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PDBsum entry 1soi
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Structural studies of the nudix hydrolase dr1025 from deinococcus radiodurans and its ligand complexes.
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Authors
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W.Ranatunga,
E.E.Hill,
J.L.Mooster,
E.L.Holbrook,
U.Schulze-Gahmen,
W.Xu,
M.J.Bessman,
S.E.Brenner,
S.R.Holbrook.
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Ref.
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J Mol Biol, 2004,
339,
103-116.
[DOI no: ]
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PubMed id
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Abstract
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We have determined the crystal structure, at 1.4A, of the Nudix hydrolase DR1025
from the extremely radiation resistant bacterium Deinococcus radiodurans. The
protein forms an intertwined homodimer by exchanging N-terminal segments between
chains. We have identified additional conserved elements of the Nudix fold,
including the metal-binding motif, a kinked beta-strand characterized by a
proline two positions upstream of the Nudix consensus sequence, and
participation of the N-terminal extension in the formation of the
substrate-binding pocket. Crystal structures were also solved of DR1025
crystallized in the presence of magnesium and either a GTP analog or Ap(4)A
(both at 1.6A resolution). In the Ap(4)A co-crystal, the electron density
indicated that the product of asymmetric hydrolysis, ATP, was bound to the
enzyme. The GTP analog bound structure showed that GTP was bound almost
identically as ATP. Neither nucleoside triphosphate was further cleaved.
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Figure 1.
Figure 1. The structure of the DR1025 dimer as observed in
the crystal. The Nudix box is colored in blue. Secondary
structure elements are labeled. The b strands are colored
yellow. The other a helices are in pink and the samarium bound
to the Nudix helix (Sm1) is in orange. The intertwining
N-terminal extension is in red. The proteins sit on a
crystallographic 2-fold axis that relates the monomer to the
dimer. Only one samarium of one monomer (Sm1) is shown.
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Figure 3.
Figure 3. Electrostatic potential surface of the DR1025
dimer as calculated by the GRASP program.[32.] The areas of high
negative charge are shaded red, while the positively charged
regions are shaded blue.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2004,
339,
103-116)
copyright 2004.
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