3BQ1

Insertion ternary complex of Dbh DNA polymerase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural insights into the generation of single-base deletions by the Y family DNA polymerase dbh.

Wilson, R.C.Pata, J.D.

(2008) Mol.Cell 29: 767-779

  • DOI: 10.1016/j.molcel.2008.01.014
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Dbh is a Y family translesion DNA polymerase that accurately bypasses some damaged forms of deoxyguanosine, but also generates single-base deletion errors at frequencies of up to 50%, in specific hot spot sequences. We describe preinsertion binary, i ...

    Dbh is a Y family translesion DNA polymerase that accurately bypasses some damaged forms of deoxyguanosine, but also generates single-base deletion errors at frequencies of up to 50%, in specific hot spot sequences. We describe preinsertion binary, insertion ternary, and postinsertion binary crystal structures of Dbh synthesizing DNA after making a single-base deletion. The skipped template base adopts an extrahelical conformation stabilized by interactions with the C-terminal domain of the enzyme. DNA translocation and positioning of the next templating base at the active site, with space opposite to accommodate incoming nucleotide, occur independently of nucleotide binding, incorporation, and pyrophosphate release. We also show that Dbh creates single-base deletions more rapidly when the skipped base is located two or three bases upstream of the nascent base pair than when it is directly adjacent to the templating base, indicating that Dbh predominantly creates single-base deletions by template slippage rather than by dNTP-stabilized misalignment.


    Organizational Affiliation

    Division of Molecular Medicine, Wadsworth Center, New York State Department of Health, The State University of New York at Albany, Albany, NY 12201-0509, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase IV
A
354Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770)Mutation(s): 0 
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: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*DGP*DAP*DAP*DGP*DCP*DCP*DGP*DGP*DCP*DG)-3')P10N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*DT*DTP*DCP*DCP*DGP*DCP*DCP*DCP*DGP*DGP*DCP*DTP*DTP*DCP*DC)-3')T15N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
DG3
Query on DG3

Download SDF File 
Download CCD File 
P
2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O12 P3
HDRRAMINWIWTNU-NTSWFWBYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.204 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 124.960α = 90.00
b = 124.960β = 90.00
c = 70.210γ = 90.00
Software Package:
Software NamePurpose
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-04-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance