Biological Assembly 1  

 3D View: Structure

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 14.67 kDa 
• Atom Count: 1102 
• Residue Count: 130 
• Unique protein chains: 1

1TBY

DISSECTION OF THE FUNCTIONAL ROLE OF STRUCTURAL ELEMENTS OF TYROSINE-63 IN THE CATALYTIC ACTION OF HUMAN LYSOZYME

• DOI: 10.2210/pdb1TBY/pdb

• Classification: HYDROLASE (O-GLYCOSYL)
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 1992-08-06 Released: 1993-01-15 
• Deposition Author(s): Harata, K., Muraki, M., Jigami, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Work: 0.182 
• R-Value Observed: 0.182 

Literature

Dissection of the functional role of structural elements of tyrosine-63 in the catalytic action of human lysozyme.

Muraki, M., Harata, K., Jigami, Y.

(1992) Biochemistry 31: 9212-9219

• PubMed: 1390708 
• DOI: 10.1021/bi00153a014
• Structures With Same Primary Citation


• PubMed Abstract: 
  

The functional role of tyrosine-63 in the catalytic action of human lysozyme (EC 3.2.1.17) has been probed by site-directed mutagenesis. In order to identify the role of Tyr63 in the interaction with substrate, both the three-dimensional structures and the enzymatic functions of the mutants, in which Tyr63 was converted to phenylalanine, tryptophan, leucine, or alanine, have been characterized in comparison with those of the wild-type enzyme. X-ray crystallographical analysis of the mutant enzyme at not less than 1.77-A resolution indicated no remarkable change in tertiary structure except the side chain of 63rd residue. The conversion of Tyr63 to Phe or Trp did not change the enzymatic properties against the noncharged substrate (or substrate analogs) largely, while the conversion to Leu or Ala markedly reduced the catalytic activity to a few percent of wild-type enzyme. Kinetic analysis using p-nitrophenyl penta-N-acetyl-beta-(1----4)-chitopentaoside (PNP-(GlcNAc)5) as a substrate revealed that the reduction of activity should mainly be attributed to the reduction of affinity between enzyme and substrate. The apparent contribution of the phenolic hydroxyl group and the phenol group in the side chain of Tyr63 was estimated to 0.4 +/- 0.4 and 2.5 +/- 0.8 kcal mol-1, respectively. The result suggested that the direct contact between the planar side-chain group of Tyr63 and the sugar residue at subsite B is a major determinant of binding specificity toward a electrostatically neutral substrate in the catalytic action of human lysozyme.

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Organizational Affiliation: 

Biological Chemistry Division, National Chemical Laboratory for Industry, Ibaraki, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
HUMAN LYSOZYME	A	130	Homo sapiens	Mutation(s): 0  Gene Names: LYZ, LZM EC: 3.2.1.17
Find proteins for P61626 (Homo sapiens) Go to UniProtKB:  P61626
NIH Common Fund Data Resources
PHAROS  P61626 GTEx  ENSG00000090382

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Work: 0.182 
• R-Value Observed: 0.182 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.19	α = 90
b = 60.9	β = 90
c = 33.01	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1992-08-06 
• Released Date: 1993-01-15 
Deposition Author(s): Harata, K., Muraki, M., Jigami, Y.

Revision History 

• Version 1.0: 1993-01-15
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-11-29
  Changes: Derived calculations, Other