 |
PDBsum entry 2gbm
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Protein binding
|
PDB id
|
|
|
|
2gbm
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
References listed in PDB file
|
|
|
Key reference
|
|
|
Title
|
|
Structures of ubiquitin insertion mutants support site-Specific reflex response to insertions hypothesis.
|
|
|
Authors
|
|
D.M.Ferraro,
D.J.Ferraro,
S.Ramaswamy,
A.D.Robertson.
|
|
|
Ref.
|
|
J Mol Biol, 2006,
359,
390-402.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
Abstract
|
|
|
We previously concluded that, judging from NMR chemical shifts, the effects of
insertions into ubiquitin on its conformation appear to depend primarily on the
site of insertion rather than the sequence of the insertion. To obtain a more
complete and atomic-resolution understanding of how these insertions modulate
the conformation of ubiquitin, we have solved the crystal structures of four
insertional mutants of ubiquitin. Insertions between residues 9 and 10 of
ubiquitin are minimally perturbing to the remainder of the protein, while larger
alterations occur when the insertion is between residues 35 and 36. Further, the
alterations in response to insertions are very similar for each mutant at a
given site. Two insertions, one at each site, were designed from structurally
homologous proteins. Interestingly, the secondary structure within these five to
seven amino acid residue insertions is conserved in the new protein. Overall,
the crystal structures support the previous conclusion that the conformational
effects of these insertions are determined largely by the site of insertion and
only secondarily by the sequence of the insert.
|
|
|
|
|
|
|
|
Figure 1.
Figure 1. Predicted effects of insertions at the 35-36 loop
on ubiquitin structure.10 Residues 9 and 10 are shown in red and
residues 35 and 36 are shown in green. The curved arrow
indicates the predicted bend of the helix away from the 35-36
loop insertion site. The straight arrows indicate the predicted
hydrogen bond lengthening of the sheet near the insertion site
and shortening away from the insertion site.
|
|
Figure 3.
Figure 3. Global alignments of loop insertion mutant
structures (green) to wild-type ubiquitin (blue). Alignments
were calculated in the program Indonesia (Madsen et al.,
unpublished) and Figures were generated using PyMol
(http://pymol.sourceforge.net/). Residues that lack electron
density are shown with transparency. (a) 9-10 G8 chain A versus
wild-type. (b) 9-10 MoaD chain A versus wild-type. (c) 35-36 G8
chain A versus wild-type. (d) 35-36 MoaD chain B versus
wild-type.
|
|
|
|
|
|
The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2006,
359,
390-402)
copyright 2006.
|
|
|
|
|
|
|
