PDBsum entry 4gc6

Transferase/DNA

PDB id: 4gc6

Contents

Protein chain

342 a.a.

DNA/RNA

Ligands

0OH

Metals

_CA ×4

Waters ×45

PDB id:

4gc6

Name:

Transferase/DNA

Title:

Crystal structure of dpo4 in complex with n-mc-damp opposite dt

Structure:

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

Source:

Sulfolobus solfataricus p2. Organism_taxid: 273057. Strain: p2. Gene: dbh, dpo4, sso2448. Expressed in: escherichia coli. Expression_system_taxid: 469008. Synthetic: yes. Other_details: chemically synthesized oligonucleotide. Other_details: chemically synthesized oligonucleotide

Resolution:

2.90Å R-factor: 0.206 R-free: 0.276

Authors:

R.L.Eoff,A.Ketkar,S.Banerjee,M.K.Zafar

Key ref:

A.Ketkar et al. (2012). Differential furanose selection in the active sites of archaeal DNA polymerases probed by fixed-conformation nucleotide analogues. Biochemistry, 51, 9234-9244. PubMed id: 23050956

Date:

29-Jul-12 Release date: 24-Oct-12

Protein chain

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

Seq: 352 a.a.

Struc: 342 a.a.

DNA/RNA chains

G-G-G-G-G-A-A-G-G-A-T-T-C-C 14 bases

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

Biochemistry 51:9234-9244 (2012)

PubMed id: 23050956

Differential furanose selection in the active sites of archaeal DNA polymerases probed by fixed-conformation nucleotide analogues.

A.Ketkar, M.K.Zafar, S.Banerjee, V.E.Marquez, M.Egli, R.L.Eoff.

ABSTRACT

DNA polymerases select for the incorporation of deoxyribonucleotide triphosphates (dNTPs) using amino acid side-chains that act as a "steric-gate" to bar improper incorporation of rNTPs. An additional factor in the selection of nucleotide substrates resides in the preferred geometry for the furanose moiety of the incoming nucleotide triphosphate. We have probed the role of sugar geometry during nucleotide selection by model DNA polymerases from Sulfolobus solfataricus using fixed conformation nucleotide analogues. North-methanocarba-dATP (N-MC-dATP) locks the central ring into a RNA-type (C2'-exo, North) conformation near a C3'-endo pucker, and South-methanocarba-dATP (S-MC-dATP) locks the central ring system into a (C3'-exo, South) conformation near a C2'-endo pucker. Dpo4 preferentially inserts N-MC-dATP and in the crystal structure of Dpo4 in complex with N-MC-dAMP, the nucleotide analogue superimposes almost perfectly with Dpo4 bound to unmodified dATP. Biochemical assays indicate that the S. solfataricus B-family DNA polymerase Dpo1 can insert and extend from both N-MC-dATP and S-MC-dATP. In this respect, Dpo1 is unexpectedly more tolerant of substrate conformation than Dpo4. The crystal structure of Dpo4 bound to S-MC-dADP shows that poor incorporation of the Southern pucker by the Y-family polymerase results from a hydrogen bond between the 3'-OH group of the nucleotide analogue and the OH group of the steric gate residue, Tyr12, shifting the S-MC-dADP molecule away from the dNTP binding pocket and distorting the base pair at the primer-template junction. These results provide insights into substrate specificity of DNA polymerases, as well as molecular mechanisms that act as a barrier against insertion of rNTPs.