, Sodium Potassium Pump PMID:30725773
  2. Rui H, Artigas P, Roux B. The selectivity of the Na(+)/K(+)-pump is controlled by binding site protonation and self-correcting occlusion. Elife. 2016 Aug 4;5. doi: 10.7554/eLife.16616. PMID:27490484 doi:http://dx.doi.org/10.7554/eLife.16616
  3. Forrest MD. The sodium-potassium pump is an information processing element in brain computation. Front Physiol. 2014 Dec 23;5:472. doi: 10.3389/fphys.2014.00472. eCollection, 2014. PMID:25566080 doi:http://dx.doi.org/10.3389/fphys.2014.00472
  4. Funck VR, Ribeiro LR, Pereira LM, de Oliveira CV, Grigoletto J, Della-Pace ID, Fighera MR, Royes LF, Furian AF, Larrick JW, Oliveira MS. Contrasting effects of Na+, K+-ATPase activation on seizure activity in acute versus chronic models. Neuroscience. 2015 Jul 9;298:171-9. doi: 10.1016/j.neuroscience.2015.04.031. Epub, 2015 Apr 20. PMID:25907445 doi:http://dx.doi.org/10.1016/j.neuroscience.2015.04.031
  5. Lees GJ. Inhibition of sodium-potassium-ATPase: a potentially ubiquitous mechanism contributing to central nervous system neuropathology. Brain Res Brain Res Rev. 1991 Sep-Dec;16(3):283-300. doi:, 10.1016/0165-0173(91)90011-v. PMID:1665097 doi:http://dx.doi.org/10.1016/0165-0173(91)90011-v
  6. Clausen T. Clinical and therapeutic significance of the Na+,K+ pump*. Clin Sci (Lond). 1998 Jul;95(1):3-17. PMID:9662481
  7. Tack CJ, Lutterman JA, Vervoort G, Thien T, Smits P. Activation of the sodium-potassium pump contributes to insulin-induced vasodilation in humans. Hypertension. 1996 Sep;28(3):426-32. doi: 10.1161/01.hyp.28.3.426. PMID:8794828 doi:http://dx.doi.org/10.1161/01.hyp.28.3.426
  8. Shrimanker I, Bhattarai S. Electrolytes PMID:31082167
  9. Geering K. Functional roles of Na,K-ATPase subunits. Curr Opin Nephrol Hypertens. 2008 Sep;17(5):526-32. doi:, 10.1097/MNH.0b013e3283036cbf. PMID:18695395 doi:http://dx.doi.org/10.1097/MNH.0b013e3283036cbf
  10. Jorgensen PL, Andersen JP. Structural basis for E1-E2 conformational transitions in Na,K-pump and Ca-pump proteins. J Membr Biol. 1988 Jul;103(2):95-120. doi: 10.1007/BF01870942. PMID:3054114 doi:http://dx.doi.org/10.1007/BF01870942
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