Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 257.53 kDa 
• Atom Count: 17546 
• Residue Count: 2160 
• Unique protein chains: 1

2DQB

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

• DOI: 10.2210/pdb2DQB/pdb

• Classification: HYDROLASE, DNA BINDING PROTEIN
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2006-05-25 Released: 2007-01-23 
• Deposition Author(s): Kondo, N., Nakagawa, N., Ebihara, A., Chen, L., Liu, Z.-J., Wang, B.-C., Yokoyama, S., Kuramitsu, S., Masui, R., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.286 
• R-Value Work: 0.223 

Literature

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

• PubMed: 17242516 
• DOI: 10.1107/S0907444906049262
• Structures With Same Primary Citation


• 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Deoxyguanosinetriphosphate triphosphohydrolase, putative	A, B, C, D, E, F	376	Thermus thermophilus HB8	Mutation(s): 5  Gene Names: TTHA0412 EC: 3.1.5.1
Find proteins for Q5SL81 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q5SL81

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	A, B, C, D, E, F	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A,B,C,D,E,F	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.286 
• R-Value Work: 0.223 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.1	α = 110.2
b = 84.2	β = 109.7
c = 108	γ = 94.4

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
SOLVE	phasing
CNS	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-05-25 
• Released Date: 2007-01-23 
Deposition Author(s): Kondo, N., Nakagawa, N., Ebihara, A., Chen, L., Liu, Z.-J., Wang, B.-C., Yokoyama, S., Kuramitsu, S., Masui, R., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History 

• 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