PDBsum entry 1ip4

Hydrolase

PDB id: 1ip4

Contents

Protein chain

130 a.a. *

Metals

_NA

Waters ×261

* Residue conservation analysis

PDB id:

1ip4

Name:

Hydrolase

Title:

G72a human lysozyme

Structure:

LysozymE C. Chain: a. Engineered: yes. Mutation: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: saccharomyces cerevisiae. Expression_system_taxid: 4932.

Resolution:

1.80Å R-factor: 0.171

Authors:

K.Takano,Y.Yamagata,K.Yutani

Key ref:

K.Takano et al. (2001). Role of amino acid residues in left-handed helical conformation for the conformational stability of a protein. Proteins, 45, 274-280. PubMed id: 11599030 DOI: 10.1002/prot.1147

Date:

20-Apr-01 Release date: 14-Nov-01

Protein chain

P61626  (LYSC_HUMAN) -  Lysozyme C from Homo sapiens

Seq: 148 a.a.

Struc: 130 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

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: 10.1002/prot.1147

Proteins 45:274-280 (2001)

PubMed id: 11599030

Role of amino acid residues in left-handed helical conformation for the conformational stability of a protein.

K.Takano, Y.Yamagata, K.Yutani.

ABSTRACT

Our previous study of six non-Gly to Gly/Ala mutant human lysozymes in a left-handed helical region showed that only one non-Gly residue at a rigid site had unfavorable strain energy as compared with Gly at the same position (Takano et al., Proteins 2001; 44:233-243). To further examine the role of left-handed residues in the conformational stability of a protein, we constructed ten Gly to Ala mutant human lysozymes. Most Gly residues in human lysozyme are located in the left-handed helix region. The thermodynamic parameters for denaturation and crystal structures were determined by differential scanning calorimetry and X-ray analysis, respectively. The difference in denaturation Gibbs energy (DeltaDeltaG) for the ten Gly to Ala mutants ranged from + 1.9 to -7.5 kJ/mol, indicating that the effect of the mutation depends on the environment of the residue. We confirm that Gly in a left-handed region is more favorable at rigid sites than non-Gly, but there is little difference in energetic cost between Gly and non-Gly at flexible sites. The present results indicate that dihedral angles in the backbone conformation and also the flexibility at the position should be considered for analyses of protein stability, and protein structural determination, prediction, and design.

Selected figure(s)

Figure 2.
Figure 2. Stereodrawings of the structures in the vicinity of the mutation sites for (a) G37A, (b) G48A, (c) G68A, (d) G72A, (e) G105A, (f) G127A, and (g) G129A of human lysozymes. The wild-type and mutant structures are superimposed.

Figure 3.
Figure 3. Ramachandran plot[1] of the Gly residues in the wild-type human lysozyme structure (open squares), and each Ala residue in the mutant structure (closed squares).

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2001, 45, 274-280) copyright 2001.

Figures were selected by an automated process.