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* Residue conservation analysis
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DOI no:
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Proc Natl Acad Sci U S A
100:5760-5765
(2003)
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PubMed id:
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The structure of nonvertebrate actin: implications for the ATP hydrolytic mechanism.
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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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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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Selected figure(s)
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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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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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J.Pfaendtner,
E.Lyman,
T.D.Pollard,
and
G.A.Voth
(2010).
Structure and dynamics of the actin filament.
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J Mol Biol,
396,
252-263.
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J.Salje,
P.Gayathri,
and
J.Löwe
(2010).
The ParMRC system: molecular mechanisms of plasmid segregation by actin-like filaments.
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Nat Rev Microbiol,
8,
683-692.
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K.Murakami,
T.Yasunaga,
T.Q.Noguchi,
Y.Gomibuchi,
K.X.Ngo,
T.Q.Uyeda,
and
T.Wakabayashi
(2010).
Structural basis for actin assembly, activation of ATP hydrolysis, and delayed phosphate release.
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Cell,
143,
275-287.
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PDB codes:
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S.Viggiano,
B.Haarer,
and
D.C.Amberg
(2010).
Correction/completion of the yeast actin, alanine scan alleles.
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Genetics,
185,
391-394.
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K.E.Bryan,
and
P.A.Rubenstein
(2009).
Allele-specific effects of human deafness gamma-actin mutations (DFNA20/26) on the actin/cofilin interaction.
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J Biol Chem,
284,
18260-18269.
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M.Morín,
K.E.Bryan,
F.Mayo-Merino,
R.Goodyear,
A.Mencía,
S.Modamio-Høybjør,
I.del Castillo,
J.M.Cabalka,
G.Richardson,
F.Moreno,
P.A.Rubenstein,
and
M.A.Moreno-Pelayo
(2009).
In vivo and in vitro effects of two novel gamma-actin (ACTG1) mutations that cause DFNA20/26 hearing impairment.
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Hum Mol Genet,
18,
3075-3089.
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T.Oda,
M.Iwasa,
T.Aihara,
Y.Maéda,
and
A.Narita
(2009).
The nature of the globular- to fibrous-actin transition.
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Nature,
457,
441-445.
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PDB code:
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E.E.Grintsevich,
S.A.Benchaar,
D.Warshaviak,
P.Boontheung,
F.Halgand,
J.P.Whitelegge,
K.F.Faull,
R.R.Loo,
D.Sept,
J.A.Loo,
and
E.Reisler
(2008).
Mapping the cofilin binding site on yeast G-actin by chemical cross-linking.
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J Mol Biol,
377,
395-409.
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K.Baek,
X.Liu,
F.Ferron,
S.Shu,
E.D.Korn,
and
R.Dominguez
(2008).
Modulation of actin structure and function by phosphorylation of Tyr-53 and profilin binding.
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Proc Natl Acad Sci U S A,
105,
11748-11753.
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PDB codes:
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M.R.Sawaya,
D.S.Kudryashov,
I.Pashkov,
H.Adisetiyo,
E.Reisler,
and
T.O.Yeates
(2008).
Multiple crystal structures of actin dimers and their implications for interactions in the actin filament.
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Acta Crystallogr D Biol Crystallogr,
64,
454-465.
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PDB codes:
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U.B.Nair,
P.B.Joel,
Q.Wan,
S.Lowey,
M.A.Rould,
and
K.M.Trybus
(2008).
Crystal structures of monomeric actin bound to cytochalasin D.
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J Mol Biol,
384,
848-864.
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PDB codes:
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B.J.Nolen,
and
T.D.Pollard
(2007).
Insights into the influence of nucleotides on actin family proteins from seven structures of Arp2/3 complex.
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Mol Cell,
26,
449-457.
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PDB codes:
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T.D.Pollard
(2007).
Regulation of actin filament assembly by Arp2/3 complex and formins.
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Annu Rev Biophys Biomol Struct,
36,
451-477.
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A.C.Martin,
M.D.Welch,
and
D.G.Drubin
(2006).
Arp2/3 ATP hydrolysis-catalysed branch dissociation is critical for endocytic force generation.
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Nat Cell Biol,
8,
826-833.
