3ACA

Crystal structure of human NUDT5 complexed with 8-oxo-dADP and manganese


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Diverse substrate recognition and hydrolysis mechanisms of human NUDT5

Arimori, T.Tamaoki, H.Nakamura, T.Kamiya, H.Ikemizu, S.Takagi, Y.Ishibashi, T.Harashima, H.Sekiguchi, M.Yamagata, Y.

(2011) Nucleic Acids Res. 39: 8972-8983

  • DOI: 10.1093/nar/gkr575
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human NUDT5 (hNUDT5) hydrolyzes various modified nucleoside diphosphates including 8-oxo-dGDP, 8-oxo-dADP and ADP-ribose (ADPR). However, the structural basis of the broad substrate specificity remains unknown. Here, we report the crystal structures ...

    Human NUDT5 (hNUDT5) hydrolyzes various modified nucleoside diphosphates including 8-oxo-dGDP, 8-oxo-dADP and ADP-ribose (ADPR). However, the structural basis of the broad substrate specificity remains unknown. Here, we report the crystal structures of hNUDT5 complexed with 8-oxo-dGDP and 8-oxo-dADP. These structures reveal an unusually different substrate-binding mode. In particular, the positions of two phosphates (α and β phosphates) of substrate in the 8-oxo-dGDP and 8-oxo-dADP complexes are completely inverted compared with those in the previously reported hNUDT5-ADPR complex structure. This result suggests that the nucleophilic substitution sites of the substrates involved in hydrolysis reactions differ despite the similarities in the chemical structures of the substrates and products. To clarify this hypothesis, we employed the isotope-labeling method and revealed that 8-oxo-dGDP is attacked by nucleophilic water at Pβ, whereas ADPR is attacked at Pα. This observation reveals that the broad substrate specificity of hNUDT5 is achieved by a diversity of not only substrate recognition, but also hydrolysis mechanisms and leads to a novel aspect that enzymes do not always catalyze the reaction of substrates with similar chemical structures by using the chemically equivalent reaction site.


    Organizational Affiliation

    Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ADP-sugar pyrophosphatase
A, B
196Homo sapiensMutation(s): 0 
Gene Names: NUDT5 (NUDIX5)
EC: 3.6.1.13
Find proteins for Q9UKK9 (Homo sapiens)
Go to Gene View: NUDT5
Go to UniProtKB:  Q9UKK9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
8DD
Query on 8DD

Download SDF File 
Download CCD File 
A, B
8-oxo-7,8-dihydro-2'-deoxy-adenosine-5'-diphosphate
C10 H15 N5 O10 P2
FEPFWQCDWZFLGY-KVQBGUIXSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.199 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 113.636α = 90.00
b = 40.701β = 121.64
c = 99.791γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data scaling
CNSphasing
PHENIXrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-01-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-11-09
    Type: Database references, Structure summary
  • Version 1.3: 2013-06-05
    Type: Database references