 |
PDBsum entry 2dqb
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Hydrolase, DNA binding protein
|
PDB id
|
|
|
|
2dqb
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
References listed in PDB file
|
|
|
Key reference
|
|
|
Title
|
|
Structure of dntp-Inducible dntp triphosphohydrolase: insight into broad specificity for dntps and triphosphohydrolase-Type hydrolysis.
|
|
|
Authors
|
|
N.Kondo,
N.Nakagawa,
A.Ebihara,
L.Chen,
Z.J.Liu,
B.C.Wang,
S.Yokoyama,
S.Kuramitsu,
R.Masui.
|
|
|
Ref.
|
|
Acta Crystallogr D Biol Crystallogr, 2007,
63,
230-239.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
