PDBsum entry 4j9m

Transferase/DNA

PDB id: 4j9m

Contents

Protein chain

429 a.a.

DNA/RNA

Ligands

XG4

GOL ×2

Metals

_MG ×2

_NA

Waters ×188

PDB id:

4j9m

Name:

Transferase/DNA

Title:

Human DNA polymerase eta-DNA ternary complex: misincorporation g opposite t after an a at the primer 3' end (aa/g)

Structure:

DNA polymerase eta. Chain: a. Fragment: catalytic core domain, unp residues 1-432. Synonym: rad30 homolog a, xeroderma pigmentosum variant type protein. Engineered: yes. DNA. Chain: t. Engineered: yes. DNA.

Source:

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

Resolution:

2.25Å R-factor: 0.183 R-free: 0.223

Authors:

Y.Zhao,M.Gregory,C.Biertumpfel,Y.Hua,F.Hanaoka,W.Yang

Key ref:

Y.Zhao et al. (2013). Mechanism of somatic hypermutation at the WA motif by human DNA polymerase η. Proc Natl Acad Sci U S A, 110, 8146-8151. PubMed id: 23630267 DOI: 10.1073/pnas.1303126110

Date:

16-Feb-13 Release date: 01-May-13

Protein chain

Q9Y253  (POLH_HUMAN) -  DNA polymerase eta from Homo sapiens

Seq: 713 a.a.

Struc: 429 a.a.

DNA/RNA chains

C-T-T-A-T-G-A-C-G-T 10 bases

T-A-C-G-T-C-A-T-A 9 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: 10.1073/pnas.1303126110

Proc Natl Acad Sci U S A 110:8146-8151 (2013)

PubMed id: 23630267

Mechanism of somatic hypermutation at the WA motif by human DNA polymerase η.

Y.Zhao, M.T.Gregory, C.Biertümpfel, Y.J.Hua, F.Hanaoka, W.Yang.

ABSTRACT

Somatic hypermutation is programmed base substitutions in the variable regions of Ig genes for high-affinity antibody generation. Two motifs, RGYW and WA (R, purine; Y, pyrimidine; W, A or T), have been found to be somatic hypermutation hotspots. Overwhelming evidence suggests that DNA polymerase η (Pol η) is responsible for converting the WA motif to WG by misincorporating dGTP opposite the templating T. To elucidate the molecular mechanism, crystal structures and kinetics of human Pol η substituting dGTP for dATP in four sequence contexts, TA, AA, GA, and CA, have been determined and compared. The T:dGTP wobble base pair is stabilized by Gln-38 and Arg-61, two uniquely conserved residues among Pol η. Weak base paring of the W (T:A or A:T) at the primer end and their distinct interactions with Pol η lead to misincorporation of G in the WA motif. Between two WA motifs, our kinetic and structural data indicate that A-to-G mutation occurs more readily in the TA context than AA. Finally, Pol η can extend the T:G mispair efficiently to complete the mutagenesis.