PDBsum entry 2f2q

Hydrolase

PDB id: 2f2q

Contents

Protein chain

175 a.a. *

Ligands

GAI

HED

Metals

_CL

Waters ×181

* Residue conservation analysis

PDB id:

2f2q

Name:

Hydrolase

Title:

High resolution crystal structure of t4 lysozyme mutant l20r63/a liganded to guanidinium ion

Structure:

Lysozyme. Chain: a. 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:

1.45Å R-factor: 0.200 R-free: 0.223

Authors:

M.S.Yousef,N.Bischoff,C.M.Dyer,W.A.Baase,B.W.Matthews

Key ref:

M.S.Yousef et al. (2006). Guanidinium derivatives bind preferentially and trigger long-distance conformational changes in an engineered T4 lysozyme. Protein Sci, 15, 853-861. PubMed id: 16600969 DOI: 10.1110/ps.052020606

Date:

17-Nov-05 Release date: 25-Apr-06

Protein chain

P00720  (ENLYS_BPT4) -  Endolysin from Enterobacteria phage T4

Seq: 164 a.a.

Struc: 175 a.a.*

* PDB and UniProt seqs differ at 17 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.052020606

Protein Sci 15:853-861 (2006)

PubMed id: 16600969

Guanidinium derivatives bind preferentially and trigger long-distance conformational changes in an engineered T4 lysozyme.

M.S.Yousef, N.Bischoff, C.M.Dyer, W.A.Baase, B.W.Matthews.

ABSTRACT

The binding of guanidinium ion has been shown to promote a large-scale translation of a tandemly duplicated helix in an engineered mutant of T4 lysozyme. The guanidinium ion acts as a surrogate for the guanidino group of an arginine side chain. Here we determine whether methyl- and ethylguanidinium provide better mimics. The results show that addition of the hydrophobic moieties to the ligand enhances the binding affinity concomitant with reduction in ligand solubility. Crystallographic analysis confirms that binding of the alternative ligands to the engineered site still drives the large-scale conformational change. Thermal analysis and NMR data show, in comparison to guanidinium, an increase in protein stability and in ligand affinity. This is presumably due to the successive increase in hydrophobicity in going from guanidinium to ethylguanidinium. A fluorescence-based optical method was developed to sense the ligand-triggered helix translation in solution. The results are a first step in the de novo design of a molecular switch that is not related to the normal function of the protein.

Selected figure(s)

Figure 2.
Stereo pair showing that the backbone structures of L20/R63A lysozyme complexed with guanidinium ion (red), methylguanidinium (yellow), and ethylguanidinium (green) are virtually identical. The structure of L20/R63A in the absence of ligand (cyan) differs substantially.

Figure 3.
Details of the stabilizing interactions of the loop at the C terminus of the engineered helix in the mutant L20/R63A in the presence of guanidinium (A), methylguanidinium (B), and ethylguanidi-nium (C). The superimposed F[o]-F[c] difference maps contoured at 3[sigma] (red) define the position of the ligands. The resolution of the maps is 1.45 A, 1.7 A, and 1.8 A, respectively. The methylated and ethylated ligands adopt alternative conformations as shown. (D) Interactions made by Arg63 in the lysozyme (Molecule B, PDB code 262L). Similar interactions are made by Arg52 in wild-type lysozyme.

The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (2006, 15, 853-861) copyright 2006.

Figures were selected by an automated process.