5L9X: Human DNA polymerase eta-DNA ternary complex: reaction with 10 mM Mn2+ for 60s

Citation:
Abstract
It is generally assumed that an enzyme-substrate (ES) complex contains all components necessary for catalysis and that conversion to products occurs by rearrangement of atoms, protons, and electrons. However, we find that DNA synthesis does not occur in a fully assembled DNA polymerase-DNA-deoxynucleoside triphosphate complex with two canonical metal ions bound. Using time-resolved x-ray crystallography, we show that the phosphoryltransfer reaction takes place only after the ES complex captures a third divalent cation that is not coordinated by the enzyme. Binding of the third cation is incompatible with the basal ES complex and requires thermal activation of the ES for entry. It is likely that the third cation provides the ultimate boost over the energy barrier to catalysis of DNA synthesis.
PDB ID: 5L9XDownload
MMDB ID: 140367
PDB Deposition Date: 2016/6/12
Updated in MMDB: 2016/06
Experimental Method:
x-ray diffraction
Resolution: 1.9  Å
Source Organism:
Homo sapiens
Similar Structures:
Biological Unit for 5L9X: trimeric; determined by software (PISA)
Molecular Components in 5L9X
Label Count Molecule
Protein (1 molecule)
1
DNA Polymerase ETA(Gene symbol: POLH)
Molecule annotation
Nucleotides(2 molecules)
1
DNA (5'-d(*cp*ap*tp*tp*ap*tp*gp*ap*cp*gp*cp*t)-3')
Molecule annotation
1
DNA (5'-d(*ap*gp*cp*gp*tp*cp*ap*tp*a)-3')
Molecule annotation
Chemicals (9 molecules)
1
3
2
1
3
3
4
1
5
1
* Click molecule labels to explore molecular sequence information.

Citing MMDB
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