PDBsum entry 3gv5

Transferase/DNA

PDB id: 3gv5

Contents

Protein chain

379 a.a. *

DNA/RNA

Ligands

GOL

ADI ×2

Metals

_CA ×8

Waters ×737

* Residue conservation analysis

PDB id:

3gv5

Name:

Transferase/DNA

Title:

Human DNA polymerase iota in complex with t template DNA and incoming ddadp

Structure:

DNA polymerase iota. Chain: b, d. Synonym: rad30 homolog b, eta2. Engineered: yes. 5'-d( Gp Tp Gp Gp Ap Tp Gp Ap G)-3'. Chain: p, e. Engineered: yes. 5'-d(p Cp Ap Tp Tp Cp Tp Cp Ap Tp Cp Cp Ap C)-3'. Chain: t, f.

Source:

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

Resolution:

2.00Å R-factor: 0.206 R-free: 0.253

Authors:

K.N.Kirouac,H.Ling

Key ref:

K.N.Kirouac and H.Ling (2009). Structural basis of error-prone replication and stalling at a thymine base by human DNA polymerase iota. Embo J, 28, 1644-1654. PubMed id: 19440206

Date:

30-Mar-09 Release date: 02-Jun-09

Protein chains

Q9UNA4  (POLI_HUMAN) -  DNA polymerase iota from Homo sapiens

Seq: 740 a.a.

Struc: 379 a.a.

DNA/RNA chains

G-T-G-G-A-T-G-A-G 9 bases

C-A-T-T-C-T-C-A-T-C-C-A-C 13 bases

G-T-G-G-A-T-G-A-G 9 bases

C-A-T-T-C-T-C-A-T-C-C-A-C 13 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

DNA(n) (Bound ligand (Het Group name = ADI) matches with 48.39% similarity) + 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate

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

Added reference

Embo J 28:1644-1654 (2009)

PubMed id: 19440206

Structural basis of error-prone replication and stalling at a thymine base by human DNA polymerase iota.

K.N.Kirouac, H.Ling.

ABSTRACT

Human DNA polymerase iota (pol iota) is a unique member of Y-family polymerases, which preferentially misincorporates nucleotides opposite thymines (T) and halts replication at T bases. The structural basis of the high error rates remains elusive. We present three crystal structures of pol complexed with DNA containing a thymine base, paired with correct or incorrect incoming nucleotides. A narrowed active site supports a pyrimidine to pyrimidine mismatch and excludes Watson-Crick base pairing by pol. The template thymine remains in an anti conformation irrespective of incoming nucleotides. Incoming ddATP adopts a syn conformation with reduced base stacking, whereas incorrect dGTP and dTTP maintain anti conformations with normal base stacking. Further stabilization of dGTP by H-bonding with Gln59 of the finger domain explains the preferential T to G mismatch. A template 'U-turn' is stabilized by pol and the methyl group of the thymine template, revealing the structural basis of T stalling. Our structural and domain-swapping experiments indicate that the finger domain is responsible for pol's high error rates on pyrimidines and determines the incorporation specificity.