PDBsum entry 3g6v

Replication/DNA

PDB id: 3g6v

Contents

Protein chain

373 a.a. *

DNA/RNA

Ligands

ATP

Metals

_MG ×2

Waters ×171

* Residue conservation analysis

PDB id:

3g6v

Name:

Replication/DNA

Title:

DNA synthesis across an abasic lesion by human DNA polymerase-iota

Structure:

DNA polymerase iota. Chain: a. Synonym: rad30 homolog b, eta2. Engineered: yes. Primer DNA strand. Chain: p. Engineered: yes. Template DNA strand. Chain: t.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: poli, rad30b. Expressed in: saccharomyces cerevisiae. Expression_system_taxid: 4932. Synthetic: yes. Other_details: oligonucleotide synthesis. Other_details: oligonucleotide synthesis

Resolution:

2.20Å R-factor: 0.214 R-free: 0.251

Authors:

D.T.Nair,A.K.Aggarwal

Key ref:

D.T.Nair et al. (2009). DNA synthesis across an abasic lesion by human DNA polymerase iota. Structure, 17, 530-537. PubMed id: 19368886 DOI: 10.1016/j.str.2009.02.015

Date:

09-Feb-09 Release date: 12-May-09

Protein chain

Q9UNA4  (POLI_HUMAN) -  DNA polymerase iota from Homo sapiens

Seq: 740 a.a.

Struc: 373 a.a.

DNA/RNA chains

A-G-G-A-C-C-DOC 7 bases

T-3DR-G-G-G-T-C-C-T 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: 10.1016/j.str.2009.02.015

Structure 17:530-537 (2009)

PubMed id: 19368886

DNA synthesis across an abasic lesion by human DNA polymerase iota.

D.T.Nair, R.E.Johnson, L.Prakash, S.Prakash, A.K.Aggarwal.

ABSTRACT

Abasic sites are among the most abundant DNA lesions formed in human cells, and they present a strong block to replication. DNA polymerase iota (Poliota) is one of the few DNA Pols that does not follow the A-rule opposite an abasic site. We present here three structures of human Poliota in complex with DNAs containing an abasic lesion and dGTP, dTTP, or dATP as the incoming nucleotide. The structures reveal a mechanism of translesion synthesis across an abasic lesion that differs from that in other Pols. Both the abasic lesion and the incoming dNTPs are intrahelical and are closely apposed across a constricted active site cleft. The dNTPs partake in distinct networks of hydrogen bonds in the "void" opposite the lesion. These different patterns of hydrogen bonds, as well as stacking interactions, may underlie Poliota's small preference for insertion of dGTP over other nucleotides opposite this common lesion.

Selected figure(s)

Figure 3.
Figure 3. Hydrogen-Bonding Networks
(A) Hydrogen bonding between the dGTP base and polymerase in the Polι[Abasic.dGTP] ternary complex. The relevant DNA and protein residues are colored according to element, the water molecules are shown as red spheres, and the hydrogen bonds are displayed as dashed lines.
(B) Hydrogen bonding between the dTTP base and polymerase in the Polι[Abasic.dTTP] ternary complex.
(C) Hydrogen bonding between the dATP base and polymerase in the Polι[Abasic.dATP] ternary complex.

Figure 4.
Figure 4. Comparison of Dpo4[Abasic.dCTP] and Polι[Abasic.dTTP] Ternary Complexes
The protein surface is displayed in light blue (Dpo4) or cyan (Polι), DNA is shown in stick representation, and putative Mg^2+ (Polι) or Ca^2+ (Dpo4) ions are shown as dark blue spheres. The abasic site and the incoming dTTP (Polι) or dCTP (Dpo4) are colored in red. The nucleotide 5′ to the abasic site in the Dpo4 complex is colored in sky blue. The abasic site is extrahelical in the Dpo4 complex (Ling et al., 2004), but remains intrahelical in the Polι complex(es).

The above figures are reprinted by permission from Cell Press: Structure (2009, 17, 530-537) copyright 2009.

Figures were selected by an automated process.