2QXF

Product bound structure of exonuclease I at 1.5 angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of Escherichia coli exonuclease I in complex with thymidine 5'-monophosphate.

Busam, R.D.

(2008) Acta Crystallogr.,Sect.D 64: 206-210

  • DOI: 10.1107/S090744490706012X

  • PubMed Abstract: 
  • In Escherichia coli, exonuclease I (ExoI) is a monomeric processive 3'-5' exonuclease that degrades single-stranded DNA. The enzyme has been implicated as primarily being involved in repairing frameshift mutations. The structure of the enzyme has pre ...

    In Escherichia coli, exonuclease I (ExoI) is a monomeric processive 3'-5' exonuclease that degrades single-stranded DNA. The enzyme has been implicated as primarily being involved in repairing frameshift mutations. The structure of the enzyme has previously been determined in a hexagonal space group at 2.4 A resolution. Here, the structure of ExoI in complex with a nucleotide product, thymidine 5'-monophosphate, is described in an orthorhombic space group at 1.5 A resolution. This new high-resolution structure provides some insight into the interactions involved in binding a nucleotide product. The conserved active site contains a unique metal-binding position when compared with orthologous sites in the Klenow fragment, T4 DNA polymerase and dnaQ. This unique difference is proposed to be a consequence of the repositioning of an important histidine, His181, away from the active site.


    Organizational Affiliation

    Institute of Molecular Biology, Howard Hughes Medical Institute and Department of Physics, 1229 University of Oregon, Eugene, OR 97403-1229, USA. robert.busam@ki.se




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Exodeoxyribonuclease I
A
482Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: sbcB (cpeA, xonA)
EC: 3.1.11.1
Find proteins for P04995 (Escherichia coli (strain K12))
Go to UniProtKB:  P04995
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
TMP
Query on TMP

Download SDF File 
Download CCD File 
A
THYMIDINE-5'-PHOSPHATE
C10 H15 N2 O8 P
GYOZYWVXFNDGLU-XLPZGREQSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 52.630α = 90.00
b = 91.849β = 90.00
c = 102.752γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
ADSCdata collection
REFMACrefinement
HKL-2000data reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2007-08-11 
  • Released Date: 2008-01-22 
  • Deposition Author(s): Busam, R.D.

Revision History 

  • Version 1.0: 2008-01-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Source and taxonomy, Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description