Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 14805.67 
• Atom Count: 1034 
• Residue Count: 130 
• Unique protein chains: 1

1JKC

HUMAN LYSOZYME MUTANT WITH TRP 109 REPLACED BY PHE

• DOI: 10.2210/pdb1JKC/pdb

• Classification: LYSOZYME
• Organism(s): Homo sapiens
• Expression System: Saccharomyces cerevisiae
• Mutation(s): 1 


• Deposited: 1996-11-13 Released: 1997-05-15 
• Deposition Author(s): Muraki, M., Harata, K., Goda, S., Nagahora, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.6 Å
• R-Value Free: 0.220 
• R-Value Work: 0.180 

Literature

Importance of van der Waals contact between Glu 35 and Trp 109 to the catalytic action of human lysozyme.

Muraki, M., Goda, S., Nagahora, H., Harata, K.

(1997) Protein Sci. 6: 473-476

• PubMed: 9041653 
• DOI: 10.1002/pro.5560060227
• Primary Citation of Related Structures:  
  1JKD, 1JKB, 1JKA


• PubMed Abstract: 
  

The importance of van der Waals contact between Glu 35 and Trp 109 to the active-site structure and the catalytic properties of human lysozyme (HL) has been investigated by site-directed mutagenesis. The X-ray analysis of mutant HLs revealed that both the replacement of Glu 35 by Asp or Ala, and the replacement of Trp 109 by Phe or Ala resulted in a significant but localized change in the active-site cleft geometry. A prominent movement of the backbone structure was detected in the region of residues 110 to 120 and in the region of residues 100 to 115 for the mutations concerning Glu 35 and Trp 109, respectively. Accompanied by the displacement of the main-chain atoms with a maximal deviation of C alpha atom position ranging from 0.7 A to 1.0 A, the mutant HLs showed a remarkable change in the catalytic properties against Micrococcus luteus cell substrate as compared with native HL. Although the replacement of Glu 35 by Ala completely abolished the lytic activity, HL-Asp 35 mutant retained a weak but a certain lytic activity, showing the possible involvement of the side-chain carboxylate group of Asp 35 in the catalytic action. The kinetic consequence derived from the replacement of Trp 109 by Phe or Ala together with the result of the structural change suggested that the structural detail of the cleft lobe composed of the residues 100 to 115 centered at Ala 108 was responsible for the turnover in the reaction of HL against the bacterial cell wall substrate. The results revealed that the van der Waals contact between Glu 35 and Trp 109 was an essential determinant in the catalytic action of HL.

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Related Citations: 

• The Roles of Conserved Aromatic Amino-Acid Residues in the Active Site of Human Lysozyme: A Site-Specific Mutagenesis Study
  Muraki, M.,Morikawa, M.,Jigami, Y.,Tanaka, H.
  (1987) Biochim.Biophys.Acta 916: 66




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Organizational Affiliation: 

Biomolecules Department, National Institute of Bioscience and Human-Technology, Ibaraki, Japan. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
LYSOZYME	A	130	Homo sapiens	Mutation(s): 1  Gene Names: LYZ (LZM) EC: 3.2.1.17
Find proteins for P61626 (Homo sapiens) Go to Gene View: LYZ Go to UniProtKB:  P61626

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
NO3	A	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.6 Å
• R-Value Free: 0.220 
• R-Value Work: 0.180 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 57.170	α = 90.00
b = 60.830	β = 90.00
c = 32.890	γ = 90.00

Software Package:

Software Name	Purpose
X-PLOR	phasing
MADNES	data collection
X-PLOR	model building
MADNES	data reduction
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1996-11-13 
• Released Date: 1997-05-15 
• Deposition Author(s): Muraki, M., Harata, K., Goda, S., Nagahora, H.

Revision History 

• Version 1.0: 1997-05-15
  Type: Initial release
• Version 1.1: 2008-03-03
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2018-04-18
  Type: Data collection, Other