Sandbox GGC2

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=='''Actin, alpha skeletal muscle (ACTA1)'''==
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==1QHA HUMAN HEXOKINASE TYPE I==
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<StructureSection load='1KXP' size='340' side='right' caption='Caption for this structure' scene=''>
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<StructureSection load='1QHA' size='340' side='right' caption='HUMAN HEXOKINASE TYPE I COMPLEXED WITH ATP ANALOGUE AMP-PNP' scene=''>
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Actin is a family of globular proteins that form microfilaments. It is the most abundant protein in eukaryotes <ref>DOI: 10.1073/pnas.122126299</ref>. They can be found in virtually all eukaryotic cells and come in two main forms, F-actin and G actin. Actin is responsible for many contraction properties in muscles.
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Vertebrates have 3 main groups of actin isoforms, alpha, beta, and gamma. Alpha actins play a major role in muscle contraction mechanism. Beta and gamma actins are involved in the regulation of cell motility. Actin has the capability to bind with other molecules, most notably myosin and ATP, in order to carry out its function.
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[[Image:C.jpg]]
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== Function ==
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<scene name='75/752269/Oliver_main/1'>Human Hexokinase 1 '1QHA'</scene> falls under the protein category of a kinase and is located within the cytosol and along the mitochondrial outer membrane <ref>PMID:27374331</ref><ref>PMID:1985912</ref>. A kinase is a protein that is responsible for the modification of a molecule through the covalent addition of the phosphate group. The source of the phosphate group is <scene name='75/752269/Oliver_atp/2'>Adenosine Triphosphate (ATP)</scene>. Human Hexokinase 1 catalyzes the phosphorylation of hexose sugars, primarily <scene name='75/752269/Oliver_glucose/2'>Glucose</scene> to form Glucose-6-Phosphate. This is typically observed during the initial step of glycolysis and is performed in order to attach a charge to the glucose, preventing it from diffusing out of the cell through the cell membrane. Typically, a <scene name='75/752269/Oliver_magnesium/1'>Magnesium</scene> cofactor also participates in a chelation complex with ATP <ref>PMID:2931560</ref>.
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Human Hexokinase 1 is seen to have a function in both innate immunity and inflammation in which the protein acts as a pattern recognition receptor for N-acetyl-D-glucosamine, a hexose present in the peptidoglycan layer of bacterial cell walls. Upon binding to N-acetyl-D-glucosamine, Human Hexokinase 1 dissociates from the mitochondria, which results in the activation of NLRP3 inflammasome <ref>PMID:27374331</ref>. Human Hexokinase 1 is also seen to play a role in tumor suppression. It does so by form a complex with voltage-dependent anion channel-1 (VDAC1) when acted phosphorylated by activating transcription factor 2 (ATF2). The HK1-VDAC1 complex functions to increase the permeability of the mitochondria outer membrane. This causes a release of mitochondrial enzymes which trigger apoptosis <ref>PMID:22304920</ref>.
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== Function ==
 
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Actins are highly conserved proteins that are involved in various types of cell motility and are ubiquitously expressed in all eukaryotic cells. The main function of ACTA1 gives directions to make the alpha (a)-actin. Actins are detrimental to cell movement and the contraction of muscle fibers. They are also used to help maintain the cytoskeleton. alpha skeletal actin is an essential component of sarcomeres, which are the basic contractile unit of muscle fibers.
 
