PDBsum entry 4f4x

Transferase/DNA

PDB id: 4f4x

Contents

Protein chain

342 a.a.

DNA/RNA

Ligands

DCP

Metals

_CA ×4

Waters ×186

PDB id:

4f4x

Name:

Transferase/DNA

Title:

Y-family DNA polymerase chimera dbh-dpo4-dpo4 #2

Structure:

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

Source:

Sulfolobus acidocaldarius, sulfolobus solfataricus. Organism_taxid: 330779, 273057. Strain: atcc 33909 / dsm 639 / jcm 8929 / nbrc 15157 / ncimb 11770. Gene: dbh, dpo4 (s. Solfataricus) and dbh (s. Acidocaldarius), saci_0554, dpo4, sso24 48. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes.

Resolution:

2.05Å R-factor: 0.220 R-free: 0.250

Authors:

J.D.Pata,R.C.Wilson

Key ref:

R.C.Wilson et al. (2013). Y-family polymerase conformation is a major determinant of fidelity and translesion specificity. Structure, 21, 20-31. PubMed id: 23245850

Date:

11-May-12 Release date: 02-Jan-13

Protein chain

Q4JB80  (DPO4_SULAC) -  DNA polymerase IV from Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770)

Seq: 354 a.a.

Struc: 342 a.a.*

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.*

* PDB and UniProt seqs differ at 157 residue positions (black crosses)

DNA/RNA chains

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

T-A-C-G-C-C-C-T-G-A-T-C-A-G-T-G-C-C 18 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

Structure 21:20-31 (2013)

PubMed id: 23245850

Y-family polymerase conformation is a major determinant of fidelity and translesion specificity.

R.C.Wilson, M.A.Jackson, J.D.Pata.

ABSTRACT

Y-family polymerases help cells tolerate DNA damage by performing translesion synthesis opposite damaged DNA bases, yet they also have a high intrinsic error rate. We constructed chimeras of two closely related Y-family polymerases that display distinctly different activity profiles and found that the polypeptide linker that tethers the catalytic polymerase domain to the C-terminal DNA-binding domain is a major determinant of overall polymerase activity, nucleotide incorporation fidelity, and abasic site-bypass ability. Exchanging just 3 out of the 15 linker residues is sufficient to interconvert the polymerase activities tested. Crystal structures of four chimeras show that the conformation of the protein correlates with the identity of the interdomain linker sequence. Thus, residues that are more than 15 Å away from the active site are able to influence many aspects of polymerase activity by altering the relative orientations of the catalytic and DNA-binding domains.