4XRH: Human Dna Polymerase Lambda- Mgdttp Binary And Complex With 6 Paired Dna

The mechanism of DNA polymerase (pol) fidelity is of fundamental importance in chemistry and biology. While high-fidelity pols have been well studied, much less is known about how some pols achieve medium or low fidelity with functional importance. Here we examine how human DNA polymerase lambda (Pol lambda) achieves medium fidelity by determining 12 crystal structures and performing pre-steady-state kinetic analyses. We showed that apo-Pol lambda exists in the closed conformation, unprecedentedly with a preformed MgdNTP binding pocket, and binds MgdNTP readily in the active conformation in the absence of DNA. Since prebinding of MgdNTP could lead to very low fidelity as shown previously, it is attenuated in Pol lambda by a hydrophobic core including Leu431, Ile492, and the Tyr505/Phe506 motif. We then predicted and demonstrated that L431A mutation enhances MgdNTP prebinding and lowers the fidelity. We also hypothesized that the MgdNTP-prebinding ability could stabilize a mismatched ternary complex and destabilize a matched ternary complex, and provided evidence with structures in both forms. Our results demonstrate that, while high-fidelity pols follow a common paradigm, Pol lambda has developed specific conformations and mechanisms for its medium fidelity. Structural comparison with other pols also suggests that different pols likely utilize different conformational changes and microscopic mechanisms to achieve their catalytic functions with varying fidelities.
PDB ID: 4XRHDownload
MMDB ID: 136667
PDB Deposition Date: 2015/1/21
Updated in MMDB: 2016/03
Experimental Method:
x-ray diffraction
Resolution: 3  Å
Source Organism:
synthetic construct
Similar Structures:
Biological Unit for 4XRH: trimeric; determined by author and by software (PISA)
Molecular Components in 4XRH
Label Count Molecule
Protein (1 molecule)
DNA Polymerase Lambda(Gene symbol: POLL)
Molecule annotation
Nucleotides(2 molecules)
DNA (5'-d(*cp*ap*gp*tp*ap*c)-3')
Molecule annotation
DNA (5'-d(p*gp*tp*ap*cp*tp*g)-3')
Molecule annotation
* Click molecule labels to explore molecular sequence information.

Citing MMDB