4J2A: Rb69 Dna Polymerase L415a Ternary Complex

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.
PDB ID: 4J2ADownload
MMDB ID: 117621
PDB Deposition Date: 2013/2/4
Updated in MMDB: 2014/02
Experimental Method:
x-ray diffraction
Resolution: 1.8  Å
Source Organism:
synthetic construct
Similar Structures:
Biological Unit for 4J2A: trimeric; determined by author and by software (PISA)
Molecular Components in 4J2A
Label Count Molecule
Protein (1 molecule)
DNA Polymerase(Gene symbol: 43)
Molecule annotation
Nucleotides(2 molecules)
DNA (5'- D(*tp*cp*gp*ap*gp*tp*ap*ap*gp*cp*ap*gp*tp*cp*cp*gp*cp*g)-3')
Molecule annotation
DNA (5'-d(*gp*cp*gp*gp*ap*cp*tp*gp*cp*tp*tp*ap*c)-3')
Molecule annotation
Chemicals (8 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB