PDBsum entry 1gft

Hydrolase

PDB id

1gft

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Contents

			Protein chain

					130 a.a. *

			Metals

					_NA

			Waters ×256

* Residue conservation analysis

PDB id:

1gft

Links
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Name:

Hydrolase

Title:

Crystal structure of mutant human lysozyme substituted at the surface positions

Structure:

Lysozyme. 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:

0.191

Authors:

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

Key ref:

J.Funahashi et al. (2002). Positive contribution of hydration structure on the surface of human lysozyme to the conformational stability. J Biol Chem, 277, 21792-21800. PubMed id: 11927576

Date:

04-Dec-00

Release date:

27-Dec-00

PROCHECK

	Headers

	References

Protein chain

P61626 (LYSC_HUMAN) - Lysozyme C from Homo sapiens

Seq: Struc:					148 a.a. 130 a.a.*

Key:

PfamA domain

Secondary structure

CATH domain

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



		Enzyme reactions

Enzyme class:

E.C.3.2.1.17 - lysozyme.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

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.

	J Biol Chem 277:21792-21800 (2002)
PubMed id: 11927576

Positive contribution of hydration structure on the surface of human lysozyme to the conformational stability.
J.Funahashi, K.Takano, Y.Yamagata, K.Yutani.

ABSTRACT

Water molecules make a hydration structure with the network of hydrogen bonds, covering on the surface of proteins. To quantitatively estimate the contribution of the hydration structure to protein stability, a series of hydrophilic mutant human lysozymes (Val to Ser, Tyr, Asp, Asn, and Arg) modified at three different positions on the surface, which are located in the alpha-helix (Val-110), the beta-sheet (Val-2), and the loop (Val-74), were constructed. Their thermodynamic parameters of denaturation and crystal structures were examined by calorimetry and by x-ray crystallography at 100 K, respectively. The introduced polar residues made hydrogen bonds with protein atoms and/or water molecules, sometimes changing the hydration structure around the mutation site. Changes in the stability of the mutant proteins can be evaluated by a unique equation that considers the conformational changes resulting from the substitutions. Using this analysis, the relationship between the changes in the stabilities and the hydration structures for mutant human lysozymes substituted on the surface could be quantitatively estimated. The analysis indicated that the hydration structure on protein surface plays an important role in determining the conformational stability of the protein.

Literature references that cite this PDB file's key reference

PubMed id

Reference

19864691

T.Nakamura, S.Meshitsuka, S.Kitagawa, N.Abe, J.Yamada, T.Ishino, H.Nakano, T.Tsuzuki, T.Doi, Y.Kobayashi, S.Fujii, M.Sekiguchi, and Y.Yamagata (2010).
Structural and dynamic features of the MutT protein in the recognition of nucleotides with the mutagenic 8-oxoguanine base.

J Biol Chem, 285, 444-452.

PDB codes:

3a6s 3a6t 3a6u 3a6v

17921497

C.Deutsch, and B.Krishnamoorthy (2007).
Four-body scoring function for mutagenesis.

Bioinformatics, 23, 3009-3015.

14747705

Y.Maruyama, N.Maruyama, B.Mikami, and S.Utsumi (2004).
Structure of the core region of the soybean beta-conglycinin alpha' subunit.

Acta Crystallogr D Biol Crystallogr, 60, 289-297.

PDB code:

1uik

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.