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PDBsum entry 4j2e
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Transferase/DNA
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PDB id
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4j2e
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References listed in PDB file
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Key reference
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Title
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Alteration in the cavity size adjacent to the active site of rb69 DNA polymerase changes its conformational dynamics.
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Authors
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S.Xia,
M.Wood,
M.J.Bradley,
E.M.De la cruz,
W.H.Konigsberg.
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Ref.
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Nucleic Acids Res, 2013,
41,
9077-9089.
[DOI no: ]
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PubMed id
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Abstract
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Internal cavities are a common feature of many proteins, often having profound
effects on the dynamics of their interactions with substrate and binding
partners. RB69 DNA polymerase (pol) has a hydrophobic cavity right below the
nucleotide binding pocket at the tip of highly conserved L415 side chain.
Replacement of this residue with Gly or Met in other B family pols resulted in
higher mutation rates. When similar substitutions for L415 were introduced into
RB69pol, only L415A and L415G had dramatic effects on pre-steady-state kinetic
parameters, reducing base selectivity by several hundred fold. On the other
hand, the L415M variant behaved like the wild-type. Using a novel tC(o)-tCnitro
Förster Resonance Energy Transfer (FRET) assay, we were able to show that the
partition of the primer terminus between pol and exonuclease (exo) domains was
compromised with the L415A and L415G mutants, but not with the L415M variant.
These results could be rationalized by changes in their structures as determined
by high resolution X-ray crystallography.
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