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: 14.73 kDa 
• Atom Count: 1142 
• Residue Count: 130 
• Unique protein chains: 1

1LAA

X-RAY STRUCTURE OF GLU 53 HUMAN LYSOZYME

• DOI: 10.2210/pdb1LAA/pdb

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


• Deposited: 1992-06-24 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: 0.179 
• R-Value Observed: 0.179 

Literature

X-ray structure of Glu 53 human lysozyme.

Harata, K., Muraki, M., Hayashi, Y., Jigami, Y.

(1992) Protein Sci 1: 1447-1453

• PubMed: 1363898 
• DOI: 10.1002/pro.5560011106
• Structures With Same Primary Citation


• PubMed Abstract: 
  

The three-dimensional structure of a modified human lysozyme (HL), Glu 53 HL, in which Asp 53 was replaced by Glu, has been determined at 1.77 A resolution by X-ray analysis. The backbone structure of Glu 53 HL is essentially the same as the structure of wild-type HL. The root mean square difference for the superposition of equivalent C alpha atoms is 0.141 A. Except for the Glu 53 residue, the structure of the active site region is largely conserved between Glu 53 HL and wild-type HL. However, the hydrogen bond network differs because of the small shift or rotation of side chain groups. The carboxyl group of Glu 53 points to the carboxyl group of Glu 35 with a distance of 4.7 A between the nearest carboxyl oxygen atoms. A water molecule links these carboxyl groups by a hydrogen bond bridge. The active site structure explains well the fact that the binding ability for substrates does not significantly differ between Glu 53 HL and wild-type HL. On the other hand, the positional and orientational change of the carboxyl group of the residue 53 caused by the mutation is considered to be responsible for the low catalytic activity (ca. 1%) of Glu 53 HL. The requirement of precise positioning for the carboxyl group suggests the possibility that the Glu 53 residue contributes more than a simple electrostatic stabilization of the intermediate in the catalysis reaction.

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Related Citations: 

• The Importance of Precise Positioning of Negatively Charged Carboxylate in the Catalytic Action of Human Lysozyme
  Muraki, M., Harata, K., Hayashi, Y., Machida, M., Jigami, Y.
  (1991) Biochim Biophys Acta 1079: 229

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Organizational Affiliation: 

Research Institute for Polymers and Textiles, 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: 0.179 
• R-Value Observed: 0.179 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.13	α = 90
b = 61.05	β = 90
c = 33.16	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: 1992-06-24 
• 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