PDBsum entry 4eyh

Transferase/DNA

PDB id: 4eyh

Contents

Protein chain

377 a.a.

DNA/RNA

Ligands

DCP

Metals

_MG ×3

Waters ×28

PDB id:

4eyh

Name:

Transferase/DNA

Title:

Human DNA polymerase iota incorporating dctp opposite n- (deoxyguanosin-8-yl)-1-aminopyrene lesion

Structure:

DNA polymerase iota. Chain: b. Fragment: unp residues 26-445. Synonym: eta2, rad30 homolog b. Engineered: yes. DNA template. Chain: t. Engineered: yes. DNA primer.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: poli, rad30b. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: synthesized. Other_details: synthesized

Resolution:

2.90Å R-factor: 0.242 R-free: 0.281

Authors:

K.Kirouac,H.Ling

Key ref:

K.N.Kirouac et al. (2013). Replication of a carcinogenic nitropyrene DNA lesion by human Y-family DNA polymerase. Nucleic Acids Res, 41, 2060-2071. PubMed id: 23268450

Date:

01-May-12 Release date: 09-Jan-13

Protein chain

Q9UNA4  (POLI_HUMAN) -  DNA polymerase iota from Homo sapiens

Seq: 740 a.a.

Struc: 377 a.a.

DNA/RNA chains

DG8-G-G-G-T-C-C-T 8 bases

A-G-G-A-C-C-C 7 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

Nucleic Acids Res 41:2060-2071 (2013)

PubMed id: 23268450

Replication of a carcinogenic nitropyrene DNA lesion by human Y-family DNA polymerase.

K.N.Kirouac, A.K.Basu, H.Ling.

ABSTRACT

Nitrated polycyclic aromatic hydrocarbons are common environmental pollutants, of which many are mutagenic and carcinogenic. 1-Nitropyrene is the most abundant nitrated polycyclic aromatic hydrocarbon, which causes DNA damage and is carcinogenic in experimental animals. Error-prone translesion synthesis of 1-nitropyrene-derived DNA lesions generates mutations that likely play a role in the etiology of cancer. Here, we report two crystal structures of the human Y-family DNA polymerase iota complexed with the major 1-nitropyrene DNA lesion at the insertion stage, incorporating either dCTP or dATP nucleotide opposite the lesion. Polι maintains the adduct in its active site in two distinct conformations. dCTP forms a Watson-Crick base pair with the adducted guanine and excludes the pyrene ring from the helical DNA, which inhibits replication beyond the lesion. By contrast, the mismatched dATP stacks above the pyrene ring that is intercalated in the helix and achieves a productive conformation for misincorporation. The intra-helical bulky pyrene mimics a base pair in the active site and facilitates adenine misincorporation. By structure-based mutagenesis, we show that the restrictive active site of human polη prevents the intra-helical conformation and A-base misinsertions. This work provides one of the molecular mechanisms for G to T transversions, a signature mutation in human lung cancer.