4j2e

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4j2e, resolution 2.02Å ()
Ligands: ,
Activity: DNA-directed DNA polymerase, with EC number 2.7.7.7
Related: 4j2a, 4j2b, 4j2d


Resources: FirstGlance, OCA, RCSB, PDBsum
Coordinates: save as pdb, mmCIF, xml


Contents

RB69 DNA Polymerase L415M Ternary Complex

Publication Abstract from PubMed

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 Forster 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.

Alteration in the cavity size adjacent to the active site of RB69 DNA polymerase changes its conformational dynamics., Xia S, Wood M, Bradley MJ, De La Cruz EM, Konigsberg WH, Nucleic Acids Res. 2013 Oct;41(19):9077-89. doi: 10.1093/nar/gkt674. Epub 2013, Aug 5. PMID:23921641

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

Function

[DPOL_BPR69] This polymerase possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single stranded DNA in the 3'- to 5'-direction.

About this Structure

4j2e is a 3 chain structure. Full crystallographic information is available from OCA.

Reference

  • Xia S, Wood M, Bradley MJ, De La Cruz EM, Konigsberg WH. Alteration in the cavity size adjacent to the active site of RB69 DNA polymerase changes its conformational dynamics. Nucleic Acids Res. 2013 Oct;41(19):9077-89. doi: 10.1093/nar/gkt674. Epub 2013, Aug 5. PMID:23921641 doi:http://dx.doi.org/10.1093/nar/gkt674

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