3AP7

Crystal structure of the galectin-8 N-terminal carbohydrate recognition domain in complex with lactose sialic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Galectin-8-N-domain recognition mechanism for sialylated and sulfated glycans

Ideo, H.Matsuzaka, T.Nonaka, T.Seko, A.Yamashita, K.

(2011) J.Biol.Chem. 286: 11346-11355

  • DOI: 10.1074/jbc.M110.195925
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Galectin-8 has much higher affinity for 3'-O-sulfated or 3'-O-sialylated glycoconjugates and a Lewis X-containing glycan than for oligosaccharides terminating in Galβ1→3/4GlcNAc, and this specificity is mainly attributed to the N-terminal carbohydrat ...

    Galectin-8 has much higher affinity for 3'-O-sulfated or 3'-O-sialylated glycoconjugates and a Lewis X-containing glycan than for oligosaccharides terminating in Galβ1→3/4GlcNAc, and this specificity is mainly attributed to the N-terminal carbohydrate recognition domain (N-domain, CRD) (Ideo, H., Seko, A., Ishizuka, I., and Yamashita, K. (2003) Glycobiology 13, 713-723). In this study, we elucidated the crystal structures of the human galectin-8-N-domain (-8N) in the absence or presence of 4 ligands. The apo molecule forms a dimer, which is different from the canonical 2-fold symmetric dimer observed for galectin-1 and -2. In a galectin-8N-lactose complex, the lactose-recognizing amino acids are highly conserved among the galectins. However, Arg(45), Gln(47), Arg(59), and the long loop region between the S3 and S4 β-strands are unique to galectin-8N. These amino acids directly or indirectly interact with the sulfate or sialic acid moieties of 3'-sialyl- and 3'-sulfolactose complexed with galectin-8N. Furthermore, in the LNF-III-galectin-8N complex, van der Waals interactions occur between the α1-3-branched fucose and galactose and between galactose and Tyr(141), and these interactions increase the affinity toward galectin-8N. Based on the findings of these x-ray crystallographic analyses, a mutagenesis study using surface plasmon resonance showed that Arg(45), Gln(47), and Arg(59) of galectin-8N are indispensable and coordinately contribute to the strong binding of galectins-8N to sialylated and sulfated oligosaccharides. Arg(59) is the most critical amino acid for binding in the S3-S4 loop region.


    Organizational Affiliation

    Innovative Research Initiatives, Tokyo Institute of Technology, Yokohama, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Galectin-8
A
154Homo sapiensMutation(s): 0 
Gene Names: LGALS8
Find proteins for O00214 (Homo sapiens)
Go to Gene View: LGALS8
Go to UniProtKB:  O00214
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
LAT
Query on LAT

Download SDF File 
Download CCD File 
A
BETA-LACTOSE
C12 H22 O11
GUBGYTABKSRVRQ-DCSYEGIMSA-N
 Ligand Interaction
SIA
Query on SIA

Download SDF File 
Download CCD File 
A
O-SIALIC ACID
C11 H19 N O9
SQVRNKJHWKZAKO-YRMXFSIDSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LATKd: 62000 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.164 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 46.360α = 90.00
b = 49.917β = 90.00
c = 70.289γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
SCALAdata scaling
ADSCdata collection
MOSFLMdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-01-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-01-15
    Type: Database references