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PDBsum entry 1nmd
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Structural protein
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PDB id
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1nmd
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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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The structure of nonvertebrate actin: implications for the ATP hydrolytic mechanism.
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Authors
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S.Vorobiev,
B.Strokopytov,
D.G.Drubin,
C.Frieden,
S.Ono,
J.Condeelis,
P.A.Rubenstein,
S.C.Almo.
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Ref.
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Proc Natl Acad Sci U S A, 2003,
100,
5760-5765.
[DOI no: ]
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PubMed id
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Abstract
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The structures of Saccharomyces cerevisiae, Dictyostelium, and Caenorhabditis
elegans actin bound to gelsolin segment-1 have been solved and refined at
resolutions between 1.9 and 1.75 A. These structures reveal several features
relevant to the ATP hydrolytic mechanism, including identification of the
nucleophilic water and the roles of Gln-137 and His-161 in positioning and
activating the catalytic water, respectively. The involvement of these residues
in the catalytic mechanism is consistent with yeast genetics studies. This work
highlights both structural and mechanistic similarities with the small and
trimeric G proteins and restricts the types of mechanisms responsible for the
considerable enhancement of ATP hydrolysis associated with actin polymerization.
The conservation of functionalities involved in nucleotide binding and catalysis
also provide insights into the mechanistic features of members of the family of
actin-related proteins.
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Figure 1.
Fig. 1. Overall structure of the yeast actin/gelsolin
segment-1 complex. Gelsolin (purple) binds to subdomains 1 and 3
of actin (yellow). Sixteen water molecules (aqua) contribute to
the actin-gelsolin binding interface. Eight water molecules
(red) form a network across the actin nucleotide binding cleft,
contacting residues in subdomains 1, 3, and 4 (red backbone).
The gelsolin-associated Ca^2+ ion is represented as pink. The
adenine nucleotide is also shown, with the Mg2+ ion in black.
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Figure 2.
Fig. 2. Details of the water-mediated hydrogen bonding
network across the nucleotide-binding cleft. Eight solvent
molecules (black) run across the nucleotide binding cleft and
may play a role in transducing changes in the nucleotide state
into structural and dynamic changes relevant to polymerization
and interactions with regulatory proteins.
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