PDBsum entry 4qw9

Transferase/DNA

PDB id: 4qw9

Contents

Protein chain

341 a.a.

DNA/RNA

Ligands

0G4

Metals

_CA ×3

Waters ×135

PDB id:

4qw9

Name:

Transferase/DNA

Title:

Ternary crystal structures of a y-family DNA polymerase dpo4 from sulfolobus solfataricus in complex with DNA and (-)ftc-ppnp

Structure:

DNA polymerase iv. Chain: a. Fragment: dpo4. Synonym: pol iv. Engineered: yes. DNA (5'-d(p Gp Gp Cp Tp Ap Cp Ap Gp Gp Ap Cp Tp C)-3'). Chain: c. Engineered: yes. DNA (5'-

Source:

Sulfolobus solfataricus. Organism_taxid: 273057. Strain: atcc 35092 / dsm 1617 / jcm 11322 / p2. Gene: dbh, dpo4, sso2448. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: random sequence, chemically synthesized. Other_details: random sequence, chemically synthesized

Resolution:

2.40Å R-factor: 0.245 R-free: 0.270

Authors:

V.Gaur,Z.Suo

Key ref:

V.Gaur et al. (2014). Structural and kinetic insights into binding and incorporation of L-nucleotide analogs by a Y-family DNA polymerase. Nucleic Acids Res, 42, 9984-9995. PubMed id: 25104018 DOI: 10.1093/nar/gku709

Date:

16-Jul-14 Release date: 27-Aug-14

Protein chain

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.

DNA/RNA chains

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

C-A-G-G-A-G-T-C-C-T-G-T-A-G-C-C 16 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: 10.1093/nar/gku709

Nucleic Acids Res 42:9984-9995 (2014)

PubMed id: 25104018

Structural and kinetic insights into binding and incorporation of L-nucleotide analogs by a Y-family DNA polymerase.

V.Gaur, R.Vyas, J.D.Fowler, G.Efthimiopoulos, J.Y.Feng, Z.Suo.

ABSTRACT

Considering that all natural nucleotides (D-dNTPs) and the building blocks (D-dNMPs) of DNA chains possess D-stereochemistry, DNA polymerases and reverse transcriptases (RTs) likely possess strongD-stereoselectivity by preferably binding and incorporating D-dNTPs over unnatural L-dNTPs during DNA synthesis. Surprisingly, a structural basis for the discrimination against L-dNTPs by DNA polymerases or RTs has not been established although L-deoxycytidine analogs (lamivudine and emtricitabine) and L-thymidine (telbivudine) have been widely used as antiviral drugs for years. Here we report seven high-resolution ternary crystal structures of a prototype Y-family DNA polymerase, DNA, and D-dCTP, D-dCDP, L-dCDP, or the diphosphates and triphosphates of lamivudine and emtricitabine. These structures reveal that relative to D-dCTP, each of these L-nucleotides has its sugar ring rotated by 180° with an unusual O4'-endo sugar puckering and exhibits multiple triphosphate-binding conformations within the active site of the polymerase. Such rare binding modes significantly decrease the incorporation rates and efficiencies of these L-nucleotides catalyzed by the polymerase.