DNA Polymerase in Thermococcus gorgonarius: Difference between revisions

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<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='1TGO' size='340' side='right' caption='DNA Polymerase-Beta' scene=''>
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== Function ==
== 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) The original DNA stands are used as templates for the synthesis of new strands of DNA. DNA polymerases are the enzymes that catalyze the attachment of nucleotides to synthesize a new DNA strand.  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 from 3’ to 5’.  DNA follows Chargaff’s rule, which states 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 roughly makes only one mistake every billion bases.  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>DOI:10.2210/rcsb_pdb/mom_2000_3</ref>
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 ==
http://tools.niehs.nih.gov/polg/
 
== Relevance ==
 
== Structural highlights ==
DNA polymerase from Thermococcus gorgonarius (Tgo) is composed of 2,319 nucleotides.  Tgo 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 nucleotides.  The thumb (red) helps position the DNA and with translocation. <ref>PMCID:PMC22340</ref>
 
There are two separate <scene name='71/713469/Disulfidebond/2'>disulfide bonds</scene> are formed at two different cysteine pairs in Thermococcus gorgonarius. Each sulfide atom is shown in yellow.  Both of the cysteines are located on the palm domain. One disulfide bonds between cysteine (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 created by cysteine (506) and cysteine (509) create more stabilization for the helix in the palm domain at a helical turn.  With these disulfide bond this molecule is more thermostable.
 


== 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>


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>


</StructureSection>
</StructureSection>
== References ==
== References ==
<references/>
<references/>

Latest revision as of 05:54, 1 October 2019

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’. [1] 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. [2] 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. [1]

Function

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). [3] Human DNA polymerase optimum temperature is around 75 degrees Celsius (167 degrees Fahrenheit). [4]

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 . 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. [3]

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. [3]

There are two separate , 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. [3]


DNA Polymerase from Thermococcus gorgonarius (PDB code 1tgo)

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ReferencesReferences

  1. ↑ 1.0 1.1 DOI:10.2210/rcsb_pdb/mom_2000_3
  2. ↑ Bell SJ, Forsdyke DR. Accounting units in DNA. J Theor Biol. 1999 Mar 7;197(1):51-61. PMID:10036207 doi:http://dx.doi.org/10.1006/jtbi.1998.0857
  3. ↑ 3.0 3.1 3.2 3.3 Hopfner KP, Eichinger A, Engh RA, Laue F, Ankenbauer W, Huber R, Angerer B. Crystal structure of a thermostable type B DNA polymerase from Thermococcus gorgonarius. Proc Natl Acad Sci U S A. 1999 Mar 30;96(7):3600-5. PMID:10097083
  4. ↑ Innis MA, Myambo KB, Gelfand DH, Brow MA. DNA sequencing with Thermus aquaticus DNA polymerase and direct sequencing of polymerase chain reaction-amplified DNA. Proc Natl Acad Sci U S A. 1988 Dec;85(24):9436-40. PMID:3200828

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