PDBsum entry 1lyh

Hydrolase(o-glycosyl)

PDB id: 1lyh

Contents

Protein chain

162 a.a. *

Ligands

BME-BME

Metals

_CL ×2

Waters ×142

* Residue conservation analysis

PDB id:

1lyh

Name:

Hydrolase(o-glycosyl)

Title:

Dissection of helix capping in t4 lysozyme by structural and thermodynamic analysis of six amino acid substitutions at thr 59

Structure:

T4 lysozyme. Chain: a. Engineered: yes

Source:

Enterobacteria phage t4. Organism_taxid: 10665.

Biol. unit:

Dimer (from PQS)

Resolution:

1.70Å R-factor: 0.163

Authors:

J.A.Bell,W.J.Becktel,U.Sauer,W.A.Baase,B.W.Matthews

Key ref:

J.A.Bell et al. (1992). Dissection of helix capping in T4 lysozyme by structural and thermodynamic analysis of six amino acid substitutions at Thr 59. Biochemistry, 31, 3590-3596. PubMed id: 1567817 DOI: 10.1021/bi00129a006

Date:

10-Aug-92 Release date: 31-Oct-93

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: 10.1021/bi00129a006

Biochemistry 31:3590-3596 (1992)

PubMed id: 1567817

Dissection of helix capping in T4 lysozyme by structural and thermodynamic analysis of six amino acid substitutions at Thr 59.

J.A.Bell, W.J.Becktel, U.Sauer, W.A.Baase, B.W.Matthews.

ABSTRACT

Threonine 59, a helix-capping residue at the amino terminus of the longest helix in T4 phage lysozyme, was substituted with valine, alanine, glycine, serine, asparagine, and aspartic acid. The valine, alanine, and glycine replacements were observed to be somewhat more destabilizing than serine, asparagine, and aspartic acid. The crystal structures of the different variants showed that changes in conformation occurred at the site of substitution, including Asp 61, which is nearby, as well as displacement of a solvent molecule that is hydrogen-bonded to the gamma-oxygen of Thr 59 in wild-type lysozyme. Neither the structures nor the stabilities of the mutant proteins support the hypothesis of Serrano and Fersht (1989) that glycine and alanine are better helix-capping residues than valine because a smaller-sized residue allows better hydration at the end of the helix. In the aspartic acid and asparagine replacements the substituted side chains form hydrogen bonds with the end of the helix, as does threonine and serine at this position. In contrast, however, the Asp and Asn side chains also make unusually close contacts with carbon atoms in Asp 61. This suggests a structural basis for the heretofore puzzling observations that asparagine is more frequently observed as a helix-capping residue than threonine [Richardson, J. S., & Richardson, D. C. (1988) Science 240, 1648-1652] yet Thr----Asn replacements at N-cap positions in barnase were found to be destabilizing [Serrano, L., & Fersht, A. R. (1989) Nature 342, 296-299].(ABSTRACT TRUNCATED AT 250 WORDS)