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PDBsum entry 2bh8
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Transcription
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PDB id
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2bh8
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References listed in PDB file
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Key reference
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Title
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A segment of cold shock protein directs the folding of a combinatorial protein.
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Authors
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S.De bono,
L.Riechmann,
E.Girard,
R.L.Williams,
G.Winter.
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Ref.
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Proc Natl Acad Sci U S A, 2005,
102,
1396-1401.
[DOI no: ]
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PubMed id
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Abstract
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It has been suggested that protein domains evolved by the non-homologous
recombination of building blocks of subdomain size. In earlier work we attempted
to recapitulate domain evolution in vitro. We took a polypeptide segment
comprising three beta-strands in the monomeric, five-stranded beta-barrel cold
shock protein (CspA) of Escherichia coli as a building block. This segment
corresponds to a complete exon in homologous eukaryotic proteins and includes
residues that nucleate folding in CspA. We recombined this segment at random
with fragments of natural proteins and succeeded in generating a range of folded
chimaeric proteins. We now present the crystal structure of one such
combinatorial protein, 1b11, a 103-residue polypeptide that includes segments
from CspA and the S1 domain of the 30S ribosomal subunit of E. coli. The
structure reveals a segment-swapped, six-stranded beta-barrel of unique
architecture that assembles to a tetramer. Surprisingly, the CspA segment
retains its structural identity in 1b11, recapitulating its original fold and
deforming the structure of the S1 segment as necessary to complete a barrel. Our
work provides structural evidence that (i) random shuffling of nonhomologous
polypeptide segments can lead to folded proteins and unique architectures, (ii)
many structural features of the segments are retained, and (iii) some segments
can act as templates around which the rest of the protein folds.
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Figure 2.
Fig. 2. Structure of 1b11. (A and B) Secondary structure
cartoons of CspA (PDB ID code 1MJC [PDB]
) with template residues 1-36 in dark blue (A) and the S1 domain
from E. coli polynucleotide phosphorylase (PDB ID code 1SRO [PDB]
) with residues 5-45 (as found in 1b11) in dark red (B). (C and
D) 1b11 tetramer (C) and dimer (D) shown with a smoothed
backbone tube; chains A and A' are gray, and B and B' are green.
(E) 1b11 barrel with strand assignments; strands  1- 4
(residues 16-72) of chain A and 5- 6 (residues 73-101) of
chain B are colored as in C and D. Strand 6 is split into 6a and
6b
to indicate its change of direction. (F) 1b11 barrel showing
origin of segments, with strand assignments of parent proteins
marked and colored as in A and B.
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Figure 3.
Fig. 3. Pattern of main-chain hydrogen bonds of -strands
of CspA and 1b11. Interstrand backbone hydrogen bonds are shown
as dashed lines, and residues are shown as circles; small
circles indicate residues pointing into the barrel. Hydrogen
bonding from 1- 3 of CspA (dark blue) to
4-
5 of
CspA (light blue) has been recapitulated in 1b11 by
hydrogen-bonding to S1-derived residues in 4 and 6 (gray).
Residues in 1b11 that are colored white have no structural
equivalent in CspA.
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