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* Residue conservation analysis
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DOI no:
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J Mol Biol
313:1045-1057
(2001)
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PubMed id:
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Refined structure of alpha beta-tubulin at 3.5 A resolution.
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J.Löwe,
H.Li,
K.H.Downing,
E.Nogales.
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ABSTRACT
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We present a refined model of the alpha beta-tubulin dimer to 3.5 A resolution.
An improved experimental density for the zinc-induced tubulin sheets was
obtained by adding 114 electron diffraction patterns at 40-60 degrees tilt and
increasing the completeness of structure factor amplitudes to 84.7 %. The
refined structure was obtained using maximum-likelihood including phase
information from experimental images, and simulated annealing Cartesian
refinement to an R-factor of 23.2 and free R-factor of 29.7. The current model
includes residues alpha:2-34, alpha:61-439, beta:2-437, one molecule of GTP, one
of GDP, and one of taxol, as well as one magnesium ion at the non-exchangeable
nucleotide site, and one putative zinc ion near the M-loop in the alpha-tubulin
subunit. The acidic C-terminal tails could not be traced accurately, neither
could the N-terminal loop including residues 35-60 in the alpha-subunit. There
are no major changes in the overall fold of tubulin with respect to the previous
structure, testifying to the quality of the initial experimental phases. The
overall geometry of the model is, however, greatly improved, and the position of
side-chains, especially those of exposed polar/charged groups, is much better
defined. Three short protein sequence frame shifts were detected with respect to
the non-refined structure. In light of the new model we discuss details of the
tubulin structure such as nucleotide and taxol binding sites, lateral contacts
in zinc-sheets, and the significance of the location of highly conserved
residues.
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Selected figure(s)
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Figure 4.
Figure 4. Stacking of aromatic residues in the N-terminal
b-sheet of a-tubulin. The Figure was generated with O.[45]
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Figure 6.
Figure 6. (a) 2F[o] -F[c] density for taxol within the
b-tubulin structure shown as C^a trace for clarity. The Figure
was generated with O.[45] (b) Stereo view of the taxol site
including residues that make direct contact with the taxol
molecule. The Figure was generated with Insight II (Biosym Inc.).
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2001,
313,
1045-1057)
copyright 2001.
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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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ChemMedChem,
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PDB codes:
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PDB codes:
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Insights into microtubule nucleation from the crystal structure of human gamma-tubulin.
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Nature,
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PDB codes:
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H.W.Wang,
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Nucleotide-dependent bending flexibility of tubulin regulates microtubule assembly.
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Curr Genet,
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Protoplasma,
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The Kavar(D) dominant female-sterile mutations of Drosophila reveal a role for the maternally provided alpha-tubulin4 isoform in cleavage spindle maintenance and elongation.
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The binding mode of epothilone A on alpha,beta-tubulin by electron crystallography.
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Science,
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PDB code:
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J.Löwe,
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Molecules of the bacterial cytoskeleton.
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Mol Biol Cell,
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PDB code:
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Structural insights into FtsZ protofilament formation.
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PDB codes:
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N.Mizuno,
S.Toba,
M.Edamatsu,
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Mol Biol Cell,
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Insight into tubulin regulation from a complex with colchicine and a stathmin-like domain.
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Nature,
428,
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PDB codes:
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R.M.Buey,
J.F.Díaz,
J.M.Andreu,
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Interaction of epothilone analogs with the paclitaxel binding site: relationship between binding affinity, microtubule stabilization, and cytotoxicity.
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KIF1A alternately uses two loops to bind microtubules.
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Science,
305,
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PDB codes:
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S.A.Sánchez,
J.E.Brunet,
D.M.Jameson,
R.Lagos,
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Tubulin equilibrium unfolding followed by time-resolved fluorescence and fluorescence correlation spectroscopy.
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The bioactive Taxol conformation on beta-tubulin: experimental evidence from highly active constrained analogs.
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Proc Natl Acad Sci U S A,
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From words to literature in structural proteomics.
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Nature,
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Regulation of KinI kinesin ATPase activity by binding to the microtubule lattice.
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J Cell Biol,
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Energetics of the cooperative assembly of cell division protein FtsZ and the nucleotide hydrolysis switch.
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PDB codes:
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T.Lila,
T.E.Renau,
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J.Philips,
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Reversible unfolding of FtsZ cell division proteins from archaea and bacteria. Comparison with eukaryotic tubulin folding and assembly.
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J Biol Chem,
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Heterologous expression and folding analysis of a beta-tubulin isotype from the Antarctic ciliate Euplotes focardii.
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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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 |
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