PDBsum entry 2b6y

Hydrolase

PDB id: 2b6y

Contents

Protein chain

162 a.a. *

Ligands

BME ×2

Metals

_CL ×2

Waters ×110

* Residue conservation analysis

PDB id:

2b6y

Name:

Hydrolase

Title:

T4 lysozyme mutant l99a at ambient pressure

Structure:

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

Source:

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

Resolution:

2.40Å R-factor: 0.163 R-free: 0.212

Authors:

M.D.Collins,M.L.Quillin,B.W.Matthews,S.M.Gruner

Key ref:

M.D.Collins et al. (2005). Cooperative water filling of a nonpolar protein cavity observed by high-pressure crystallography and simulation. Proc Natl Acad Sci U S A, 102, 16668-16671. PubMed id: 16269539 DOI: 10.1073/pnas.0508224102

Date:

03-Oct-05 Release date: 08-Nov-05

Protein chain

P00720  (ENLYS_BPT4) -  Endolysin from Enterobacteria phage T4

Seq: 164 a.a.

Struc: 162 a.a.*

* PDB and UniProt seqs differ at 5 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: 10.1073/pnas.0508224102

Proc Natl Acad Sci U S A 102:16668-16671 (2005)

PubMed id: 16269539

Cooperative water filling of a nonpolar protein cavity observed by high-pressure crystallography and simulation.

M.D.Collins, G.Hummer, M.L.Quillin, B.W.Matthews, S.M.Gruner.

ABSTRACT

Formation of a water-expelling nonpolar core is the paradigm of protein folding and stability. Although experiment largely confirms this picture, water buried in "hydrophobic" cavities is required for the function of some proteins. Hydration of the protein core has also been suggested as the mechanism of pressure-induced unfolding. We therefore are led to ask whether even the most nonpolar protein core is truly hydrophobic (i.e., water-repelling). To answer this question we probed the hydration of an approximately 160-A(3), highly hydrophobic cavity created by mutation in T4 lysozyme by using high-pressure crystallography and molecular dynamics simulation. We show that application of modest pressure causes approximately four water molecules to enter the cavity while the protein itself remains essentially unchanged. The highly cooperative filling is primarily due to a small change in bulk water activity, which implies that changing solvent conditions or, equivalently, cavity polarity can dramatically affect interior hydration of proteins and thereby influence both protein activity and folding.

Selected figure(s)

Figure 1.
Fig. 1. Electron density in the main cavity of T4 lysozyme mutant L99A at high pressure. Helix E is shown behind a cut-away view of the 160-Å^3 cavity. (A) Experimental density at 100 MPa (yellow), 150 MPa (cyan), and 200 MPa (magenta) is contoured at 0.1 electrons per Å^3. (B) Experimental electron density at 150 MPa (cyan) compared with simulation density at 200 MPa (magenta), contoured at 0.1 electrons per Å^3, viewed as described above. The distribution of atoms at 100 MPa (using the occupancies of N = 1, 2, 3, 4, 5 at 200 MPa) is shown in yellow for comparison.

Figure 3.
Fig. 3. Probability distribution (logarithmic scale) of the number N of water molecules in the cavity from computer simulations. Symbols show results from MD simulations at 0.1, 100, and 200 MPa. Lines are the results of perturbation theory using the 200-MPa simulations as a reference point. Error bars indicate statistical uncertainties corresponding to one estimated standard deviation.

Figures were selected by an automated process.