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{{Template:Oberholser_Sandbox_Reservation}}
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<scene name='Sandbox_38/Adenylate_kinase_overall/1'>Adenylate kinase</scene> is an enzyme that catalyzes the reaction ATP + AMP = 2ADP. It consists of two identical subunits, A (shown in blue) and B (shown in green). For simplicity's sake, only the A chain will be shown in subsequent green links.


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==Basic structural elements==
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<Structure load='1AKE' size='500' frame='true' align='right' caption='Adenylate Kinase' scene='Insert optional scene name here' />
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Like many proteins, the <scene name='Sandbox_38/Adenylate_kinase_2o_structure/12'>secondary structure</scene> of adenylate kinase consists of two elements: alpha-helices, which are shown in light green, and beta-sheets, which are shown in dark green. Some of these are parallel, while others are anti-parallel. (Non-repetitive structural elements are shown in light blue/gray.) In addition to the regular hydrogen bonding that results in the secondary structure of the protein, additional <scene name='Sandbox_38/Adenylate_kinase_2o_structure/15'>hydrogen bonding</scene> is present in the backbone of adenylate kinase (shown in yellow), which also contributes to the overall stability/folding of the molecule.
An additional, significant factor in the structural stability/folding of the molecule is the polarity of the amino acid residues. The <scene name='Sandbox_38/Adenylate_kinase_2o_structure/18'>hydrophobic</scene> (nonpolar) residues are shown in gray, while the <scene name='Sandbox_38/Adenylate_kinase_2o_structure/17'>hydrophilic</scene> (polar/charged) residues are shown in red.


= '''Papain''' =
==Reactive structural elements==
As mentioned above, adenylate kinase catalyzes the reaction ATP + AMP = 2ADP. The <scene name='Sandbox_38/Adenylate_kinase_2o_structure/19'>catalytic residues</scene> that interact with the substrate to accomplish this are shown in purple. The amino acids that comprise these residues are Arg, Asp, and Lys.
However, the enzyme does not only interact with the ATP and AMP--it also interacts with <scene name='Sandbox_38/Adenylate_kinase_2o_structure/20'>Bis(adenosine)-5'-Pentaphosphate</scene> (shown in red), a non-hydrolysable substrate with structural similarity to the enzyme's actual substrate. The <scene name='Sandbox_38/Adenylate_kinase_2o_structure/29'>contact residues</scene>, i.e. the residues that are in contact with the ligand, can be seen (cationic residues are shown in blue, whereas anionic residues are shown in bright red). Similar to the catalytic residues, which have positively-charged side chains, most of the side chains that interact with the ligand are also charged, although oxygen (primarily from Thr side chains) interacts with it as well. Furthermore, the carbonyl and nitrogen parts of the amino acid backbone also interact with the ligand.
NOTE: The highlighted contact residues are actually those that are within 4 angstroms of the ligand, and all of them may not actually be in contact with it (although most of them are).


 
==Water Accessibility==
==Introduction==
Of course, this enzyme is not reacting with its substrate or ligand in a vacuum, but rather in solvent, such as water. However,  the molecule has a specific <scene name='Sandbox_38/Adenylate_kinase_2o_structure/24'>solvent accessibility</scene> (water is shown in blue, the enzyme shown in white, and the ligand is shown in red). Because of the protein's folding, the solvent can't interact with every part of it; usually the outside is covered in solvent molecules, while the inside has less interaction with the solvent. It should be noted, however, that even some of the <scene name='Sandbox_38/Adenylate_kinase_2o_structure/27'>internal residues</scene> are in contact with the solvent.
[[Image:Papain_cartoon.png|200px|left|thumb|Cartoon Peak at Pepsin]]
 
DID YOU KNOW?
 
<scene name='Sandbox_35/Papain/1'>Papain</scene>. Meat tenderizer. Old time home remedy for insect, jellyfish, and stingray stings<ref>[http://www.ameriden.com/products/advanced-digestive-enzyme/] Ameridan International</ref>. Who would have thought that a sulfhydryl protease from the latex of the papaya fruit, ''Carica papaya'' and ''Vasconcellea cundinamarcensis'' would have such a practical application beyond proteopedia?
 
 
 
This protease belongs to an extended family of aminopeptidases, dipeptidyl peptidases, endopeptidases, and other enzymes having both exo- and endo-peptidase activity. The inactivated zymogen with N-terminal propeptide regions - helping to stabilize against alkalinity and enabling proper folding - is activated through removal of the propeptide regions <ref>PMID: 7845226</ref><ref>PMID: 12188906</ref>.
 
<StructureSection load='9pap' size='500' side='right' caption='Structure of Papain (PDB entry [[9PAP]])' scene=''>
==Structure==
Its polypeptide chain consists of 212 amino acid residues folded to form a groove between its two domains containing the active site.
<scene name='Sandbox_35/Secondary_structure_papain/2'>secondary structure</scene>
 
<scene name='Sandbox_35/2nd_struc_papain_beta/2'>beta sheets</scene>
 
<scene name='Sandbox_35/2nd_struc_papain_helix/2'>alpha helix</scene> <ref name="9PAP PDB">[http://www.pdb.org/pdb/explore/explore.do?structureId=9PAP]9PAP PDB</ref>
 
<scene name='Sandbox_35/Active_site_papain/3'>active site</scene> <ref>PMID: 8140097</ref>
<scene name='Sandbox_35/Active_site_asp_158_papain/1'>TextToBeDisplayed</scene>
 
===Distribution of Residues===
<scene name='Sandbox_35/Papain_acid_and_basic_residues/1'>acidic and basic residues</scene>
 
<scene name='Sandbox_35/Hydrophobicity_papain/3'>polar and non-polar residue</scene>
 
<scene name='Sandbox_35/Papain_polar/1'>polar residues</scene>
 
<scene name='Sandbox_35/Nonpolar_papain/2'>non-polar residues</scene>
 
===Ligands interactions===
<scene name='Sandbox_35/Cathepsin_l_specific_inhibitor/2'>Cathepsin L specific inhibitor</scene>
Primarily hydrogen bonds with non-water and hydrophobic interactions
 
<scene name='Sandbox_35/Cathepsin_interaction/3'>interaction</scene>
</StructureSection>
 
==Catalytic Mechanism==
[[Image:Papainmech6.jpg|200px|left|thumb| General mechanism of papain catalysis<ref>[http://chemistry.umeche.maine.edu/CHY431/Peptidase10.html] University of Maine</ref>.]]
 
==References==
<references />
<ref group="xtra">PMID:8140097</ref>
 
http://www.pdb.org/pdb/explore/explore.do?structureId=2PAD
• Show the secondary structures.
• Compare the distribution of polar residues to that of nonpolar residues.
• Highlight the active site.
• If you can find a PDB file of the enzyme that contains a pseudo-substrate (may be inhibitor), highlight it.
• Show the contacts or attractions that are present between the pseudo-substrate and the protein, and if the enzyme has multiple subunits, show the contacts between the subunits.
• Identify any other ligands that are present in the structure and the types of contacts that are present between them and the protein
 
http://proteopedia.org/wiki/index.php/Sandbox_55#cite_note-18
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