4F4W

Y-family DNA polymerase chimera Dbh-Dpo4-Dpo4 #1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.898 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

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

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

(2013) Structure 21: 20-31

  • DOI: 10.1016/j.str.2012.11.005
  • Primary Citation of Related Structures:  4F4X, 4F4Y, 4F4Z, 4F50, 4HYK

  • PubMed 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 disti ...

    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.


    Organizational Affiliation

    Wadsworth Center, New York State Department of Health, Albany, NY 12201-0509, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase IV
A, B
361Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770)Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
This entity is chimeric
Gene Names: dbh, dbh (dpo4)
EC: 2.7.7.7 2.7.7.7
Find proteins for Q4JB80 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
Go to UniProtKB:  Q4JB80
Find proteins for Q97W02 (Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Go to UniProtKB:  Q97W02
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*GP*CP*AP*CP*TP*GP*AP*TP*CP*GP*GP*C)-3')P,E13N/A
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*TP*AP*CP*GP*GP*CP*CP*GP*AP*TP*CP*AP*GP*TP*GP*CP*C)-3')T,F18N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DCP
Query on DCP

Download SDF File 
Download CCD File 
A, B
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
C9 H16 N3 O13 P3
RGWHQCVHVJXOKC-SHYZEUOFSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.898 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 52.820α = 90.00
b = 99.655β = 90.16
c = 101.625γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data reduction
CBASSdata collection
HKL-2000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-02
    Type: Initial release
  • Version 1.1: 2013-02-13
    Type: Database references
  • Version 1.2: 2014-01-29
    Type: Source and taxonomy
  • Version 1.3: 2014-02-12
    Type: Source and taxonomy
  • Version 1.4: 2017-08-16
    Type: Refinement description, Source and taxonomy