1JKB|pdb_00001jkb

HUMAN LYSOZYME MUTANT WITH GLU 35 REPLACED BY ALA

PDB DOI: https://doi.org/10.2210/pdb1JKB/pdb

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

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.66 Å
R-Value Free:
0.202 (Depositor)
R-Value Work:
0.178 (Depositor), 0.180 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model:experimental
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wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1002/pro.5560060227
Primary Citation of Related Structures:
1JKA,1JKB,1JKC,1JKD

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.

Organizational Affiliation

Biomolecules Department, National Institute of Bioscience and Human-Technology, Ibaraki, Japan. muraki@nibh.go.jp

Macromolecule Content

Total Structure Weight: 14.79 kDa
Atom Count: 1,122
Modeled Residue Count: 130
Deposited Residue Count: 130
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LYSOZYME	A	130	Homo sapiens	Mutation(s): 1 Gene Names: A SYNTHETIC GENE OF HUMAN LYSO EC: 3.2.1.17
UniProt & NIH Common Fund Data Resources
Find proteins for P61626 (Homo sapiens) Explore P61626 Go to UniProtKB: P61626
PHAROS: P61626 GTEx: ENSG00000090382
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P61626
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NO3 Query on NO3 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]