Sandbox 46

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{{STRUCTURE_1w68 | PDB=1w68 | SCENE= }}
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{{STRUCTURE_1w69 | PDB=1w69 | SCENE= }}
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{{Template:Oberholser_Sandbox_Reservation}}
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==Mouse Ribonucleotide Reductase R2==
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<!-- PLEASE ADD YOUR CONTENT BELOW HERE -->
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Protein ID:
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<Structure load='1AKE A' size='500' frame='true' align='right' caption='Adenylate Kinase' scene='Sandbox_46/1ake_main/2' />
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=Adenylate Kinase=
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<scene name='Sandbox_46/1ake_main/2'>Adenylate kinase</scene> is a enzyme that catalyzes the conversion of 2 units of ADP into a unit of ATP and a unit of AMP. It is because of this catalytic role that adenylate kinase is an important part of homeostasis. Consisting of only 211 amino acids, adenylate kinase is not that large of an enzyme, despite its vital role in metabolism.
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=Structure=
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The <scene name='Sandbox_46/1ake_secondary/1'>secondary structure</scene> of adenylate kinase shows alpha helices (blue) and beta sheets (teal) surrounding the non-hydrolysable substrate analogue. The enzyme is comprised of 9 helices and 9 sheets constituting the secondary structure. As with any enzyme, the <scene name='Sandbox_46/1ake_hydrogen/1'>hydrogen bonds</scene> (May not load) between the residues of the peptide chains supply the final folded protein with structural stability which helps hold it in its folded configuration.
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<scene name='Sandbox_46/1w68/2'>1w68 (under oxidizing conditions)</scene>
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This secondary structure is oriented as such so that the <scene name='Sandbox_46/1ake_phobicphilic/2'>hydrophobic and hydrophilic residues</scene> are buried or exposed depending on their individual properties. The hydrophobic, represented in grey, are buried as to avoid as much contact with water as possible. Similarly, the hydrophilic, or polar, residues are colored purple and exposed as much to water as possible. This is further illustrated by the <scene name='Sandbox_46/1ake_water/1'>water solvation</scene> model, displaying water molecules as pink orbs and the enzyme as a translucent white. These hydrophobic interactions, burying of non polar residues and exposure of polar ones, is another main driving force conserving the tertiary structure of the enzyme.
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<scene name='Sandbox_46/1w69/2'>1w69 (under reducing conditions)</scene><ref>http://blast.ncbi.nlm.nih.gov/Blast.cgi</ref>
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The model of adenylate kinases shows displays the non-hydrolysable substrate as the ligand. The <scene name='Sandbox_46/1ake_ligandinteract/1'>residues interacting with the ligand</scene> are polar as the substrate is also highly negatively charged. The ligand can be seen in the active site of the enzyme, and shown in standard atomic coloring scheme. The <scene name='Sandbox_46/1ake_catalytic/1'>catalytic residues</scene> are the residues that directly interact with the ligand, and can be seen in yellow.
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==Introduction==
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Mouse ribonucleotide reductase is a class I enzyme. Class I enzymes consist of two different subunits. These two subunits are connected via hydrogen bonds. This enzyme acts primarily to catalyze the reduction of nucleoside diphosphates to deoxynucleoside diphosphates. Within DNA synthesis, this is the first dedicated step. The R2 subunit, a homodimer, is the smaller of the two subunits in this enzyme and serves as a limiting agent for overall enzyme activity. This subunit acts to maintain the tyrosil radical neighboring a diiron carboxylate site. In the mouse R2 subunit, the tyrosine residue is Tyr177. Through the process of catalysis, it has been proposed that the oxidation equivalent stored in the tyrosil subunit is passed along a pathway to a cysteine residue at an active site. Both subunits act as electron transfer pathways to the iron site. An arginine residue, Arg 265, has proven to be key to the activity of this particular enzyme. <ref>http://www.jbc.org/cgi/content/full/281/36/26022</ref>
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==Activity Within DNA Synthesis==
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Ribonucleotide reductase is essential in the formation of new deoxyribonucleotides. These are essential for the repair and replication of DNA with organisms. This reaction is highly regulated, which is important; since levels of deoxyribonucleotides must be correct to lower chances of cell death or genetic abnormalities. With mice and humans, the two subunits are coded for by genes located on different chromosomes. The R2 subunit determines the activity of the enzyme, since its levels vary while the levels of the R1 subunit are quite constant. DNA damage induces transcription of the R1 gene only. The transcription of R2 is induced by p53 during the S phase of the cell. One interesting fact about this gene is that the human ribonucleotide reductase R2 promoter can activate transcription of the human R2 gene in a mouse cell. The human R2 gene can be expressed in a functional R2 protein within a mouse cell. The same is true for a mouse R2 gene in a human cell. This illustrates close relatedness of the genes. <ref>http://www.jbc.org/cgi/content/full/279/11/10796</ref>
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==Structual Properties==
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While both forms of this enzyme both interact with iron, there are some structural differences due to the different conditions.
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1w68:
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16 α-helices
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8 β-turns
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1w69:
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15 α-helices
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10 β-turns<ref>http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/</ref>
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==Protein Sequence==
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For the enzyme under oxidizing conditions (1w68):
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VEDEPLLRENPRRFVVFPIEYHDIWQMYKKAEASFWTAEEVDLSKDIQHWEALKPDERHFISHVLAFFA
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ASDGIVNENLVERFSQEVQVTEARCFYGFQIAMENIHSEMYSLLIDTYIKDPKEREYLFNAIETMPCVK
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KKADWALRWIGDKEATYGERVVAFAAVEGIFFSGSFASIFWLKKRGLMPGLTFSNELISRDEGLHCDFA
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CLMFKHLVHKPAEQRVREIITNAVRIEQEFLTEALPVKLIGMNCTLMKQYIEFVADRLMLELGFNKIFR
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VENPF
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For the enzyme under reducing conditions(1w69):
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VEDEPLLRENPRRFVVFPIEYHDIWQMYKKAEASFWTAEEVDLSKDIQHWEALKPDERHFISHVLAFFA
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ASDGIVNENLVERFSQEVQVTEARCFYGFQIAMENIHSEMYSLLIDTYIKDPKEREYLFNAIETMPCVK
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KKADWALRWIGDKEATYGERVVAFAAVEGIFFSGSFASIFWLKKRGLMPGLTFSNELISRDEGLHCDFA
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CLMFKHLVHKPAEQRVREIITNAVRIEQEFLTEALPVKLIGMNCTLMKQYIEFVADRLMLELGFNKIFR
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VENPF<ref>http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/</ref>
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==References==
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<references/>
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BLAST: Basic Local Alignment Search Tool, National Center for Biotechnology Information
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Gräslund A, Narváez AJ, Thelander L, Voevodskaya N. 2006 "The Involvement of Arg265 of Mouse Ribonucleotide Reductase R2 Protein in Proton Transfer and Catalysis." J. Biol. Chem., 281(36): 26022-26028.
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Björklund S, Chabes AL, Thelander L. 2004 "S Phase-specific Transcription of the Mouse Ribonucleotide Reductase R2 Gene Requires Both a Proximal Repressive E2F-binding Site and an Upstream Promoter Activating Region." J. Biol. Chem., 279(11): 10796-10807.
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PDBSum: European Bioinformatics Institution
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Current revision

