2DRY

Crystal structure of the earthworm lectin C-terminal domain mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.234 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Tailoring a novel sialic acid-binding lectin from a ricin-B chain-like galactose-binding protein by natural evolution-mimicry

Yabe, R.Suzuki, R.Kuno, A.Fujimoto, Z.Jigami, Y.Hirabayashi, J.

(2007) J Biochem 141: 389-399

  • DOI: https://doi.org/10.1093/jb/mvm043
  • Primary Citation of Related Structures:  
    2DRY, 2DRZ, 2DS0

  • PubMed Abstract: 

    Sialic acid (Sia) is a typical terminal sugar, which modifies various types of glycoconjugates commonly found in higher animals. Its regulatory roles in diverse biological phenomena are frequently triggered by interaction with Sia-binding lectins. When using natural Sia-binding lectins as probes, however, there have been practical problems concerning their repertoire and availability. Here, we show a rational creation of a Sia-binding lectin based on the strategy 'natural evolution-mimicry', where Sia-binding lectins are engineered by error-prone PCR from a Gal-binding lectin used as a scaffold protein. After selection with fetuin-agarose using a recently reinforced ribosome display system, one of the evolved mutants SRC showed substantial affinity for alpha2-6Sia, which the parental Gal-binding lectin EW29Ch lacked. SRC was found to have additional practical advantages in productivity and in preservation of affinity for Gal. Thus, the developed novel Sia-recognition protein will contribute as useful tools to sialoglycomics.


  • Organizational Affiliation

    Research Center for Glycoscience, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8568, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
29-kDa galactose-binding lectin
A, B
130Lumbricus terrestrisMutation(s): 6 
UniProt
Find proteins for O96048 (Lumbricus terrestris)
Explore O96048 
Go to UniProtKB:  O96048
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO96048
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.234 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.151α = 90
b = 89.562β = 116.39
c = 41.67γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-02-06
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-10-25
    Changes: Data collection, Refinement description