2iso
From Proteopedia
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| - | [[Image:2iso.gif|left|200px]] | + | [[Image:2iso.gif|left|200px]] |
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| - | '''Ternary complex of DNA Polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-difluoromethylene triphosphate''' | + | {{Structure |
| + | |PDB= 2iso |SIZE=350|CAPTION= <scene name='initialview01'>2iso</scene>, resolution 2.10Å | ||
| + | |SITE= | ||
| + | |LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene> and <scene name='pdbligand=GFF:2'-DEOXY-5'-O-[({[DIFLUORO(PHOSPHONO)METHYL](HYDROXY)PHOSPHORYL}OXY)(HYDROXY)PHOSPHORYL]GUANOSINE'>GFF</scene> | ||
| + | |ACTIVITY= [http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] | ||
| + | |GENE= POLB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]) | ||
| + | }} | ||
| + | |||
| + | '''Ternary complex of DNA Polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-difluoromethylene triphosphate''' | ||
| + | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
| - | 2ISO is a [ | + | 2ISO is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ISO OCA]. |
==Reference== | ==Reference== | ||
| - | Modifying the beta,gamma leaving-group bridging oxygen alters nucleotide incorporation efficiency, fidelity, and the catalytic mechanism of DNA polymerase beta., Sucato CA, Upton TG, Kashemirov BA, Batra VK, Martinek V, Xiang Y, Beard WA, Pedersen LC, Wilson SH, McKenna CE, Florian J, Warshel A, Goodman MF, Biochemistry. 2007 Jan 16;46(2):461-71. PMID:[http:// | + | Modifying the beta,gamma leaving-group bridging oxygen alters nucleotide incorporation efficiency, fidelity, and the catalytic mechanism of DNA polymerase beta., Sucato CA, Upton TG, Kashemirov BA, Batra VK, Martinek V, Xiang Y, Beard WA, Pedersen LC, Wilson SH, McKenna CE, Florian J, Warshel A, Goodman MF, Biochemistry. 2007 Jan 16;46(2):461-71. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17209556 17209556] |
[[Category: DNA-directed DNA polymerase]] | [[Category: DNA-directed DNA polymerase]] | ||
[[Category: Homo sapiens]] | [[Category: Homo sapiens]] | ||
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[[Category: polymerase]] | [[Category: polymerase]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 17:32:50 2008'' |
Revision as of 15:32, 20 March 2008
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| , resolution 2.10Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , and | ||||||
| Gene: | POLB (Homo sapiens) | ||||||
| Activity: | DNA-directed DNA polymerase, with EC number 2.7.7.7 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Ternary complex of DNA Polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-difluoromethylene triphosphate
Overview
DNA polymerase catalysis and fidelity studies typically compare incorporation of "right" versus "wrong" nucleotide bases where the leaving group is pyrophosphate. Here we use dGTP analogues replacing the beta,gamma-bridging O with CH2, CHF, CF2, or CCl2 to explore leaving-group effects on the nucleotidyl transfer mechanism and fidelity of DNA polymerase (pol) beta. T.G mismatches occur with fidelities similar to dGTP with the exception of the CH2 analogue, which is incorporated with 5-fold higher fidelity. All analogues are observed to bind opposite template C with Kds between 1 and 4 microM, and structural evidence suggests that the analogues bind in essentially the native conformation, making them suitable substrates for probing linear free energy relationships (LFERs) in transient-kinetics experiments. Importantly, Brnsted correlations of log(kpol) versus leaving-group pKa for both right and wrong base incorporation reveal similar sensitivities (betalg approximately -0.8) followed by departures from linearity, suggesting that a chemical step rather than enzyme conformational change is rate-limiting for either process. The location of the breaks relative to pKas of CF2, O, and the sterically bulky CCl2-bridging compounds suggests a modification-induced change in the mechanism by stabilization of leaving-group elimination. The results are addressed theoretically in terms of the energetics of successive primer 3'-O addition (bond forming) and pyrophosphate analogue elimination (bond breaking) reaction energy barriers.
About this Structure
2ISO is a Single protein structure of sequence from Homo sapiens. Full crystallographic information is available from OCA.
Reference
Modifying the beta,gamma leaving-group bridging oxygen alters nucleotide incorporation efficiency, fidelity, and the catalytic mechanism of DNA polymerase beta., Sucato CA, Upton TG, Kashemirov BA, Batra VK, Martinek V, Xiang Y, Beard WA, Pedersen LC, Wilson SH, McKenna CE, Florian J, Warshel A, Goodman MF, Biochemistry. 2007 Jan 16;46(2):461-71. PMID:17209556
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