PDBsum entry 2b7x

Hydrolase

PDB id: 2b7x

Contents

Protein chains

157 a.a. *

Ligands

SO4 ×8

* Residue conservation analysis

PDB id:

2b7x

Name:

Hydrolase

Title:

Sequential reorganization of beta-sheet topology by insertion of a single strand

Structure:

Lysozyme. Chain: a, b, c, d. Synonym: lysis protein, muramidase, endolysin. Engineered: yes. Mutation: yes

Source:

Enterobacteria phage t4. Organism_taxid: 10665. Gene: e. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

3.00Å R-factor: 0.239 R-free: 0.319

Authors:

M.Sagermann,B.W.Matthews

Key ref:

M.Sagermann et al. (2006). Sequential reorganization of beta-sheet topology by insertion of a single strand. Protein Sci, 15, 1085-1092. PubMed id: 16597830 DOI: 10.1110/ps.052018006

Date:

05-Oct-05 Release date: 01-Aug-06

Protein chains

P00720  (ENLYS_BPT4) -  Endolysin from Enterobacteria phage T4

Seq: 164 a.a.

Struc: 157 a.a.*

* PDB and UniProt seqs differ at 6 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.2.1.17 - lysozyme.
• Reaction: Hydrolysis of the 1,4-beta-linkages between N-acetyl-D-glucosamine and N-acetylmuramic acid in peptidoglycan heteropolymers of the prokaryotes cell walls.

DOI no: 10.1110/ps.052018006

Protein Sci 15:1085-1092 (2006)

PubMed id: 16597830

Sequential reorganization of beta-sheet topology by insertion of a single strand.

M.Sagermann, W.A.Baase, B.W.Matthews.

ABSTRACT

Insertions, duplications, and deletions of sequence segments are thought to be major evolutionary mechanisms that increase the structural and functional diversity of proteins. Alternative splicing, for example, is an intracellular editing mechanism that is thought to generate isoforms for 30%-50% of all human genes. Whereas the inserted sequences usually display only minor structural rearrangements at the insertion site, recent observations indicate that they may also cause more dramatic structural displacements of adjacent structures. In the present study we test how artificially inserted sequences change the structure of the beta-sheet region in T4 lysozyme. Copies of two different beta-strands were inserted into two different loops of the beta-sheet, and the structures were determined. Not surprisingly, one insert "loops out" at its insertion site and forms a new small beta-hairpin structure. Unexpectedly, however, the second insertion leads to displacement of adjacent strands and a sequential reorganization of the beta-sheet topology. Even though the insertions were performed at two different sites, looping out occurred at the C-terminal end of the same beta-strand. Reasons as to why a non-native sequence would be recruited to replace that which occurs in the native protein are discussed. Our results illustrate how sequence insertions can facilitate protein evolution through both local and nonlocal changes in structure.

Selected figure(s)

Figure 1.
Schematic representation of the [beta]-sheet of T4 lysozyme. The sheet structure consists of Strands I, II, and III and turns T-1, T-2, and T-3. The sequences to be inserted are shown in red. In mutant L30c, the inserted amino acid sequence corresponds to Strand II plus Turn T-2 and is inserted after Tyr24. In mutant L31d, the inserted sequence corresponds to Turn T-2 plus Strand III and is inserted after residue Leu33. The color-coding shown here is maintained in all figures.

Figure 2.
Illustration of some possible folds of the [beta]-sheet domain as a result of the insertion L30c. The inserted sequence (red) contains Strand II and Turn T-2. (A) In the simplest scenario, the inserted structure loops out at the insertion site, i.e., at Turn T-1. The neighboring structure retains the native conformation, leaving the identical parent sequence (yellow) unchanged. (B) In a second scenario, the insert sequence displaces the identical parent sequence, forcing it to loop out at Turn T-2. (C) In yet another scenario (the one that is observed), the sequence that is displaced in B continues so as to displace the sequence in Strand III. The structure will then be forced to loop out at T-3. In going from scenario B to C, the wild-type turn structure T-2 (Gly-Ile-Gly) is restored. In contrast, however, Strand II now replaces Strand III, causing substitutions in this region.

The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (2006, 15, 1085-1092) copyright 2006.

Figures were selected by an automated process.