PDBsum entry 2pij

Transcription

PDB id: 2pij

Contents

Protein chains

59 a.a. *

Ligands

SO4 ×4

BCT

DTT

Waters ×61

* Residue conservation analysis

PDB id:

2pij

Name:

Transcription

Title:

Structure of the cro protein from prophage pfl 6 in pseudomonas fluorescens pf-5

Structure:

Prophage pfl 6 cro. Chain: a, b. Engineered: yes

Source:

Pseudomonas fluorescens. Organism_taxid: 220664. Strain: pf-5. Gene: prophage pfl 6 cro. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.70Å R-factor: 0.221 R-free: 0.271

Authors:

C.G.Roessler,S.A.Roberts,W.R.Montfort,M.H.J.Cordes

Key ref:

C.G.Roessler et al. (2008). Transitive homology-guided structural studies lead to discovery of Cro proteins with 40% sequence identity but different folds. Proc Natl Acad Sci U S A, 105, 2343-2348. PubMed id: 18227506 DOI: 10.1073/pnas.0711589105

Date:

13-Apr-07 Release date: 04-Mar-08

Protein chains

J3IU59  (J3IU59_9PSED) -  Cro from Pseudomonas sp. GM80

Seq: 67 a.a.

Struc: 59 a.a.*

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

DOI no: 10.1073/pnas.0711589105

Proc Natl Acad Sci U S A 105:2343-2348 (2008)

PubMed id: 18227506

Transitive homology-guided structural studies lead to discovery of Cro proteins with 40% sequence identity but different folds.

C.G.Roessler, B.M.Hall, W.J.Anderson, W.M.Ingram, S.A.Roberts, W.R.Montfort, M.H.Cordes.

ABSTRACT

Proteins that share common ancestry may differ in structure and function because of divergent evolution of their amino acid sequences. For a typical diverse protein superfamily, the properties of a few scattered members are known from experiment. A satisfying picture of functional and structural evolution in relation to sequence changes, however, may require characterization of a larger, well chosen subset. Here, we employ a "stepping-stone" method, based on transitive homology, to target sequences intermediate between two related proteins with known divergent properties. We apply the approach to the question of how new protein folds can evolve from preexisting folds and, in particular, to an evolutionary change in secondary structure and oligomeric state in the Cro family of bacteriophage transcription factors, initially identified by sequence-structure comparison of distant homologs from phages P22 and lambda. We report crystal structures of two Cro proteins, Xfaso 1 and Pfl 6, with sequences intermediate between those of P22 and lambda. The domains show 40% sequence identity but differ by switching of alpha-helix to beta-sheet in a C-terminal region spanning approximately 25 residues. Sedimentation analysis also suggests a correlation between helix-to-sheet conversion and strengthened dimerization.

Selected figure(s)

Figure 3.
Comparison of Xfaso 1 and Pfl 6. (A and B) Crystal structures of Xfaso 1 (A) and Pfl 6 (B) with ribbon diagrams for the biological dimers shown. The Xfaso 1 asymmetric unit has a third subunit (data not shown). Cys 42 and Cys 55 are indicated for one subunit of Xfaso 1 to show spatial proximity in the reduced form. (C) One possible sequence alignment of Xfaso 1 and Pfl 6, annotated with secondary structures. This alignment gives 40% sequence identity across 65 residues, with two gaps. The unstructured C termini of Xfaso 1 (16 residues) and Pfl 6 (7 residues) are not included in the alignment.

Figure 4.
Summary of stepping-stone results and working model for Cro structural evolution. Hypothetical or qualitative aspects are gray. For example, structures of the common ancestor and Afe01 are known only at the level of general fold either from previous outgroup analysis (ancestor) or from low-resolution data in the present study (Afe01). One possible phylogenetic tree topology is indicated by dashed gray lines. The different colors of the second subunits shown for Pfl 6 Cro (gold) and λ Cro (red) are intended to indicate the stronger dimerization of the latter. (Insets) Residues in the ball-and-socket region of Pfl 6 Cro and λ Cro.

Figures were selected by an automated process.