PDBsum entry 1ovh

Hydrolase

PDB id: 1ovh

Contents

Protein chain

162 a.a. *

Ligands

BME ×3

2CM

Metals

_CL ×2

Waters ×62

* Residue conservation analysis

PDB id:

1ovh

Name:

Hydrolase

Title:

T4 lysozyme cavity mutant l99a/m102q bound with 2-chloro-6-methyl- aniline

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

Biol. unit:

Dimer (from PQS)

Resolution:

1.95Å R-factor: 0.185

Authors:

B.Q.Wei,W.A.Baase,L.H.Weaver,B.W.Matthews,B.K.Shoichet

Key ref:

B.Q.Wei et al. (2004). Testing a flexible-receptor docking algorithm in a model binding site. J Mol Biol, 337, 1161-1182. PubMed id: 15046985 DOI: 10.1016/j.jmb.2004.02.015

Date:

26-Mar-03 Release date: 06-Apr-04

Protein chain

P00720  (ENLYS_BPT4) -  Endolysin from Enterobacteria phage T4

Seq: 164 a.a.

Struc: 162 a.a.*

* PDB and UniProt seqs differ at 4 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.2004.02.015

J Mol Biol 337:1161-1182 (2004)

PubMed id: 15046985

Testing a flexible-receptor docking algorithm in a model binding site.

B.Q.Wei, L.H.Weaver, A.M.Ferrari, B.W.Matthews, B.K.Shoichet.

ABSTRACT

Sampling receptor flexibility is challenging for database docking. We consider a method that treats multiple flexible regions of the binding site independently, recombining them to generate different discrete conformations. This algorithm scales linearly rather than exponentially with the receptor's degrees of freedom. The method was first evaluated for its ability to identify known ligands of a hydrophobic cavity mutant of T4 lysozyme (L99A). Some 200000 molecules of the Available Chemical Directory (ACD) were docked against an ensemble of cavity conformations. Surprisingly, the enrichment of known ligands from among a much larger number of decoys in the ACD was worse than simply docking to the apo conformation alone. Large decoys, accommodated in the larger cavity conformations sampled in the ensemble, were ranked better than known small ligands. The calculation was redone with an energy correction term that considered the cost of forming the larger cavity conformations. Enrichment improved, as did the balance between high-ranking large and small ligands. In a second retrospective test, the ACD was docked against a conformational ensemble of thymidylate synthase. Compared to docking against individual enzyme conformations, the flexible receptor docking approach improved enrichment of known ligands. Including a receptor conformational energy weighting term improved enrichment further. To test the method prospectively, the ACD database was docked against another cavity mutant of lysozyme (L99A/M102Q). A total of 18 new compounds predicted to bind this polar cavity and to change its conformation were tested experimentally; 14 were found to bind. The bound structures for seven ligands were determined by X-ray crystallography. The predicted geometries of these ligands all corresponded to the observed geometries to within 0.7A RMSD or better. Significant conformational changes of the cavity were observed in all seven complexes. In five structures, part of the observed accommodations were correctly predicted; in two structures, the receptor conformational changes were unanticipated and thus never sampled. These results suggest that although sampling receptor flexibility can lead to novel ligands that would have been missed when docking a rigid structure, it is also important to consider receptor conformational energy.

Selected figure(s)

Figure 6.
Figure 6. Stereo views of difference electron density maps for seven ligands bound to L99A/M102Q. a, 2-n-Propyl aniline; b, 2-allyl-6-methyl phenol; c, 3-fluoro-2-methyl aniline; d, 2-allyl phenol; e, 2-chloro-6-methyl aniline; f, 4-fluorophenethyl alcohol; and g, N-allyl aniline. The coefficients are (F[o] -F[c]), where the F[o] are the observed structure amplitudes for the ligand-bound complex and the F[c] and phases were calculated from the refined model with all atoms removed from the cavity. Maps are contoured at +3s (continuous lines) and -3s (broken lines).

Figure 8.
Figure 8. Docking against the apo L99A/M102Q cavity (PDB entry 1LGU) led to incorrect prediction of the binding geometry of a, 2-chloro-6-methyl aniline and b, 3-fluoro-2-methyl aniline. Color scheme is the same as in Figure 7. The pictures are in stereo.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 337, 1161-1182) copyright 2004.

Figures were selected by an automated process.