2DQB

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

PDB DOI: https://doi.org/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)

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1107/S0907444906049262
Primary Citation of Related Structures:
2DQB

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.

Macromolecule Content

Total Structure Weight: 257.53 kDa
Atom Count: 17,546
Modelled Residue Count: 2,160
Deposited Residue Count: 2,256
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deoxyguanosinetriphosphate triphosphohydrolase, putative	A, B, C, D, E A, B, C, D, E, F	376	Thermus thermophilus HB8	Mutation(s): 5 Gene Names: TTHA0412 EC: 3.1.5.1
UniProt
Find proteins for Q5SL81 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SL81 Go to UniProtKB: Q5SL81
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5SL81
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain I [auth C] SDF format, chain J [auth D] SDF format, chain K [auth E] SDF format, chain L [auth F] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth C] MOL2 format, chain J [auth D] MOL2 format, chain K [auth E] MOL2 format, chain L [auth F]	G [auth A] H [auth B] I [auth C] J [auth D] K [auth E] G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth D] Focus chain K [auth E] Focus chain L [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth D] Focus chain K [auth E] Focus chain L [auth F]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E 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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-01-23

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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