DNA Polymerase in Thermococcus gorgonarius: Difference between revisions

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OCA, Kayla Briley, Michal Harel, Jaime Prilusky

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-{{Sandbox_Reserved_JMeans}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE -->
+<StructureSection load='1TGO' size='340' side='right' caption='DNA Polymerase from Thermococcus gorgonarius (PDB code [[1tgo]]) ' scene=''>
-==DNA Polymerase==
+'''DNA polymerase''' is an enzyme, which synthesizes new stands of DNA from preexisting DNA. DNA polymerases are the enzymes which catalyze the attachment of nucleotides one by one to synthesize a new DNA strand.  The new DNA strands are always synthesized from 5’ to the 3’ direction.  DNA polymerase I is composed of a single polypeptide that removes the RNA primers and replaces them with DNA. DNA polymerase III is responsible for the majority of the DNA replication and the proofreading of new DNA from 3’ to 5’. <ref name="PDBDNAPOL">DOI:10.2210/rcsb_pdb/mom_2000_3</ref>  DNA follows Chargaff’s rule, which states there is an equal amount of purines to pyrimidines.  From Chargaff’s rule it is known that cytosine binds to guanine and adenine binds to thymine. <ref>PMID:10036207</ref> Each time a cell divides, DNA polymerase duplicates all of the cell’s DNA, and the cell passes one copy of DNA to each daughter cell.  DNA polymerase makes roughly only one mistake per every billion base.  Although Chargaff’s rule help makes the replication on DNA polymerase easier, an extra step of proofreading and cutting out the mismatched bases, after replication, is the reason why DNA polymerase is the most accurate enzyme. <ref name="PDBDNAPOL">DOI:10.2210/rcsb_pdb/mom_2000_3</ref>
-<StructureSection load='7icg' size='340' side='right' caption='DNA Polymerase-Beta' scene=''>
-This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; 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 name="structure">PMID:21638687</ref> to the rescue.<ref name="structure" />
 == Function ==
-DNA polymerase has an important role in the development of life.  DNA polymerase is an enzyme, which synthesizes new stands of DNA from preexisting DNA.  It does this by adding one nucleotide at a time to the 3’ end of a growing strand.  The new DNA strands are always synthesized from 5’ to the 3’ direction. (GENETICS BOOK)  Each time a cell divides, DNA polymerase duplicates all of the cell’s DNA, and the cell passes one copy of DNA to each daughter cell.  DNA polymerase roughly makes only one mistake every billion bases.  The binding of cytosine to guanine and adenine to thymine help make the replication on DNA polymerase easier, but an extra step of proofreading and cutting out mismatched bases after replication is the reason why DNA polymerase is the most accurate enzyme. (http://www.rcsb.org/pdb/101/motm.do?momID=3)
+The function of DNA polymerase in ''Thermococcus gorgonarius'' (''Tgo'') plays an important role in the development of life for this organism.  In ''Tgo'', DNA polymerase take on the same role of synthesizing new DNA as it does in every organism.  Although ''Tgo''’s DNA polymerase plays the same role, it does deffer from the human DNA polymerase.  The DNA polymerase in ''Tgo'' is more thermally stable.  Its stability can withstand temperature up to around 95 degrees Celsius (203 degrees Fahrenheit). <ref name="Thermococcus">PMID:10097083</ref>  Human DNA polymerase optimum temperature is around 75 degrees Celsius (167 degrees Fahrenheit). <ref>PMID:3200828</ref>
-== Disease ==
+== Structural Highlights ==
+DNA polymerase from ''Thermococcus gorgonarius'' (''Tgo'') is composed of 2,319 nucleotides.  ''Tgo'' is a single polypeptide chain made up of 773 amino acids which are folded into five domains.  The five domains in ''Tgo'' are the N-terminal, 3’ to 5’ exonuclease, palm, fingers, and the thumb.  These five domain are arranged to form a ring shaped molecule.  The structure of DNA polymerase can be described by using the “right hand model” which has a <scene name='71/713469/Palmthumbfinger/1'>“palm”, “fingers”, and “thumb” regions</scene>.  The palm region (blue) catalyzes the phosphoric transfer.  The finger region (green) interacts with the newly incoming nucleotides and the template bases that are paired together with the preexisting base.  The thumb (red) helps the positioning of the DNA and with translocation. <ref name="Thermococcus">PMID:10097083</ref>
+== Stabilization ==
+''Thermococcus gorgonarius'' (''Tgo'') is a very thermophilic molecule with a growth range between 55-95 degrees Celsius (131-203 degrees Fahrenheit).  In order to replicate properly, the DNA polymerase must be stable and  be able to tolerate binding to the substrate DNA.  ''Tgo'' polymerase contains 41% helix, 22% beta-stands, and 19% turns and also has an increase in hydrogen bonding. <ref name="Thermococcus">PMID:10097083</ref>
-== Relevance ==
+There are two separate <scene name='71/713469/Disulfidebond/2'>disulfide bonds</scene>, which are formed at two different cysteine pairs in ''Thermococcus gorgonarius''. Each sulfur atom is shown in yellow.  Both of the cysteines are located within the palm domain.  One disulfide bonds between cysteine (residue 428) and cysteine (442) stabilize the molecule at one of the folds between a helix in the palm domain and a helix located in the finger domain.  While the other disulfide bond composed of cysteine (506) and cysteine (509) creates more stabilization for the helix in the palm domain at a helical turn.  Sulfurs can withstand high temperature because their melting point is about 115 degrees Celsius (239 degrees Fahrenheit).  With these disulfide bond and structural folding this molecule is more thermostable. <ref name="Thermococcus">PMID:10097083</ref>
-== Structural highlights ==
-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.
 </StructureSection>
 == References ==
 <references/>