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J.H.Willis,
E.Munro,
R.Lyczak,
and
B.Bowerman
(2006).
Conditional dominant mutations in the Caenorhabditis elegans gene act-2 identify cytoplasmic and muscle roles for a redundant actin isoform.
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Mol Biol Cell,
17,
1051-1064.
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T.J.Minehardt,
P.A.Kollman,
R.Cooke,
and
E.Pate
(2006).
The open nucleotide pocket of the profilin/actin x-ray structure is unstable and closes in the absence of profilin.
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Biophys J,
90,
2445-2449.
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V.F.Waingeh,
C.D.Gustafson,
E.I.Kozliak,
S.L.Lowe,
H.R.Knull,
and
K.A.Thomasson
(2006).
Glycolytic enzyme interactions with yeast and skeletal muscle F-actin.
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Biophys J,
90,
1371-1384.
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V.Procaccio,
G.Salazar,
S.Ono,
M.L.Styers,
M.Gearing,
A.Davila,
R.Jimenez,
J.Juncos,
C.A.Gutekunst,
G.Meroni,
B.Fontanella,
E.Sontag,
J.M.Sontag,
V.Faundez,
and
B.H.Wainer
(2006).
A mutation of beta -actin that alters depolymerization dynamics is associated with autosomal dominant developmental malformations, deafness, and dystonia.
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Am J Hum Genet,
78,
947-960.
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W.Chen,
K.K.Wen,
A.E.Sens,
and
P.A.Rubenstein
(2006).
Differential interaction of cardiac, skeletal muscle, and yeast tropomyosins with fluorescent (pyrene235) yeast actin.
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Biophys J,
90,
1308-1318.
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Y.L.Shih,
and
L.Rothfield
(2006).
The bacterial cytoskeleton.
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Microbiol Mol Biol Rev,
70,
729-754.
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A.C.Martin,
X.P.Xu,
I.Rouiller,
M.Kaksonen,
Y.Sun,
L.Belmont,
N.Volkmann,
D.Hanein,
M.Welch,
and
D.G.Drubin
(2005).
Effects of Arp2 and Arp3 nucleotide-binding pocket mutations on Arp2/3 complex function.
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J Cell Biol,
168,
315-328.
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D.S.Kudryashov,
M.R.Sawaya,
H.Adisetiyo,
T.Norcross,
G.Hegyi,
E.Reisler,
and
T.O.Yeates
(2005).
The crystal structure of a cross-linked actin dimer suggests a detailed molecular interface in F-actin.
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Proc Natl Acad Sci U S A,
102,
13105-13110.
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PDB code:
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J.Muller,
Y.Oma,
L.Vallar,
E.Friederich,
O.Poch,
and
B.Winsor
(2005).
Sequence and comparative genomic analysis of actin-related proteins.
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Mol Biol Cell,
16,
5736-5748.
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B.J.Nolen,
R.S.Littlefield,
and
T.D.Pollard
(2004).
Crystal structures of actin-related protein 2/3 complex with bound ATP or ADP.
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Proc Natl Acad Sci U S A,
101,
15627-15632.
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PDB codes:
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O.Drory,
F.Frolow,
and
N.Nelson
(2004).
Crystal structure of yeast V-ATPase subunit C reveals its stator function.
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EMBO Rep,
5,
1148-1152.
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PDB code:
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D.S.Kudryashov,
and
E.Reisler
(2003).
Solution properties of tetramethylrhodamine-modified G-actin.
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Biophys J,
85,
2466-2475.
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E.van Wijk,
E.Krieger,
M.H.Kemperman,
E.M.De Leenheer,
P.L.Huygen,
C.W.Cremers,
F.P.Cremers,
and
H.Kremer
(2003).
A mutation in the gamma actin 1 (ACTG1) gene causes autosomal dominant hearing loss (DFNA20/26).
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J Med Genet,
40,
879-884.
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J.Q.Guan,
S.C.Almo,
E.Reisler,
and
M.R.Chance
(2003).
Structural reorganization of proteins revealed by radiolysis and mass spectrometry: G-actin solution structure is divalent cation dependent.
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Biochemistry,
42,
11992-12000.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
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Links