== Disease ==
== Disease ==
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Mutations in the human skeletal muscle alpha-actin gene (ACTA1) are associated with different muscle diseases, two of which are '''congenital myopathy''', with an excess of thin myofilaments (actin myopathy), and '''nemaline myopathy'''. Both diseases can be identified by the abnormalities of the muscle fibers and variable degrees of muscle weakness<ref>DOI: 10.1038/13837</ref>. Congenital myopathies are a group of genetic muscle disorders that are identified with muscle weakness. Myopathy, congenital, with fiber-type disproportion (CFTD) is a genetically heterogeneous disorder in which there is relative hypotrophy of type 1 muscle fibers compared to type 2 fibers on skeletal muscle biopsy. However, these findings are not specific and can be found in many different myopathic and neuropathic conditions <ref>DOI: 10.1002/ana.20260</ref>. Another type of mutation is in the form of '''actin-accumulation myopathy'''. This type of mutation usually changes a single amino acid. These mutations can alter the way actin binds to ATP. This is problematic as ATP provides energy for cells and is used during thin filament formation, leading to impaired muscle contractions and weakened muscles. '''Cap myopathy''' is a form of missense mutation seen in the ACTA1 gene. It is a disorder that acts on skeletal muscles. Those diagnosed with it are familiar with muscles that have been weakened and are poor in tone. The mutation replaces methionine with valine. It can be identified by cap-like structures that are made of disorganized thin filaments, leading to impaired muscle contraction and muscle weakness.
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== Relevance ==
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There are multiple diseases associated with Human Hexokinase 1. It is possible for illness to arise from a deficiency in the protein. A deficiency is a rare autosomal recessive disease in which the <scene name='75/752269/Oliver_leu529/3'>Leucine</scene> and <scene name='75/752269/Oliver_thr680/1'>Threonine</scene> residues in the 529 and the 680 positions are mutated and translated as a Serine. This disease results in nonspherocytic hemolytic anemia <ref>PMID:7655856</ref>.
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The ACTA1 protein is a key component in various structures. One is its involvement in the actin cytoskeleton, which is a network of actin and its binding proteins that work together with microtubules and intermediate filaments that regular functions like cell migration <ref>DOI: 10.1093/hmg/ddh185</ref>. ACTA1 is also associated with the stress fiber, a contractile actin bundle of actin filaments made of short actin filaments with alternating polarities. The skeletal alpha-actin expression is induced by stimuli and conditions known to cause muscle formation. Since the ACTA1 gene is an isoform in adult skeletal muscle, it forms the core of sarcomere's thin filaments. These thin filaments are what interact with different proteins like myosin <ref>doi: 10.1002/humu.21059</ref>. In order for muscle contractions to occur, the sarcomere must shorten. This is the result of myosin binding to actin which then leads to the movement of the filaments. When the muscles begin to shorten, myosin heads need to bind to actin to pull it in, however, this process requires energy in the form of ATP. Myosin has two binding sites one for actin and the other for ATP. When ATP binds the myosin is forced to release actin causing a detachment and the formation of ADP. This puts the myosin head in a high energy conformation state or a "cocked" position. The head goes through what is called a power stroke and afterward, ADP is released. Actin and myosin are bound together again and ATP can then rebind allowing for the continuation of the contraction cycle.
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Also, diseases of Human Hexokinase can also result in diseases that affect the nervous system. A nervous system disease associated with the protein is neuropathy, '''hereditary motor and sensory, Russe type (HMSNR)''', also known as '''Charcot-Marie-Tooth''' disease. Laboratory studies suggest that this disease is caused by a mutation in a 26 kb range in upstream exons in the Human Hexokinase 1 gene. HMSNR is also autosomal recessive and is usually apparent in the first 10 years of life, characterized by muscular atrophy and impairment in the distal lower limbs. This weakness and atrophy results in those affected by the disease experiencing difficulty walking. HMSNR can later develop into weakness in the distal upper limbs and the proximal lower limbs. It is suspected that this disease is a result of demyelination of the neuronal axon which in turn has negative effects on neuron action potential velocity <ref>PMID:19536174</ref>.
