4HYK

Dbh Ternary Complex (substrates partially disordered)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.802 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.1 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:  4F4W, 4F4X, 4F4Y, 4F4Z, 4F50

  • 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
354Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770)Gene Names: dbh
EC: 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
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*GP*GP*AP*AP*GP*CP*CP*GP*G)-3')P10synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*TP*CP*CP*GP*CP*CP*CP*CP*GP*GP*CP*TP*TP*CP*CP*C)-3')T17synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.802 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.234 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 122.642α = 90.00
b = 122.642β = 90.00
c = 69.923γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
CrystalCleardata collection

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