PDBsum entry 1llh

Hydrolase

PDB id: 1llh

Contents

Protein chain

162 a.a. *

Ligands

BME

Metals

_CL ×2

Waters ×59

* Residue conservation analysis

PDB id:

1llh

Name:

Hydrolase

Title:

Are carboxy terminii of helices coded by the local sequence or by tertiary structure contacts

Structure:

Lysozyme. Chain: a. Synonym: lysis protein. Engineered: yes. Mutation: yes

Source:

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

Biol. unit:

Dimer (from PQS)

Resolution:

1.80Å R-factor: 0.200 R-free: 0.242

Authors:

M.Sagermann,L.-G.Martensson,W.A.Baase,B.W.Matthews

Key ref:

M.Sagermann et al. (2002). A test of proposed rules for helix capping: implications for protein design. Protein Sci, 11, 516-521. PubMed id: 11847274 DOI: 10.1110/ps.39802

Date:

28-Apr-02 Release date: 15-May-02

Supersedes:

1joz

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: 10.1110/ps.39802

Protein Sci 11:516-521 (2002)

PubMed id: 11847274

A test of proposed rules for helix capping: implications for protein design.

M.Sagermann, L.G.Mårtensson, W.A.Baase, B.W.Matthews.

ABSTRACT

alpha-helices within proteins are often terminated (capped) by distinctive configurations of the polypeptide chain. Two common arrangements are the Schellman motif and the alternative alpha(L) motif. Rose and coworkers developed stereochemical rules to identify the locations of such motifs in proteins of unknown structure based only on their amino acid sequences. To check the effectiveness of these rules, they made specific predictions regarding the structural and thermodynamic consequences of certain mutations in T4 lysozyme. We have constructed these mutants and show here that they have neither the structure nor the stability that was predicted. The results show the complexity of the protein-folding problem. Comparison of known protein structures may show that a characteristic sequence of amino acids (a sequence motif) corresponds to a conserved structural motif. In any particular protein, however, changes in other parts of the sequence may result in a different conformation. The structure is determined by sequence as a whole, not by parts considered in isolation.

Selected figure(s)

Figure 1.
Fig. 1. (a) Schematic illustration of the hydrogen-bonding interactions (red lines) in a Schellman motif. As noted by Aurora et al. (1994) such motifs have a preference for glycine at C` and an apolar residue at C". (b) Schematic illustration showing the backbone hydrogen-bonding interactions (red lines) in a typical [L] capping motif, as well as the sequence of the subject motif in T4 lysozyme (in blue). Such motifs commonly have a glycine at the C position and a polar residue at C". (In her original article, Schellman [1980] proposed the name [L] for the conformation shown in panel a. Aurora et al. [1994] renamed this the Schellman motif and used [L] to designate the conformation shown in panel b.)

The above figure is reprinted by permission from the Protein Society: Protein Sci (2002, 11, 516-521) copyright 2002.

Figure was selected by an automated process.