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Another nervous system disease is a '''neurodevelopmental disorder with visual defects and brain anomalies (NEDVIBA)'''. This disease is found to primarily impact the brain, eyes, and heart. NEDVIBA is characterized by speech delay, intellectual disability, structural brain abnormalities, and visual impairments. The disease is caused by mutations in the 414 position (G → E), the 418 position (K → E), the 445 position (S → L), and in the 457 position (T → M) <ref>PMID:30778173</ref>.
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'''Retinitis pigmentosa''' is also a disease caused by mutation of the <scene name='75/752269/Oliver_glu847/2'>Glutamate</scene> residue in the 847 positions to a Lysine in Human Hexokinase 1. This disease is an autosomal dominant disease. Retinitis pigmentosa is a form of retinal dystrophy and is characterized by retinal pigment deposits. There is also a loss of both the rod and cone photoreceptors in the eye. Patients typically experience visual difficulty in poorly lit environments and loss of the mid-peripheral visual field. As the condition progresses, patients continue to experience deterioration of the visual field <ref>PMID:25190649</ref><ref>PMID:25316723</ref>.
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== Structural highlights ==
== Structural highlights ==
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The structure shown to the right is the crystal structure of the vitamin D-binding protein (shown in yellow) and its complex with skeletal actin (shown in blue). Under normal conditions, the macromolecule is present in a <scene name='75/752269/Dimeric_form/1'>dimeric form</scene>. "A homeostatic mechanism, termed the actin-scavenger system, is responsible for the depolymerization and removal of actin from the circulation. During the first phase of this mechanism, gelsolin severs the actin filaments. In the second phase, the vitamin D-binding protein (DBP) traps the actin monomers, which accelerates their clearance." <ref>DOI: 10.1073/pnas.122126299</ref>. The contacts between actin and DBP are a combination of hydrophobic and electrostatic interactions including direct hydrogen bonds (a total of 10), two salt bridges (connecting actin residues Asp-288 and Lys-328 and DBP residues Arg-218 and Glu-143, respectively), and a large number of contacts mediated by solvent molecules. There are many molecules or ligands that facilitate specific processes with actin. One of the unique ligands is <scene name='75/752269/Atp_ligand/2'>ATP</scene>. The binding of ATP, in this case, allows the ACTA1 gene to bind efficiently to DBP. The hydrolysis of ATP gives the actin the necessary energy to perform certain tasks and without it, actin will release the DBP. It is also noted that in this complex ATP is either blocked or slowed down dramatically. This observation may be an indication that during ATP hydrolysis actin undergoes certain conformational transitions that cannot take place when it is bound to certain proteins. Attached to the ATP molecule there is the metal ion, <scene name='75/752269/Mg_ligand/1'>magnesium</scene>, bound to the nucleotide site.The <scene name='75/752269/2n_struc/1'>secondary structure</scene> displays the positions of the alpha-helices and beta-strands. As seen the protein is mostly comprised of alpha-helices (shown in magenta) with the beta-sheets in minority (shown in yellow).
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The Human Hexokinase 1 protein is a homodimer formed from an <scene name='75/752269/Oliver_main_chaina/1'>"A" chain</scene> and <scene name='75/752269/Oliver_main_chainb/1'>"B" chain</scene>. There are only a few post-translational modifications that the Human Hexokinase 1 protein undergoes, those being acetylation at the Methionine residue in the 1 position and phosphorylation of the Serine residue in the 337 position, a modification that is also seen in the Rattus norvegicus (Rat) variation of the gene <ref>PMID:19413330</ref><ref>PMID:22673903</ref>. This serine phosphorylation results in the presence of a phosphoserine.
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There are several relevant regions of importance in the Human Hexokinase 1 protein. The N-terminal spanning from residue 1-10, are responsible for the binding interaction between the Human Hexokinase 1 protein and the mitochondria<ref>PMID:1985912</ref>. Further, there are multiple Glucose-6-Phosphate binding domains. These binding domains are seen at residues <scene name='75/752269/Oliver_residues_84-91/1'>84-91</scene>, 413-415, 532-536, and 861-863. There are also multiple glucose binding sites present at residues <scene name='75/752269/Oliver_substrate_binding_site/1'>172-173</scene>, 208-209, and 291-294 <ref>PMID:9493266</ref><ref>PMID:9735292</ref><ref>PMID:10574795</ref><ref>PMID:10686099</ref>.
</StructureSection>
</StructureSection>
== References ==
== References ==
<references/>
<references/>

