Crystal structure of dNTP triphosphohydrolase from Thermus thermophilus HB8, which is homologous to dGTP triphosphohydrolase

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.223 

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Structure of dNTP-inducible dNTP triphosphohydrolase: insight into broad specificity for dNTPs and triphosphohydrolase-type hydrolysis

Kondo, N.Nakagawa, N.Ebihara, A.Chen, L.Liu, Z.-J.Wang, B.-C.Yokoyama, S.Kuramitsu, S.Masui, R.

(2007) Acta Crystallogr D Biol Crystallogr 63: 230-239

  • DOI: https://doi.org/10.1107/S0907444906049262
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Deoxyribonucleoside triphosphate triphosphohydrolase from Thermus thermophilus (Tt-dNTPase) has a unique regulatory mechanism for the degradation of deoxyribonucleoside triphosphates (dNTPs). Whereas the Escherichia coli homologue specifically hydrolyzes dGTP alone, dNTPs act as both substrate and activator for Tt-dNTPase. Here, the crystal structure of Tt-dNTPase has been determined at 2.2 A resolution, representing the first report of the tertiary structure of a dNTPase homologue belonging to the HD superfamily, a diverse group of metal-dependent phosphohydrolases that includes a variety of uncharacterized proteins. This enzyme forms a homohexamer as a double ring of trimers. The subunit is composed of 19 alpha-helices; the inner six helices include the region annotated as the catalytic domain of the HD superfamily. Structural comparison with other HD-superfamily proteins indicates that a pocket at the centre of the inner six helices, formed from highly conserved charged residues clustered around a bound magnesium ion, constitutes the catalytic site. Tt-dNTPase also hydrolyzed noncanonical dNTPs, but hardly hydrolyzed dNDP and dNMP. The broad substrate specificity for different dNTPs might be rationalized by the involvement of a flexible loop during molecular recognition of the base moiety. Recognition of the triphosphate moiety crucial for the activity might be attained by highly conserved positively charged residues. The possible mode of dNTP binding is discussed in light of the structure.

  • Organizational Affiliation

    Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Deoxyguanosinetriphosphate triphosphohydrolase, putative
A, B, C, D, E
A, B, C, D, E, F
376Thermus thermophilus HB8Mutation(s): 5 
Gene Names: TTHA0412
Find proteins for Q5SL81 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SL81 
Go to UniProtKB:  Q5SL81
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SL81
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.223 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.1α = 110.2
b = 84.2β = 109.7
c = 108γ = 94.4
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2007-01-23
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2021-11-10
    Changes: Database references, Derived calculations