5DGA: Crystal Structure Of Human Dna Polymerase Eta Extending An 1,n6- Ethenodeoxyadenosine : Dt Pair By Inserting Dtmpnpp Opposite Template Da

1,N(6)-Ethenodeoxyadenosine (1,N(6)-dA) is the major etheno lesion formed in the reaction of DNA with epoxides substituted with good leaving groups (e.g. vinyl chloride epoxide). This lesion is also formed endogenously in DNA from lipid oxidation. Recombinant human DNA polymerase eta (hpol eta) can replicate oligonucleotide templates containing 1,N(6)-dA. In steady-state kinetic analysis, hpol eta preferred to incorporate dATP and dGTP, compared with dTTP. Mass spectral analysis of incorporation products also showed preferred purine (A, G) incorporation and extensive -1 frameshifts, suggesting pairing of the inserted purine and slippage before further replication. Five x-ray crystal structures of hpol eta ternary complexes were determined, three at the insertion and two at the extension stage. Two insertion complexes revealed incoming non-hydrolyzable dATP or dGTP analogs not pairing with but instead in a staggered configuration relative to 1,N(6)-dA in the anti conformation, thus opposite the 5'-T in the template, explaining the proclivity for frameshift misincorporation. In another insertion complex, dTTP was positioned opposite 1,N(6)-dA, and the adduct base was in the syn conformation, with formation of two hydrogen bonds. At the extension stage, with either an incorporated dA or dT opposite 1,N(6)-dA and 2'-deoxythymidine-5'-[(alpha,beta)-imido]triphosphate opposite the 5'-A, the 3'-terminal nucleoside of the primer was disordered, consistent with the tendency not to incorporate dTTP opposite 1,N(6)-dA. Collectively, the results show a preference for purine pairing opposite 1,N(6)-dA and for -1 frameshifts.
PDB ID: 5DGADownload
MMDB ID: 139881
PDB Deposition Date: 2015/8/27
Updated in MMDB: 2017/10
Experimental Method:
x-ray diffraction
Resolution: 2.3  Å
Source Organism:
Similar Structures:
Biological Unit for 5DGA: trimeric; determined by author and by software (PISA)
Molecular Components in 5DGA
Label Count Molecule
Protein (1 molecule)
DNA Polymerase ETA(Gene symbol: POLH)
Molecule annotation
Nucleotides(2 molecules)
DNA (5'-d(*cp*ap*tp*ap*(eda)p*tp*gp*ap*cp*gp*cp*t)-3')
Molecule annotation
DNA (5'-d(*ap*gp*cp*gp*tp*cp*ap*t)-3')
Molecule annotation
Chemicals (3 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB