User:Karl E. Zahn/Sandbox RB69 1/palm-domain

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The two-metal ion mechanism employed during the pol catalytic cycle of DNA pols relies on coordination of divalent cations by conserved motifs in the palm domain<ref>PMID:8341661</ref><ref>PMID:9440688</ref>. The palm domain of RB69 DNA pol (residues 383-468, 573-729) contains such <scene name='User:Karl_E._Zahn/Sandbox_RB69_1/palm-domain/Activesite_2ozs/1'>motifs</scene> (DTD) that are particularly appropriate for family B DNA pols. Interestingly, the residue T622 in this sequence must obtain a high energy conformation in order to correctly orient the Asp residues. This property is evident in Ramachandran plots of RB69 DNA pol where T622 is an obvious out-layer.
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The two-metal ion mechanism employed during the DNA pol catalytic cycle relies on coordination of divalent cations by conserved motifs in the palm domain<ref>PMID:8341661</ref><ref>PMID:9440688</ref>. The palm domain of RB69 DNA pol (residues 383-468, 573-729) contains such <scene name='User:Karl_E._Zahn/Sandbox_RB69_1/palm-domain/Activesite_2ozs/1'>motifs</scene> (DTD) that are particularly conserved in family B DNA pols. Interestingly, the residue T622 in this sequence must obtain a high energy conformation in order to correctly orient the Asp residues. This property is evident in Ramachandran plots of RB69 DNA pol where T622 is an obvious out-layer.
<applet load='2ozs' size='300' frame='true' align='right' caption='Active Site of RB69 polymerase: 2ozs' />
<applet load='2ozs' size='300' frame='true' align='right' caption='Active Site of RB69 polymerase: 2ozs' />

Revision as of 20:40, 22 April 2009

The two-metal ion mechanism employed during the DNA pol catalytic cycle relies on coordination of divalent cations by conserved motifs in the palm domain[1][2]. The palm domain of RB69 DNA pol (residues 383-468, 573-729) contains such (DTD) that are particularly conserved in family B DNA pols. Interestingly, the residue T622 in this sequence must obtain a high energy conformation in order to correctly orient the Asp residues. This property is evident in Ramachandran plots of RB69 DNA pol where T622 is an obvious out-layer.

Active Site of RB69 polymerase: 2ozs

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References

  1. ↑ Steitz TA, Steitz JA. A general two-metal-ion mechanism for catalytic RNA. Proc Natl Acad Sci U S A. 1993 Jul 15;90(14):6498-502. PMID:8341661
  2. ↑ Doublie S, Tabor S, Long AM, Richardson CC, Ellenberger T. Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 A resolution. Nature. 1998 Jan 15;391(6664):251-8. PMID:9440688 doi:http://dx.doi.org/10.1038/34593

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Karl E. Zahn

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