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PDBsum entry 2c9o
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References listed in PDB file
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Key reference
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Title
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Crystal structure of the human aaa+ protein ruvbl1.
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Authors
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P.M.Matias,
S.Gorynia,
P.Donner,
M.A.Carrondo.
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Ref.
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J Biol Chem, 2006,
281,
38918-38929.
[DOI no: ]
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PubMed id
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Abstract
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RuvBL1 is an evolutionarily highly conserved eukaryotic protein belonging to the
AAA(+)-family of ATPases (ATPase associated with diverse cellular activities).
It plays important roles in essential signaling pathways such as the c-Myc and
Wnt pathways in chromatin remodeling, transcriptional and developmental
regulation, and DNA repair and apoptosis. Herein we present the
three-dimensional structure of the selenomethionine variant of human RuvBL1
refined using diffraction data to 2.2A of resolution. The crystal structure of
the hexamer is formed of ADP-bound RuvBL1 monomers. The monomers contain three
domains, of which the first and the third are involved in ATP binding and
hydrolysis. Although it has been shown that ATPase activity of RuvBL1 is needed
for several in vivo functions, we could only detect a marginal activity with the
purified protein. Structural homology and DNA binding studies demonstrate that
the second domain, which is unique among AAA(+) proteins and not present in the
bacterial homolog RuvB, is a novel DNA/RNA-binding domain. We were able to
demonstrate that RuvBL1 interacted with single-stranded DNA/RNA and
double-stranded DNA. The structure of the RuvBL1.ADP complex, combined with our
biochemical results, suggest that although RuvBL1 has all the structural
characteristics of a molecular motor, even of an ATP-driven helicase, one or
more as yet undetermined cofactors are needed for its enzymatic activity.
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Figure 2.
FIGURE 2. The DNA binding region in RuvBL1 domain II. A,
stereoview of the protein C^  trace (gold) and ssDNA
ball-and-stick representation (carbon, nitrogen, oxygen, and
phosphorus atoms are colored gray, blue, red, and green,
respectively) of the RPA molecule (PDB 1JMC) superimposed onto
the DNA binding region of RuvBL1 DII (residues 127-233; cyan).
The long loops in the N-terminal domain of RPA that interact
with ssDNA (arrows 1 and 3) correspond to a disordered loop and
a much shorter loop (arrow 2) in RuvBL1 DII. B, view of the
electrostatic potential of the RPA molecule mapped at its
molecular surface. The molecular surface was calculated with
MSMS (65) using a probe radius of 1.4 Å, and the
electrostatic potential was calculated with MEAD (66) using an
ionic strength of 0.1 M, dielectric constants of 4.0 and 80.0
for the protein and the exterior, respectively, and a
temperature of 300 K. The range of potentials shown spans -5
(red) to +5 kT/e (blue) units. C, view of the electrostatic
potential of the DNA binding region of RuvBL1 DII mapped at its
molecular surface. The molecular surface and the electrostatic
potential were calculated as described above for the whole
RuvBL1 hexamer, but for clarity only the DNA binding region of
RuvBL1 DII is represented. As a visual aid, the ssDNA molecule
bound to RPA is represented in ball-and-stick (Carbon, nitrogen,
oxygen, and phosphorus atoms are colored gray, blue, red, and
green, respectively). The view in B and C is the same as in Fig.
2A. Drawings were prepared with DINO.
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Figure 3.
FIGURE 3. The RuvBL1 hexamer. A, ribbon diagram of the
RuvBL1 hexamer (side view). Adjacent monomers are colored light
gray and gold. One gold monomer is colored in the same way as in
Fig. 1B to highlight its domain structure. The hexamer herein
represented is the crystallographic hexamer, formed by monomers
A around the crystallographic 6-fold axis. The bound ADP
molecules are depicted in space-filling mode, where each atom is
represented by a sphere with a diameter twice its conventional
van der Waals radius. Carbon, nitrogen, oxygen, and phosphorus
atoms are colored gray, blue, red, and green, respectively. B,
ribbon diagram of the RuvBL1 hexamer (top view). The coloring
scheme is as in A. Drawings were prepared with DINO.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2006,
281,
38918-38929)
copyright 2006.
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Secondary reference #1
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Title
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Expression, Purification, Crystallization and preliminary x-Ray analysis of the human ruvb-Like protein ruvbl1.
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Authors
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S.Gorynia,
P.M.Matias,
S.Gonçalves,
R.Coelho,
G.Lopes,
M.Thomaz,
M.Huber,
B.Haendler,
P.Donner,
M.A.Carrondo.
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Ref.
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Acta Crystallograph Sect F Struct Biol Cryst Commun, 2006,
62,
61-66.
[DOI no: ]
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PubMed id
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Figure 1.
Figure 1 (a) Crystal of native RuvBL1; (b) crystal of
SeMet-substituted RuvBL1.
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The above figure is
reproduced from the cited reference
which is an Open Access publication published by the IUCr
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