PDBsum entry 2ds0

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Sugar binding protein PDB id
Protein chains
130 a.a.
SO4 ×5
Waters ×211
PDB id:
Name: Sugar binding protein
Title: Crystal structure of the earthworm lectin c-terminal domain mutant in complex with 6'-sialyllactose
Structure: 29-kda galactose-binding lectin. Chain: a, b. Fragment: c-terminal domain. Engineered: yes. Mutation: yes
Source: Lumbricus terrestris. Common earthworm. Organism_taxid: 6398. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
1.80Å     R-factor:   0.209     R-free:   0.241
Authors: R.Suzuki,Z.Fujimoto
Key ref: R.Yabe et al. (2007). Tailoring a novel sialic acid-binding lectin from a ricin-B chain-like galactose-binding protein by natural evolution-mimicry. J Biochem, 141, 389-399. PubMed id: 17234683 DOI: 10.1093/jb/mvm043
16-Jun-06     Release date:   06-Feb-07    
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Protein chains
Pfam   ArchSchema ?
O96048  (O96048_LUMTE) -  29-kDa galactose-binding lectin
260 a.a.
130 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 6 residue positions (black crosses)


DOI no: 10.1093/jb/mvm043 J Biochem 141:389-399 (2007)
PubMed id: 17234683  
Tailoring a novel sialic acid-binding lectin from a ricin-B chain-like galactose-binding protein by natural evolution-mimicry.
R.Yabe, R.Suzuki, A.Kuno, Z.Fujimoto, Y.Jigami, J.Hirabayashi.
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.

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21544837 J.Hirabayashi, A.Kuno, and H.Tateno (2011).
Lectin-based structural glycomics: A practical approach to complex glycans.
  Electrophoresis, 32, 1118-1128.  
19292877 H.Hemmi, A.Kuno, S.Ito, R.Suzuki, T.Hasegawa, and J.Hirabayashi (2009).
NMR studies on the interaction of sugars with the C-terminal domain of an R-type lectin from the earthworm Lumbricus terrestris.
  FEBS J, 276, 2095-2105.  
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