PDBsum entry 5dg9

Transferase/DNA

PDB id: 5dg9

Contents

Protein chain

430 a.a.

DNA/RNA

Ligands

XG4

GOL

Metals

_MG ×2

Waters ×345

PDB id:

5dg9

Name:

Transferase/DNA

Title:

Crystal structure of human DNA polymerase eta inserting dgmpnpp across a DNA template containing 1,n6-ethenodeoxyadenosine lesion

Structure:

DNA polymerase eta. Chain: a. Fragment: unp residues 1-432. Synonym: rad30 homolog a,xeroderma pigmentosum variant type protein. Engineered: yes. DNA (5'-d( Cp Ap Tp (Eda)p Ap Tp Gp Ap Cp Gp Cp T)-3'). Chain: t. Engineered: yes. DNA (5'-d( Ap Gp Cp Gp Tp Cp Ap T)-3').

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: polh, rad30, rad30a, xpv. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic construct. Organism_taxid: 32630.

Resolution:

2.15Å R-factor: 0.173 R-free: 0.222

Authors:

A.Patra,M.Egli

Key ref:

A.Patra et al. (2016). Structural and Kinetic Analysis of Miscoding Opposite the DNA Adduct 1,N6-Ethenodeoxyadenosine by Human Translesion DNA Polymerase η. J Biol Chem, 291, 14134-14145. PubMed id: 27226627 DOI: 10.1074/jbc.M116.732487

Date:

27-Aug-15 Release date: 08-Jun-16

Protein chain

Q9Y253  (POLH_HUMAN) -  DNA polymerase eta from Homo sapiens

Seq: 713 a.a.

Struc: 430 a.a.

DNA/RNA chains

C-A-T-EDA-A-T-G-A-C-G-C-T 12 bases

A-G-C-G-T-C-A-T 8 bases

Enzyme reactions

• Enzyme class: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1074/jbc.M116.732487

J Biol Chem 291:14134-14145 (2016)

PubMed id: 27226627

Structural and Kinetic Analysis of Miscoding Opposite the DNA Adduct 1,N6-Ethenodeoxyadenosine by Human Translesion DNA Polymerase η.

A.Patra, Y.Su, Q.Zhang, K.M.Johnson, F.P.Guengerich, M.Egli.

ABSTRACT

1,N(6)-Ethenodeoxyadenosine (1,N(6)-ϵdA) 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 η (hpol η) can replicate oligonucleotide templates containing 1,N(6)-ϵdA. In steady-state kinetic analysis, hpol η 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 η 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)-ϵdA 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)-ϵdA, 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)-ϵdA and 2'-deoxythymidine-5'-[(α,β)-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)-ϵdA. Collectively, the results show a preference for purine pairing opposite 1,N(6)-ϵdA and for -1 frameshifts.