PDBsum entry 1b5y

Hydrolase

PDB id: 1b5y

Contents

Protein chain

130 a.a. *

Metals

_NA

Waters ×168

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Contribution of hydrogen bonds to the conformational stability of human lysozyme: calorimetry and X-Ray analysis of six ser --≫ ala mutants.

Authors

K.Takano, Y.Yamagata, M.Kubota, J.Funahashi, S.Fujii, K.Yutani.

Ref.

Biochemistry, 1999, 38, 6623-6629. [DOI no: 10.1021/bi9901228]

PubMed id

10350481

Abstract

To further examine the contribution of hydrogen bonds to the conformational stability of the human lysozyme, six Ser to Ala mutants were constructed. The thermodynamic parameters for denaturation of these six Ser mutant proteins were investigated by differential scanning calorimetry (DSC), and the crystal structures were determined by X-ray analysis. The denaturation Gibbs energy (DeltaG) of the Ser mutant proteins was changed from 2.0 to -5.7 kJ/mol, compared to that of the wild-type protein. With an analysis in which some factors that affected the stability due to mutation were considered, the contribution of hydrogen bonds to the stability (Delta DeltaGHB) was extracted on the basis of the structures of the mutant proteins. The results showed that hydrogen bonds between protein atoms and between a protein atom and a water bound with the protein molecule favorably contribute to the protein stability. The net contribution of one intramolecular hydrogen bond to protein stability (DeltaGHB) was 8.9 +/- 2.6 kJ/mol on average. However, the contribution to the protein stability of hydrogen bonds between a protein atom and a bound water molecule was smaller than that for a bond between protein atoms.

Secondary reference #1

Title

A general rule for the relationship between hydrophobic effect and conformational stability of a protein: stability and structure of a series of hydrophobic mutants of human lysozyme.

Authors

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

Ref.

J Mol Biol, 1998, 280, 749-761. [DOI no: 10.1006/jmbi.1998.1906]

PubMed id

9677301

Figure 4.
Figure 4. Stereodrawing (Johnson, 1976) showing the structure in the vicinity of residue 59. (a) I59V (filled bonds) and 4SS (open bonds) structures are superimposed. (b) I59V-3SS (filled bonds) and 3SS (open bonds) structures are superimposed. Solvent water molecules are drawn as crossed circles. The broken lines indicate hydrogen bonds.

Figure 8.
Figure 8. Amino acid sequences of the wild-type (4SS), V93A, 3SS and V93A-3SS between residues 89 and 101. The substituted residues are represented in red.

The above figures are reproduced from the cited reference with permission from Elsevier

Secondary reference #2

Title

Contribution of hydrogen bonds to the conformational stability of human lysozyme: calorimetry and X-Ray analysis of six tyrosine --≫ phenylalanine mutants.

Authors

Y.Yamagata, M.Kubota, Y.Sumikawa, J.Funahashi, K.Takano, S.Fujii, K.Yutani.

Ref.

Biochemistry, 1998, 37, 9355-9362. [DOI no: 10.1021/bi980431i]

PubMed id

9649316

Secondary reference #3

Title

Contribution of the hydrophobic effect to the stability of human lysozyme: calorimetric studies and X-Ray structural analyses of the nine valine to alanine mutants.

Authors

K.Takano, Y.Yamagata, S.Fujii, K.Yutani.

Ref.

Biochemistry, 1997, 36, 688-698. [DOI no: 10.1021/bi9621829]

PubMed id

9020766

Secondary reference #4

Title

Contribution of water molecules in the interior of a protein to the conformational stability.

Authors

K.Takano, J.Funahashi, Y.Yamagata, S.Fujii, K.Yutani.

Ref.

J Mol Biol, 1997, 274, 132-142. [DOI no: 10.1006/jmbi.1997.1365]

PubMed id

9398521

Figure 2.
Figure 2. Structures in the vicinity of the residue 56 in the wild-type (a) and I56A (b) to (d), and those of the residue 59 in the wild-type (e) and I59A (f). In (c) and (d), dummy water molecules, which were estimated to be energetically favorable using the program, X-PLOR [Brunger 1992], are drawn. The dummy water molecules in (c) and (d) made hydrogen bonds with O^γ of Ser36 and an internal water molecule, respectively. The side-chain atoms of the residues 56 and 59, carbon atoms, oxygen and nitrogen atoms, interior water molecules, introduced water molecules and the dummy water molecules are represented by green, yellow, orange, blue, dark blue and purple, respectively.

Figure 3.
Figure 3. Correlation of ΔΔASA[HP] (changes in hydrophobic surface area exposed upon denaturation) with ΔΔG for the mutant proteins with empty cavities (a) and with solvated cavities (b). The mutants with solvated cavities are shown as open symbols and labeled. The mutants of the type I are represented by black filled up-triangles (with empty cavity). The black continuous line shows the linear regression of the type I mutants with empty cavity (black filled up-triangles). The mutants of the type II are represented by blue filled (with empty cavity) and open (with solvated cavity) circles. The blue broken line shows the linear regression of the type II mutants with solvated cavity (blue open circles). The mutants of the type III are represented by red filled (with empty cavity) and open (with solvated cavity) squares. The red continuous line shows the linear regression of the type III mutants with empty cavity (red filled squares). The red broken line is drawn with reference to the red continuous line. The ASA values were calculated using the procedure of [Connolly 1993].

The above figures are reproduced from the cited reference with permission from Elsevier

Secondary reference #5

Title

The structure, Stability, And folding process of amyloidogenic mutant human lysozyme.

Authors

J.Funahashi, K.Takano, K.Ogasahara, Y.Yamagata, K.Yutani.

Ref.

J Biochem (tokyo), 1996, 120, 1216-1223.

PubMed id

9010773

Secondary reference #6

Title

Contribution of hydrophobic residues to the stability of human lysozyme: calorimetric studies and X-Ray structural analysis of the five isoleucine to valine mutants.

Authors

K.Takano, K.Ogasahara, H.Kaneda, Y.Yamagata, S.Fujii, E.Kanaya, M.Kikuchi, M.Oobatake, K.Yutani.

Ref.

J Mol Biol, 1995, 254, 62-76. [DOI no: 10.1006/jmbi.1995.0599]

PubMed id

7473760

Figure 2.
Figure 2. Typical excess heat capacity curves of the mutant human lysozyme (I106V) at pH 2.70 (a), 2.92 (b), 3.04 (c), 3.10 (d), and 3.14 (e). The increments of excess heat capacity were 10 kJ/mol K.

Figure 5.
Figure 5. Stereo drawings (Johnson, 1976) showing the mutant structure in the vicinity of the mutation sites. The wild-type (open bonds) and mutant structures (filled bonds) are superimposed. (a) I23V; (b) I56V; (c) I59V; (d) I89V; and (e) I106V. Solvent water molecules are drawn as cross-circles. Broken lines indicate hydrogen bonds.

The above figures are reproduced from the cited reference with permission from Elsevier