Please do NOT make changes to this Sandbox. Sandboxes 30-60 are reserved for use by Biochemistry 410 & 412 at Messiah College taught by Dr. Hannah Tims during Fall 2012 and Spring 2013.

Adenylate Kinase

Drag the structure with the mouse to rotate

Adenylate Kinase

is a enzyme that catalyzes the conversion of 2 units of ADP into a unit of ATP and a unit of AMP. It is because of this catalytic role that adenylate kinase is an important part of homeostasis. Consisting of only 211 amino acids, adenylate kinase is not that large of an enzyme, despite its vital role in metabolism.

Structure

The of adenylate kinase shows alpha helices (blue) and beta sheets (teal) surrounding the non-hydrolysable substrate analogue. The enzyme is comprised of 9 helices and 9 sheets constituting the secondary structure. As with any enzyme, the (May not load) between the residues of the peptide chains supply the final folded protein with structural stability which helps hold it in its folded configuration.

This secondary structure is oriented as such so that the are buried or exposed depending on their individual properties. The hydrophobic, represented in grey, are buried as to avoid as much contact with water as possible. Similarly, the hydrophilic, or polar, residues are colored purple and exposed as much to water as possible. This is further illustrated by the model, displaying water molecules as pink orbs and the enzyme as a translucent white. These hydrophobic interactions, burying of non polar residues and exposure of polar ones, is another main driving force conserving the tertiary structure of the enzyme.

The model of adenylate kinases shows displays the non-hydrolysable substrate as the ligand. The are polar as the substrate is also highly negatively charged. The ligand can be seen in the active site of the enzyme, and shown in standard atomic coloring scheme. The are the residues that directly interact with the ligand, and can be seen in yellow.

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