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PDBsum entry 1s1d
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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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Structure and protein design of a human platelet function inhibitor.
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Authors
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J.Dai,
J.Liu,
Y.Deng,
T.M.Smith,
M.Lu.
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Ref.
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Cell, 2004,
116,
649-659.
[DOI no: ]
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PubMed id
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Abstract
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Hematophagous arthropods secrete a salivary apyrase that inhibits platelet
activation by catabolizing ADP released from damaged tissues and blood cells. We
report the X-ray crystal structures of a human enzyme of the soluble apyrase
family in its apo state and bound to a substrate analog. The structures reveal a
nucleotide binding domain comprising a five-blade beta propeller, binding
determinants of the substrate and the active site, and an unusual calcium
binding site with a potential regulatory function. Using a comparative
structural biology approach, we were able to redesign the human apyrase so as to
enhance its ADPase activity by more than 100-fold. The engineered enzyme is a
potent inhibitor of platelet aggregation and may serve as the basis for the
development of a new class of antithrombotic agents.
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Figure 1.
Figure 1. Structure of Apo Human ApyraseRibbon diagram of
the human apyrase propeller structure as viewed along (A) or
perpendicular to (B) the central tunnel. The sheets are numbered
1 to 5 and organized sequentially in a counterclockwise
direction, and the four antiparallel β strands within each
sheet are denoted a to d in the order from axis to perimeter.
The β propeller is circularized by juxtaposition of the 1a and
1b strands. The polypeptide chain is colored from blue at the N
terminus through to red at the C terminus. The Ca^2+ ion (green
sphere) is located in the middle of the central tunnel.(C)
Superposition of the α carbon traces of the five blades of the
human apyrase propeller. Blades 2 and 5 (green and light blue)
have the shortest loops between β strands. Blades 1, 3, and 4
(gray, yellow, and pink) have at least one long loop projecting
from the top face of the β propeller.(D) Stereoview of the
2F[o] − F[c] electron density map (contoured at 1.5σ) showing
the coordination geometry of the Ca^2+ ion (green sphere)
connecting the five blades of the human apyrase propeller. Water
molecules are shown as red spheres, and calcium coordinations
are denoted by dotted lines.(E) Sequence alignment of the five
blades of the human apyrase propeller. The approximate
boundaries of the β strands are highlighted. φ designates
conserved hydrophobic residues.
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Figure 2.
Figure 2. Structure-Based Alignment of Human Apyrase with
Other Apyrase ProteinsThe sequence of human apyrase (residues
Pro1–Ile333) is shown with the elements of secondary structure
indicated above the alignment. Gray arrows and cylinders mark β
strands and α helices, respectively, with crosses denoting
residues that are disordered in the present apo and substrate
analog structures. The sequences of human, rat, bed bug, and
sand fly (Phlebotomus) are shown; in these cases the enzymatic
activity has been established by biochemical analysis. Residues
that are important for nucleotide and Ca^2+ binding are
indicated by pluses and asterisks, respectively. Chemically
similar residues in the apyrase family are colored red and
residues conserved in the vertebrate and insect subfamilies in
blue and green, respectively. We refer to the human apyrase
structure using the numbering system of the mature protein.
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The above figures are
reprinted
by permission from Cell Press:
Cell
(2004,
116,
649-659)
copyright 2004.
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