3IRH

Structure of an Enterococcus Faecalis HD-domain protein complexed with dGTP and dATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Characterization of the deoxynucleotide triphosphate triphosphohydrolase (dNTPase) activity of the EF1143 protein from Enterococcus faecalis and crystal structure of the activator-substrate complex.

Vorontsov, I.I.Minasov, G.Kiryukhina, O.Brunzelle, J.S.Shuvalova, L.Anderson, W.F.

(2011) J.Biol.Chem. 286: 33158-33166

  • DOI: 10.1074/jbc.M111.250456
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The EF1143 protein from Enterococcus faecalis is a distant homolog of deoxynucleotide triphosphate triphosphohydrolases (dNTPases) from Escherichia coli and Thermus thermophilus. These dNTPases are important components in the regulation of the dNTP p ...

    The EF1143 protein from Enterococcus faecalis is a distant homolog of deoxynucleotide triphosphate triphosphohydrolases (dNTPases) from Escherichia coli and Thermus thermophilus. These dNTPases are important components in the regulation of the dNTP pool in bacteria. Biochemical assays of the EF1143 dNTPase activity demonstrated nonspecific hydrolysis of all canonical dNTPs in the presence of Mn(2+). In contrast, with Mg(2+) hydrolysis required the presence of dGTP as an effector, activating the degradation of dATP and dCTP with dGTP also being consumed in the reaction with dATP. The crystal structure of EF1143 and dynamic light scattering measurements in solution revealed a tetrameric oligomer as the most probable biologically active unit. The tetramer contains four dGTP specific allosteric regulatory sites and four active sites. Examination of the active site with the dATP substrate suggests an in-line nucleophilic attack on the α-phosphate center as a possible mechanism of the hydrolysis and two highly conserved residues, His-129 and Glu-122, as an acid-base catalytic dyad. Structural differences between EF1143 apo and holo forms revealed mobility of the α3 helix that can regulate the size of the active site binding pocket and could be stabilized in the open conformation upon formation of the tetramer and dGTP effector binding.


    Organizational Affiliation

    Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HD domain protein
A, B, C, D
480Enterococcus faecalis (strain ATCC 700802 / V583)Mutation(s): 0 
Find proteins for Q836G9 (Enterococcus faecalis (strain ATCC 700802 / V583))
Go to UniProtKB:  Q836G9
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DTP
Query on DTP

Download SDF File 
Download CCD File 
B, D
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
C10 H16 N5 O12 P3
SUYVUBYJARFZHO-RRKCRQDMSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
DGT
Query on DGT

Download SDF File 
Download CCD File 
A, B, C, D
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
HAAZLUGHYHWQIW-KVQBGUIXSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.185 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 149.253α = 90.00
b = 188.660β = 90.00
c = 67.822γ = 90.00
Software Package:
Software NamePurpose
MAR345data collection
HKL-2000data reduction
PHASERphasing
REFMACrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-09-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Source and taxonomy, Version format compliance
  • Version 1.2: 2011-11-23
    Type: Database references
  • Version 1.3: 2017-11-01
    Type: Refinement description