2RST

NMR structure of the C-terminal domain of EW29


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

NMR structure and dynamics of the C-terminal domain of R-type lectin from the earthworm Lumbricus terrestris

Hemmi, H.Kuno, A.Hirabayashi, J.

(2013) FEBS J 280: 70-82

  • DOI: https://doi.org/10.1111/febs.12050
  • Primary Citation of Related Structures:  
    2RST

  • PubMed Abstract: 

    The C-terminal domain (Ch; C-half) of the R-type earthworm 29-kDa lectin (EW29), isolated from the earthworm Lumbricus terrestris, has two sugar-binding sites, in subdomains α and γ, and the protein uses the two sugar-binding sites for its function as a single domain-type haemagglutinin. Our previous NMR titration experiments showed that the α sugar-binding site is a high-affinity site and the γ sugar-binding site is a low-affinity site. However, it remains unclear why the α sugar-binding site of EW29Ch binds to lactose much more strongly because the crystal structure of lactose-bound EW29Ch showed that the interaction between the α sugar-binding site and lactose was almost same as that between the γ sugar-binding site and lactose. In the present study, we have determined the NMR structure of EW29Ch in the sugar-free state and performed (15)N relaxation experiments for EW29Ch in both the sugar-free state and the lactose-bound states. The conformation of EW29Ch in the sugar-free state was similar to that of EW29Ch in complex with lactose. Conformational changes upon binding of lactose were observed only for the α sugar-binding site. By contrast, the (15)N relaxation experiments revealed a conformational exchange at the α sugar-binding site in the sugar-free state, which was suppressed in the lactose-bound state. The conformational exchange phenomenon observed for the α sugar-binding site was not observed for the γ sugar-binding site. Differences in the conformational change and the backbone dynamics between subdomains α and γ may be associated with the difference of the sugar-binding modes between the two sugar-binding sites. Structural data for the NMR structure of EW29Ch in the sugar-free state have been deposited in the Protein Data Bank database under accession number 2RST.


  • Organizational Affiliation

    National Food Research Institute, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan. hemmi@affrc.go.jp


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
29-kDa galactose-binding lectin132Lumbricus terrestrisMutation(s): 0 
UniProt
Find proteins for O96048 (Lumbricus terrestris)
Explore O96048 
Go to UniProtKB:  O96048
Entity Groups  
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UniProt GroupO96048
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2013-04-17 
  • Deposition Author(s): Hemmi, H.

Revision History  (Full details and data files)

  • Version 1.0: 2013-04-17
    Type: Initial release
  • Version 1.1: 2023-06-14
    Changes: Data collection, Database references, Other
  • Version 1.2: 2024-05-15
    Changes: Data collection, Database references