PDBsum entry 3dmx

Hydrolase

PDB id: 3dmx

Contents

Protein chain

164 a.a. *

Ligands

PO4 ×2

HED ×2

BNZ

Metals

_CL

Waters ×248

* Residue conservation analysis

PDB id:

3dmx

Name:

Hydrolase

Title:

Benzene binding in the hydrophobic cavity of t4 lysozyme l99a mutant

Structure:

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

Source:

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

Resolution:

1.80Å R-factor: 0.183 R-free: 0.208

Authors:

L.Liu,B.W.Matthews

Key ref:

L.Liu et al. (2009). Halogenated benzenes bound within a non-polar cavity in T4 lysozyme provide examples of I...S and I...Se halogen-bonding. J Mol Biol, 385, 595-605. PubMed id: 19014950 DOI: 10.1016/j.jmb.2008.10.086

Date:

01-Jul-08 Release date: 27-Jan-09

Protein chain

P00720  (ENLYS_BPT4) -  Endolysin from Enterobacteria phage T4

Seq: 164 a.a.

Struc: 164 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: 10.1016/j.jmb.2008.10.086

J Mol Biol 385:595-605 (2009)

PubMed id: 19014950

Halogenated benzenes bound within a non-polar cavity in T4 lysozyme provide examples of I...S and I...Se halogen-bonding.

L.Liu, W.A.Baase, B.W.Matthews.

ABSTRACT

We showed earlier that the mutation of Leu99 to alanine in bacteriophage T4 lysozyme creates an internal cavity of volume approximately 150 A(3) that binds benzene and a variety of other ligands. As such, this cavity provides an excellent target to study protein-ligand interaction. Here, we use low-temperature crystallography and related techniques to analyze the binding of halogen-incorporated benzenes typified by C(6)F(5)X, where X=H, F, Cl, Br or I, and C(6)H(5)X, where X=H or I was also studied. Because of the increased electron density of fluorine relative to hydrogen, the geometry of binding of the fluoro compounds can often be determined more precisely than their hydrogen-containing analogs. All of the ligands bind in essentially the same plane but the center of the phenyl ring can translate by up to 1.2 A. In no case does the ligand rotate freely within the cavity. The walls of the cavity consist predominantly of hydrocarbon atoms, and in several cases it appears that van der Waals interactions define the geometry of binding. In comparing the smallest with the largest ligand, the cavity volume increases from 181 A(3) to 245 A(3). This shows that the protein is flexible and adapts to the size and shape of the ligand. There is a remarkably close contact of 3.0 A between the iodine atom on C(6)F(5)I and the sulfur or selenium atom of Met or SeMet102. This interaction is 1.0 A less than the sum of the van der Waals radii and is a clear example of a so-called halogen bond. Notwithstanding this close approach, the increase in binding energy for the halogen bond relative to a van der Waals contact is estimated to be only about 0.5-0.7 kcal/mol.

Selected figure(s)

Figure 1.
Fig. 1. Electron density maps showing the location of ligands bound in the L99A cavity. Maps have amplitudes (F[obs,complex] – F[obs,L99A]) and phases from the refined structure of L99A. Resolution as in Table 1; maps contoured at 3.0σ. (a) C[6]H[6], ligand in dark blue. (b) C[6]F[6], fluorine atoms in green. (c) C[6]HF[5]. An alternative binding mode, not shown, is rotated 60° clockwise. (d) Stereo figure superimposing the C[6]F[6] complex (carbon atoms in orange, fluorine in green) on that for C[6]H[6] (atoms in blue). The side chain of Met102 is at the top left with the sulfur atom in yellow. All figures were rendered with PyMOL [http://www.pymol.org].

Figure 5.
Fig. 5. (a) Maps showing the binding of C[6]F[5]I to selenium-substituted L99A. The isomorphous difference map has amplitudes (F[obs,complex] – F[obs,L99A]) and phases from the refined structure of L99A. It is shown in red, and contoured at 3.0σ. C[6]F[5]I has density for the bound ligand and, due to the replacement of Met102, with the more electron-dense selenomethionine (top left). The map based on the anomalous scattering differences, contoured in green, is contoured at 3.0σ. (b) Electron density maps, as in panel a, for C[6]H[5]I bound to selenomethionine L99A. The ligand occupies the position shown as well as one rotated 180°.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2009, 385, 595-605) copyright 2009.

Figures were selected by an automated process.