Crystal structure of NDX2 from thermus thermophilus HB8

Experimental Data Snapshot

  • Resolution: 1.84 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.224 

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Structural basis for different substrate specificities of two ADP-ribose pyrophosphatases from Thermus thermophilus HB8

Wakamatsu, T.Nakagawa, N.Kuramitsu, S.Masui, R.

(2008) J Bacteriol 190: 1108-1117

  • DOI: https://doi.org/10.1128/JB.01522-07
  • Primary Citation of Related Structures:  
    2YVM, 2YVN, 2YVO, 2YVP

  • PubMed Abstract: 

    ADP-ribose (ADPR) is one of the main substrates of Nudix proteins. Among the eight Nudix proteins of Thermus thermophilus HB8, we previously determined the crystal structure of Ndx4, an ADPR pyrophosphatase (ADPRase). In this study we show that Ndx2 of T. thermophilus also preferentially hydrolyzes ADPR and flavin adenine dinucleotide and have determined its crystal structure. We have determined the structures of Ndx2 alone and in complex with Mg2+, with Mg2+ and AMP, and with Mg2+ and a nonhydrolyzable ADPR analogue. Although Ndx2 recognizes the AMP moiety in a manner similar to those for other ADPRases, it recognizes the terminal ribose in a distinct manner. The residues responsible for the recognition of the substrate in Ndx2 are not conserved among ADPRases. This may reflect the diversity in substrate specificity among ADPRases. Based on these results, we propose the classification of ADPRases into two types: ADPRase-I enzymes, which exhibit high specificity for ADPR; and ADPRase-II enzymes, which exhibit low specificity for ADPR. In the active site of the ternary complexes, three Mg2+ ions are coordinated to the side chains of conserved glutamate residues and water molecules. Substitution of Glu90 and Glu94 with glutamine suggests that these residues are essential for catalysis. These results suggest that ADPRase-I and ADPRase-II enzymes have nearly identical catalytic mechanisms but different mechanisms of substrate recognition.

  • Organizational Affiliation

    Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MutT/nudix family protein182Thermus thermophilus HB8Mutation(s): 0 
Gene Names: ndx2
EC: 3.6.1
Find proteins for Q5SJY9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SJY9 
Go to UniProtKB:  Q5SJY9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SJY9
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.84 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.224 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.175α = 90
b = 101.201β = 90
c = 97.559γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-02-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Source and taxonomy, Version format compliance
  • Version 1.2: 2023-10-25
    Changes: Data collection, Database references, Refinement description