PDBsum entry 2v4r

Transferase

PDB id: 2v4r

Contents

Protein chain

343 a.a. *

DNA/RNA

Ligands

DGT

Metals

_CA ×3

Waters ×134

* Residue conservation analysis

PDB id:

2v4r

Name:

Transferase

Title:

Non-productive complex of the y-family DNA polymerase dpo4 with dgtp skipping the m1dg adduct to pair with the next template cytosine

Structure:

DNA polymerase iv. Chain: a. Engineered: yes. Other_details: y-family DNA polymerase from sulfolobus solfataricus. 5'-d( Gp Gp Gp Gp Gp Ap Ap Gp Gp Ap Tp Tp C)-3'. Chain: p. Engineered: yes. Other_details: 13 base primer DNA 5'-ggg gga agg att c-3'. 5'-d( Tp Cp Ap Cp M1gp Gp Ap Ap Tp Cp Cp

Source:

Sulfolobus solfataricus. Organism_taxid: 273057. Strain: p2. Atcc: 35092. Expressed in: escherichia coli. Expression_system_taxid: 469008. Synthetic: yes. Synthetic construct. Organism_taxid: 32630.

Resolution:

2.50Å R-factor: 0.218 R-free: 0.273

Authors:

R.L.Eoff,J.B.Stafford,J.Szekely,C.J.Rizzo,M.Egli,F.P.Guengerich, L.J.Marnett

Key ref:

R.L.Eoff et al. (2009). Structural and functional analysis of Sulfolobus solfataricus Y-family DNA polymerase Dpo4-catalyzed bypass of the malondialdehyde-deoxyguanosine adduct. Biochemistry, 48, 7079-7088. PubMed id: 19492857

Date:

26-Sep-08 Release date: 16-Jun-09

Protein chain

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

Seq: 352 a.a.

Struc: 343 a.a.

DNA/RNA chains

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

C-A-C-M1G-G-A-A-T-C-C-T-T-C-C-C-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

Biochemistry 48:7079-7088 (2009)

PubMed id: 19492857

Structural and functional analysis of Sulfolobus solfataricus Y-family DNA polymerase Dpo4-catalyzed bypass of the malondialdehyde-deoxyguanosine adduct.

R.L.Eoff, J.B.Stafford, J.Szekely, C.J.Rizzo, M.Egli, F.P.Guengerich, L.J.Marnett.

ABSTRACT

Oxidative stress can induce the formation of reactive electrophiles, such as DNA peroxidation products, e.g., base propenals, and lipid peroxidation products, e.g., malondialdehyde. Base propenals and malondialdehyde react with DNA to form adducts, including 3-(2'-deoxy-beta-D-erythro-pentofuranosyl)pyrimido[1,2-alpha]purin-10(3H)-one (M1dG). When paired opposite cytosine in duplex DNA at physiological pH, M1dG undergoes ring opening to form N2-(3-oxo-1-propenyl)-dG (N2-OPdG). Previous work has shown that M1dG is mutagenic in bacteria and mammalian cells and that its mutagenicity in Escherichia coli is dependent on induction of the SOS response, indicating a role for translesion DNA polymerases in the bypass of M1dG. To probe the mechanism by which translesion polymerases bypass M1dG, kinetic and structural studies were conducted with a model Y-family DNA polymerase, Dpo4 from Sulfolobus solfataricus. The level of steady-state incorporation of dNTPs opposite M1dG was reduced 260-2900-fold and exhibited a preference for dATP incorporation. Liquid chromatography-tandem mass spectrometry analysis of the full-length extension products revealed a spectrum of products arising principally by incorporation of dC or dA opposite M1dG followed by partial or full-length extension. A greater proportion of -1 deletions were observed when dT was positioned 5' of M1dG. Two crystal structures were determined, including a "type II" frameshift deletion complex and another complex with Dpo4 bound to a dC.M1dG pair located in the postinsertion context. Importantly, M1dG was in the ring-closed state in both structures, and in the structure with dC opposite M1dG, the dC residue moved out of the Dpo4 active site, into the minor groove. The results are consistent with the reported mutagenicity of M1dG and illustrate how the lesion may affect replication events.