3LOJ

Structure of Mycobacterium tuberculosis dUTPase H145A mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.128 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Aromatic stacking between nucleobase and enzyme promotes phosphate ester hydrolysis in dUTPase

Pecsi, I.Leveles, I.Harmat, V.Vertessy, B.G.Toth, J.

(2010) Nucleic Acids Res 38: 7179-7186

  • DOI: https://doi.org/10.1093/nar/gkq584
  • Primary Citation of Related Structures:  
    3HZA, 3LOJ

  • PubMed Abstract: 

    Aromatic interactions are well-known players in molecular recognition but their catalytic role in biological systems is less documented. Here, we report that a conserved aromatic stacking interaction between dUTPase and its nucleotide substrate largely contributes to the stabilization of the associative type transition state of the nucleotide hydrolysis reaction. The effect of the aromatic stacking on catalysis is peculiar in that uracil, the aromatic moiety influenced by the aromatic interaction is relatively distant from the site of hydrolysis at the alpha-phosphate group. Using crystallographic, kinetics, optical spectroscopy and thermodynamics calculation approaches we delineate a possible mechanism by which rate acceleration is achieved through the remote π-π interaction. The abundance of similarly positioned aromatic interactions in various nucleotide hydrolyzing enzymes (e.g. most families of ATPases) raises the possibility of the reported phenomenon being a general component of the enzymatic catalysis of phosphate ester hydrolysis.


  • Organizational Affiliation

    Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Budapest, Hungary.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Deoxyuridine 5'-triphosphate nucleotidohydrolase174Mycobacterium tuberculosisMutation(s): 1 
Gene Names: dutMT2771MTCY05A6.18cRv2697c
EC: 3.6.1.23
UniProt
Find proteins for P9WNS5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WNS5 
Go to UniProtKB:  P9WNS5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WNS5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DUP
Query on DUP

Download Ideal Coordinates CCD File 
B [auth A]2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
C9 H16 N3 O13 P3
XZLLMTSKYYYJLH-SHYZEUOFSA-N
TRS
Query on TRS

Download Ideal Coordinates CCD File 
E [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
G [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.128 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.591α = 90
b = 54.591β = 90
c = 83.051γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
SHELXrefinement
PDB_EXTRACTdata extraction
MAR345data collection
XDSdata reduction
SHELXL-97refinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-08-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-02-12
    Changes: Database references
  • Version 1.3: 2017-11-01
    Changes: Advisory, Refinement description
  • Version 1.4: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description