5N41

Archaeal DNA polymerase holoenzyme - SSO6202 at 1.35 Ang resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.351 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Identification and characterization of a heterotrimeric archaeal DNA polymerase holoenzyme.

Yan, J.Beattie, T.R.Rojas, A.L.Schermerhorn, K.Gristwood, T.Trinidad, J.C.Albers, S.V.Roversi, P.Gardner, A.F.Abrescia, N.G.A.Bell, S.D.

(2017) Nat Commun 8: 15075-15075

  • DOI: 10.1038/ncomms15075
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Since their initial characterization over 30 years ago, it has been believed that the archaeal B-family DNA polymerases are single-subunit enzymes. This contrasts with the multi-subunit B-family replicative polymerases of eukaryotes. Here we reveal t ...

    Since their initial characterization over 30 years ago, it has been believed that the archaeal B-family DNA polymerases are single-subunit enzymes. This contrasts with the multi-subunit B-family replicative polymerases of eukaryotes. Here we reveal that the highly studied PolB1 from Sulfolobus solfataricus exists as a heterotrimeric complex in cell extracts. Two small subunits, PBP1 and PBP2, associate with distinct surfaces of the larger catalytic subunit and influence the enzymatic properties of the DNA polymerase. Thus, multi-subunit replicative DNA polymerase holoenzymes are present in all three domains of life. We reveal the architecture of the assembly by a combination of cross-linking coupled with mass spectrometry, X-ray crystallography and single-particle electron microscopy. The small subunits stabilize the holoenzyme assembly and the acidic tail of one small subunit mitigates the ability of the enzyme to perform strand-displacement synthesis, with important implications for lagging strand DNA synthesis.


    Organizational Affiliation

    Department of Molecular and Cellular Biochemistry, Indiana University, Simon Hall MSB, 212 S Hawthorne Dr, Bloomington, Indiana 47405, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PolB1 Binding Protein 2
A
76Saccharolobus solfataricusMutation(s): 0 
Find proteins for A0A0E3GTJ4 (Saccharolobus solfataricus)
Go to UniProtKB:  A0A0E3GTJ4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.351 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.160 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 61.752α = 90.00
b = 61.752β = 90.00
c = 35.363γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data reduction
PHENIXrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-05-17
    Type: Initial release
  • Version 1.1: 2017-12-06
    Type: Structure summary