3HL8

Crystal structure of exonuclease I in complex with inhibitor BCBP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Small-molecule tools for dissecting the roles of SSB/protein interactions in genome maintenance

Lu, D.Bernstein, D.A.Satyshur, K.A.Keck, J.L.

(2010) Proc.Natl.Acad.Sci.USA 107: 633-638

  • DOI: 10.1073/pnas.0909191107
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bacterial single-stranded DNA-binding proteins (SSBs) help to recruit a diverse array of genome maintenance enzymes to their sites of action through direct protein interactions. For all cases examined to date, these interactions are mediated by the e ...

    Bacterial single-stranded DNA-binding proteins (SSBs) help to recruit a diverse array of genome maintenance enzymes to their sites of action through direct protein interactions. For all cases examined to date, these interactions are mediated by the evolutionarily conserved C terminus of SSB (SSB-Ct). The essential nature of SSB protein interactions makes inhibitors that block SSB complex formation valuable biochemical tools and attractive potential antibacterial agents. Here, we identify four small molecules that disrupt complexes formed between Escherichia coli SSB and Exonuclease I (ExoI), a well-studied SSB-interacting enzyme. Each compound disrupts ExoI/SSB-Ct peptide complexes and abrogates SSB stimulation of ExoI nuclease activity. Structural and biochemical studies support a model for three of the compounds in which they compete with SSB for binding to ExoI. The fourth appears to rely on an allosteric mechanism to disrupt ExoI/SSB complexes. Subsets of the inhibitors block SSB-Ct complex formation with two other SSB-interaction partners as well, which highlights their utility as reagents for investigating the roles of SSB/protein interactions in diverse DNA replication, recombination, and repair reactions.


    Organizational Affiliation

    Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA.




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 4 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
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

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Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
BBP
Query on BBP

Download SDF File 
Download CCD File 
A
(5R)-3-tert-butyl-1-(6-chloro-1,3-benzothiazol-2-yl)-4,5-dihydro-1H-pyrazol-5-ol
C14 H16 Cl N3 O S
SDNWRBUDQKRGSP-GFCCVEGCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BBPKi: 32000 nM BINDINGMOAD
BBPKi: 32000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 53.823α = 90.00
b = 91.966β = 90.00
c = 106.280γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
REFMACrefinement
SCALEPACKdata scaling
MAR345data collection
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-05-27 
  • Released Date: 2010-01-19 
  • Deposition Author(s): Satyshur, K.A.

Revision History 

  • Version 1.0: 2010-01-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Source and taxonomy, Version format compliance
  • Version 1.2: 2014-05-28
    Type: Other
  • Version 1.3: 2017-11-01
    Type: Refinement description