5DQO

Crystal structure of Y347F mutant of human primase p58 iron-sulfur cluster domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.251 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The [4Fe4S] cluster of human DNA primase functions as a redox switch using DNA charge transport.

O'Brien, E.Holt, M.E.Thompson, M.K.Salay, L.E.Ehlinger, A.C.Chazin, W.J.Barton, J.K.

(2017) Science 355: --

  • DOI: 10.1126/science.aag1789
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • DNA charge transport chemistry offers a means of long-range, rapid redox signaling. We demonstrate that the [4Fe4S] cluster in human DNA primase can make use of this chemistry to coordinate the first steps of DNA synthesis. Using DNA electrochemistry ...

    DNA charge transport chemistry offers a means of long-range, rapid redox signaling. We demonstrate that the [4Fe4S] cluster in human DNA primase can make use of this chemistry to coordinate the first steps of DNA synthesis. Using DNA electrochemistry, we found that a change in oxidation state of the [4Fe4S] cluster acts as a switch for DNA binding. Single-atom mutations that inhibit this charge transfer hinder primase initiation without affecting primase structure or polymerization. Generating a single base mismatch in the growing primer duplex, which attenuates DNA charge transport, inhibits primer truncation. Thus, redox signaling by [4Fe4S] clusters using DNA charge transport regulates primase binding to DNA and illustrates chemistry that may efficiently drive substrate handoff between polymerases during DNA replication.


    Organizational Affiliation

    Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA primase large subunit
A, B, C, D
197Homo sapiensMutation(s): 1 
Gene Names: PRIM2 (PRIM2A)
EC: 2.7.7.-
Find proteins for P49643 (Homo sapiens)
Go to Gene View: PRIM2
Go to UniProtKB:  P49643
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
A, B, C, D
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.251 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 60.398α = 90.00
b = 60.398β = 90.00
c = 246.729γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM65484

Revision History 

  • Version 1.0: 2016-09-21
    Type: Initial release
  • Version 1.1: 2016-10-05
    Type: Database references
  • Version 1.2: 2017-03-08
    Type: Database references
  • Version 1.3: 2017-09-13
    Type: Author supporting evidence