PDBsum entry 2dqb

Hydrolase, DNA binding protein

PDB id: 2dqb

Contents

Protein chains

(+ 0 more) 363 a.a. *

Metals

_MG ×6

Waters ×305

* Residue conservation analysis

PDB id:

2dqb

Name:

Hydrolase, DNA binding protein

Title:

Crystal structure of dntp triphosphohydrolase from thermus thermophilus hb8, which is homologous to dgtp triphosphohydrolase

Structure:

Deoxyguanosinetriphosphate triphosphohydrolase, putative. Chain: a, b, c, d, e, f. Synonym: dntp triphosphohydrolase. Engineered: yes. Mutation: yes

Source:

Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Gene: ttha0412. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.20Å R-factor: 0.223 R-free: 0.286

Authors:

N.Kondo,N.Nakagawa,A.Ebihara,L.Chen,Z.-J.Liu,B.-C.Wang,S.Yokoyama, S.Kuramitsu,R.Masui,Riken Structural Genomics/proteomics Initiative (Rsgi)

Key ref:

N.Kondo et al. (2007). Structure of dNTP-inducible dNTP triphosphohydrolase: insight into broad specificity for dNTPs and triphosphohydrolase-type hydrolysis. Acta Crystallogr D Biol Crystallogr, 63, 230-239. PubMed id: 17242516 DOI: 10.1107/S0907444906049262

Date:

25-May-06 Release date: 23-Jan-07

Protein chains

Q5SL81  (Q5SL81_THET8) -  Deoxyguanosinetriphosphate triphosphohydrolase-like protein from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 376 a.a.

Struc: 363 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.1.5.1 - dGTPase.
• Reaction: dGTP + H2O = 2'-deoxyguanosine + triphosphate + H⁺

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1107/S0907444906049262

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

PubMed id: 17242516

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

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

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.

Selected figure(s)

Figure 2.
Figure 2 Architecture of the hexameric organization. (a) Top view. (b) Side view. Chain A is represented in the same colours as in Fig. 1-. The subunits coloured purple, brown, orange, grey and green indicate chains B, C, D, E and F, respectively. The view shown in (b) represents a 90° rotation from that in (a), so that chains F and B are hidden.

Figure 7.
Figure 7 Putative dNTP-binding site. Chains C and F are coloured orange and green, respectively. The residues comprising the putative binding site predicted by WHAT IF (Vriend, 1990[Vriend, G. (1990). J. Mol. Graph. 8, 52-56.]) are represented in deep colours. The cavity detected by VOIDOO (Kleywegt & Jones, 1994[Kleywegt, G. J. & Jones, T. A. (1994). Acta Cryst. D50, 178-185.]) is represented as a yellow mesh.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2007, 63, 230-239) copyright 2007.

Figures were selected by an automated process.