Current revision

1QHA HUMAN HEXOKINASE TYPE I

HUMAN HEXOKINASE TYPE I COMPLEXED WITH ATP ANALOGUE AMP-PNP

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References

  1. Wolf AJ, Reyes CN, Liang W, Becker C, Shimada K, Wheeler ML, Cho HC, Popescu NI, Coggeshall KM, Arditi M, Underhill DM. Hexokinase Is an Innate Immune Receptor for the Detection of Bacterial Peptidoglycan. Cell. 2016 Jul 28;166(3):624-636. doi: 10.1016/j.cell.2016.05.076. Epub 2016 Jun , 30. PMID:27374331 doi:http://dx.doi.org/10.1016/j.cell.2016.05.076
  2. Magnani M, Serafini G, Bianchi M, Casabianca A, Stocchi V. Human hexokinase type I microheterogeneity is due to different amino-terminal sequences. J Biol Chem. 1991 Jan 5;266(1):502-5. PMID:1985912
  3. Garfinkel L, Garfinkel D. Magnesium regulation of the glycolytic pathway and the enzymes involved. Magnesium. 1985;4(2-3):60-72. PMID:2931560
  4. Wolf AJ, Reyes CN, Liang W, Becker C, Shimada K, Wheeler ML, Cho HC, Popescu NI, Coggeshall KM, Arditi M, Underhill DM. Hexokinase Is an Innate Immune Receptor for the Detection of Bacterial Peptidoglycan. Cell. 2016 Jul 28;166(3):624-636. doi: 10.1016/j.cell.2016.05.076. Epub 2016 Jun , 30. PMID:27374331 doi:http://dx.doi.org/10.1016/j.cell.2016.05.076
  5. Lau E, Kluger H, Varsano T, Lee K, Scheffler I, Rimm DL, Ideker T, Ronai ZA. PKCepsilon promotes oncogenic functions of ATF2 in the nucleus while blocking its apoptotic function at mitochondria. Cell. 2012 Feb 3;148(3):543-55. doi: 10.1016/j.cell.2012.01.016. PMID:22304920 doi:http://dx.doi.org/10.1016/j.cell.2012.01.016
  6. Bianchi M, Magnani M. Hexokinase mutations that produce nonspherocytic hemolytic anemia. Blood Cells Mol Dis. 1995;21(1):2-8. doi: 10.1006/bcmd.1995.0002. PMID:7655856 doi:http://dx.doi.org/10.1006/bcmd.1995.0002
  7. Hantke J, Chandler D, King R, Wanders RJ, Angelicheva D, Tournev I, McNamara E, Kwa M, Guergueltcheva V, Kaneva R, Baas F, Kalaydjieva L. A mutation in an alternative untranslated exon of hexokinase 1 associated with hereditary motor and sensory neuropathy -- Russe (HMSNR). Eur J Hum Genet. 2009 Dec;17(12):1606-14. doi: 10.1038/ejhg.2009.99. Epub 2009, Jun 17. PMID:19536174 doi:http://dx.doi.org/10.1038/ejhg.2009.99
  8. Okur V, Cho MT, van Wijk R, van Oirschot B, Picker J, Coury SA, Grange D, Manwaring L, Krantz I, Muraresku CC, Hulick PJ, May H, Pierce E, Place E, Bujakowska K, Telegrafi A, Douglas G, Monaghan KG, Begtrup A, Wilson A, Retterer K, Anyane-Yeboa K, Chung WK. De novo variants in HK1 associated with neurodevelopmental abnormalities and visual impairment. Eur J Hum Genet. 2019 Jul;27(7):1081-1089. doi: 10.1038/s41431-019-0366-9. Epub, 2019 Feb 18. PMID:30778173 doi:http://dx.doi.org/10.1038/s41431-019-0366-9
  9. Sullivan LS, Koboldt DC, Bowne SJ, Lang S, Blanton SH, Cadena E, Avery CE, Lewis RA, Webb-Jones K, Wheaton DH, Birch DG, Coussa R, Ren H, Lopez I, Chakarova C, Koenekoop RK, Garcia CA, Fulton RS, Wilson RK, Weinstock GM, Daiger SP. A dominant mutation in hexokinase 1 (HK1) causes retinitis pigmentosa. Invest Ophthalmol Vis Sci. 2014 Sep 4;55(11):7147-58. doi: 10.1167/iovs.14-15419. PMID:25190649 doi:http://dx.doi.org/10.1167/iovs.14-15419
  10. Wang F, Wang Y, Zhang B, Zhao L, Lyubasyuk V, Wang K, Xu M, Li Y, Wu F, Wen C, Bernstein PS, Lin D, Zhu S, Wang H, Zhang K, Chen R. A missense mutation in HK1 leads to autosomal dominant retinitis pigmentosa. Invest Ophthalmol Vis Sci. 2014 Oct 14;55(11):7159-64. doi:, 10.1167/iovs.14-15520. PMID:25316723 doi:http://dx.doi.org/10.1167/iovs.14-15520
  11. Gauci S, Helbig AO, Slijper M, Krijgsveld J, Heck AJ, Mohammed S. Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach. Anal Chem. 2009 Jun 1;81(11):4493-501. PMID:19413330 doi:http://dx.doi.org/10.1021/ac9004309
  12. Lundby A, Secher A, Lage K, Nordsborg NB, Dmytriyev A, Lundby C, Olsen JV. Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues. Nat Commun. 2012 Jun 6;3:876. doi: 10.1038/ncomms1871. PMID:22673903 doi:http://dx.doi.org/10.1038/ncomms1871
  13. Magnani M, Serafini G, Bianchi M, Casabianca A, Stocchi V. Human hexokinase type I microheterogeneity is due to different amino-terminal sequences. J Biol Chem. 1991 Jan 5;266(1):502-5. PMID:1985912
  14. Aleshin AE, Zeng C, Bourenkov GP, Bartunik HD, Fromm HJ, Honzatko RB. The mechanism of regulation of hexokinase: new insights from the crystal structure of recombinant human brain hexokinase complexed with glucose and glucose-6-phosphate. Structure. 1998 Jan 15;6(1):39-50. PMID:9493266
  15. Aleshin AE, Zeng C, Bartunik HD, Fromm HJ, Honzatko RB. Regulation of hexokinase I: crystal structure of recombinant human brain hexokinase complexed with glucose and phosphate. J Mol Biol. 1998 Sep 18;282(2):345-57. PMID:9735292 doi:10.1006/jmbi.1998.2017
  16. Rosano C, Sabini E, Rizzi M, Deriu D, Murshudov G, Bianchi M, Serafini G, Magnani M, Bolognesi M. Binding of non-catalytic ATP to human hexokinase I highlights the structural components for enzyme-membrane association control. Structure. 1999 Nov 15;7(11):1427-37. PMID:10574795
  17. Aleshin AE, Kirby C, Liu X, Bourenkov GP, Bartunik HD, Fromm HJ, Honzatko RB. Crystal structures of mutant monomeric hexokinase I reveal multiple ADP binding sites and conformational changes relevant to allosteric regulation. J Mol Biol. 2000 Mar 3;296(4):1001-15. PMID:10686099 doi:10.1006/jmbi.1999.3494
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