PDBsum entry 1llh

Hydrolase

PDB id

1llh

Contents

			Protein chain

					162 a.a. *

			Ligands

					BME

			Metals

					_CL ×2

			Waters ×59

* Residue conservation analysis

References listed in PDB file

Key reference

Title

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

Authors

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

Ref.

Protein Sci, 2002, 11, 516-521. [DOI no: 10.1110/ps.39802]

PubMed id

11847274

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.



	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.)