 |
PDBsum entry 2plm
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Unknown function
|
PDB id
|
|
|
|
2plm
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
References listed in PDB file
|
|
|
Key reference
|
|
|
Title
|
|
Structure-Based activity prediction for an enzyme of unknown function.
|
|
|
Authors
|
|
J.C.Hermann,
R.Marti-Arbona,
A.A.Fedorov,
E.Fedorov,
S.C.Almo,
B.K.Shoichet,
F.M.Raushel.
|
|
|
Ref.
|
|
Nature, 2007,
448,
775-779.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
Abstract
|
|
|
With many genomes sequenced, a pressing challenge in biology is predicting the
function of the proteins that the genes encode. When proteins are unrelated to
others of known activity, bioinformatics inference for function becomes
problematic. It would thus be useful to interrogate protein structures for
function directly. Here, we predict the function of an enzyme of unknown
activity, Tm0936 from Thermotoga maritima, by docking high-energy intermediate
forms of thousands of candidate metabolites. The docking hit list was dominated
by adenine analogues, which appeared to undergo C6-deamination. Four of these,
including 5-methylthioadenosine and S-adenosylhomocysteine (SAH), were tested as
substrates, and three had substantial catalytic rate constants (10(5) M(-1
)s(-1)). The X-ray crystal structure of the complex between Tm0936 and the
product resulting from the deamination of SAH, S-inosylhomocysteine, was
determined, and it corresponded closely to the predicted structure. The
deaminated products can be further metabolized by T. maritima in a previously
uncharacterized SAH degradation pathway. Structure-based docking with
high-energy forms of potential substrates may be a useful tool to annotate
enzymes for function.
|
|
|
|
|
|
|
|
Figure 1.
Figure 1: Sample transformations of metabolites from their
ground state structure into the high-energy intermediate forms
that were used for docking. Transformations were computed
according to the conserved reaction mechanism of
amidohydrolases, a nucleophilic attack of a hydroxide at an
electrophilic centre atom. Every transformable functional group
for each molecule was processed independently. If the
high-energy structure was chiral, all stereoisomers were
calculated. Reactions catalysed by the amidohydrolases cytosine
deaminase (CDA), adenosine deaminase (ADA), dihydroorotase
(DHO), D-hydantoinase (HYD), isoaspartyl-d-dipeptidase (IAD),
N-acetyl-D-glucosamine-6-phosphate deacetylase (NaGA) and
phosphotriesterase (PTE) are shown.
|
|
Figure 3.
Figure 3: Comparing the docking prediction and the
crystallographic result.
Figure 3 : Comparing the docking
prediction and the crystallographic result.
Superposition of the crystal structure of Tm0936 in complex
with SIH (red) and the docking predicted structure of the
high-energy intermediate of SAH (carbons in green). Enzyme
carbons are coloured light blue, SAH and enzyme oxygen atoms are
coloured red, nitrogens blue and sulphurs orange. The purple
sphere represents the divalent metal ion. An F[O] – F[C] omit
electron density map for SIH is shown, contoured at 4.1  .
The structure was determined at 2.1 Å resolution.
|
|
|
|
|
|
The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nature
(2007,
448,
775-779)
copyright 2007.
|
|
|
|
|
|
|
