PDBsum entry 3khh

Transferase/DNA

PDB id: 3khh

Contents

Protein chains

341 a.a. *

DNA/RNA

Ligands

DGT ×2

_AF ×2

Metals

_CA ×6

Waters ×92

* Residue conservation analysis

PDB id:

3khh

Name:

Transferase/DNA

Title:

Dpo4 extension ternary complex with a c base opposite the 2- aminofluorene-guanine [af]g lesion

Structure:

DNA polymerase iv. Chain: a, b. Synonym: pol iv. Engineered: yes. 5'-d( Gp Tp Tp Gp Gp Ap Tp Gp Gp Tp Ap Gp (Doc))-3'. Chain: d, h. Engineered: yes. Other_details: DNA primer strand (dideoxy-terminated at the 3'-end). 5'-d( Cp Cp Tp A Ap Cp Gp Cp Tp Ap Cp Cp Ap Tp Cp Cp Ap Ap

Source:

Sulfolobus solfataricus p2. Organism_taxid: 273057. Strain: p2 / dsm 1617 / jcm 11322. Gene: dbh, dpo4, sso2448. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: DNA primer strand (dideoxy-terminated at the 3'-end). Other_details: DNA [af]g-modified template strand

Resolution:

2.70Å R-factor: 0.195 R-free: 0.252

Authors:

O.Rechkoblit,L.Malinina,D.J.Patel

Key ref:

O.Rechkoblit et al. (2010). Mechanism of error-free and semitargeted mutagenic bypass of an aromatic amine lesion by Y-family polymerase Dpo4. Nat Struct Biol, 17, 379-388. PubMed id: 20154704

Date:

30-Oct-09 Release date: 16-Feb-10

Protein chains

Q97W02  (DPO4_SULSO) -  DNA polymerase IV from Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)

Seq: 352 a.a.

Struc: 341 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DNA/RNA chains

G-T-T-G-G-A-T-G-G-T-A-G-DOC 13 bases

A-C-G-C-T-A-C-C-A-T-C-C-A-A-C-C 16 bases

G-T-T-G-G-A-T-G-G-T-A-G-DOC 13 bases

A-A-C-G-C-T-A-C-C-A-T-C-C-A-A-C-C 17 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

Nat Struct Biol 17:379-388 (2010)

PubMed id: 20154704

Mechanism of error-free and semitargeted mutagenic bypass of an aromatic amine lesion by Y-family polymerase Dpo4.

O.Rechkoblit, A.Kolbanovskiy, L.Malinina, N.E.Geacintov, S.Broyde, D.J.Patel.

ABSTRACT

The aromatic amine carcinogen 2-aminofluorene (AF) forms covalent adducts with DNA, predominantly with guanine at the C8 position. Such lesions are bypassed by Y-family polymerases such as Dpo4 via error-free and error-prone mechanisms. We show that Dpo4 catalyzes elongation from a correct 3'-terminal cytosine opposite [AF]G in a nonrepetitive template sequence with low efficiency. This extension leads to cognate full-length product, as well as mis-elongated products containing base mutations and deletions. Crystal structures of the Dpo4 ternary complex, with the 3'-terminal primer cytosine base opposite [AF]G in the anti conformation and with the AF moiety positioned in the major groove, reveal both accurate and misalignment-mediated mutagenic extension pathways. The mutagenic template-primer-dNTP arrangement is promoted by interactions between the polymerase and the bulky lesion rather than by a base pair-stabilized misaligment. Further extension leads to semitargeted mutations via this proposed polymerase-guided mechanism.