1IY3

Solution Structure of the Human lysozyme at 4 degree C


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 20 
  • Conformers Submitted: 
  • Selection Criteria: structures with the least restraint violations,structures with the lowest energy 

wwPDB Validation   3D Report Full Report

Currently 1IY3 does not have a validation slider image.


This is version 1.4 of the entry. See complete history


Literature

Low-temperature-induced structural changes in human lysozyme elucidated by three-dimensional NMR spectroscopy

Kumeta, H.Miura, A.Kobashigawa, Y.Miura, K.Oka, C.Nemoto, N.Nitta, K.Tsuda, S.

(2003) Biochemistry 42: 1209-1216

  • DOI: https://doi.org/10.1021/bi026730w
  • Primary Citation of Related Structures:  
    1IY3, 1IY4

  • PubMed Abstract: 

    The three-dimensional solution structures of human lysozyme were determined at 35 and 4 degrees C using the heteronuclear multidimensional NMR spectroscopy, which were compared with each other to clarify the structural response of this enzyme to lowering of the temperature. Together with the data of the temperature dependence experiments of the lytic activity against Micrococcus luteus, we consider the implication of the observed structural change for the low-temperature-induced reduction of the activity of human lysozyme. The structures of human lysozyme determined at the two temperatures are found to be similar, both of which comprise four alpha-helices (A- to D-helices) and three antiparallel beta-strands (beta(1)-beta(3)), leading to the constructions of the alpha- and beta-domains as previously identified in the X-ray crystal structure. A significant structural change was observed for the "active site lobe" comprising the loop region connecting C- and D-helices and the following D-helix, which moves toward the active site cleft located between the alpha- and beta-domains so as to obstruct the cleft according to the temperature lowering. It further appeared that the total volume as well as the accessible surface area of human lysozyme decreases with lowering of the temperature, suggesting that the internal cavity of this enzyme shrinks under low temperature environment. Because in human lysozyme the region comprising the active site lobe is responsible for turnover of the enzymatic reaction against the substrate, the low-temperature-induced structural change of the active site lobe presumably controls the efficiency of the lytic activity under low temperatures.


  • Organizational Affiliation

    Protein Structure Research Group, Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1, Tsukisamu-Higashi, Toyohira, Sapporo 062-8517, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysozyme130Homo sapiensMutation(s): 0 
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61626
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 20 
  • Conformers Submitted: 
  • Selection Criteria: structures with the least restraint violations,structures with the lowest energy 

Structure Validation

View Full Validation Report

Currently 1IY3 does not have a validation slider image.



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-07-31
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-02-23
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-12-27
    Changes: Data collection