PDBsum entry 2bh8

Transcription

PDB id: 2bh8

Contents

Protein chains

85 a.a. *

Waters ×144

* Residue conservation analysis

PDB id:

2bh8

Name:

Transcription

Title:

Combinatorial protein 1b11

Structure:

1b11. Chain: a, b. Engineered: yes. Other_details: 1b11 is a polypeptide that includes segments from cspa and the s1 domain of the 30s ribosomal subunit of escherichia coli

Source:

Escherichia coli. Organism_taxid: 83333. Strain: k12. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Expression_system_variant: c41.

Biol. unit:

Tetramer (from PDB file)

Resolution:

1.90Å R-factor: 0.197 R-free: 0.251

Authors:

S.De Bono,L.Riechmann,E.Girard,R.L.Williams,G.Winter

Key ref:

S.de Bono et al. (2005). A segment of cold shock protein directs the folding of a combinatorial protein. Proc Natl Acad Sci U S A, 102, 1396-1401. PubMed id: 15671167 DOI: 10.1073/pnas.0407298102

Date:

07-Jan-05 Release date: 07-Feb-05

Protein chains

P0A9X9  (CSPA_ECOLI) -  Cold shock protein CspA from Escherichia coli (strain K12)

Seq: 70 a.a.

Struc: 85 a.a.*

* PDB and UniProt seqs differ at 33 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1073/pnas.0407298102

Proc Natl Acad Sci U S A 102:1396-1401 (2005)

PubMed id: 15671167

A segment of cold shock protein directs the folding of a combinatorial protein.

S.de Bono, L.Riechmann, E.Girard, R.L.Williams, G.Winter.

ABSTRACT

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.

Selected figure(s)

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.

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.

Figures were selected by an automated process.