6M5M image
Entry Detail
PDB ID:
6M5M
Title:
SPL-1 - GlcNAc complex
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2020-03-11
Release Date:
2020-06-10
Method Details:
Experimental Method:
Resolution:
1.70 Å
R-Value Free:
0.21
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
P 65
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:N-acetylglucosamine-specific lectin
Chain IDs:A
Chain Length:158
Number of Molecules:1
Biological Source:Saxidomus purpuratus
Polymer Type:polypeptide(L)
Description:N-acetylglucosamine-specific lectin
Chain IDs:B
Chain Length:159
Number of Molecules:1
Biological Source:Saxidomus purpuratus
Primary Citation
Novel carbohydrate-recognition mode of the invertebrate C-type lectin SPL-1 from Saxidomus purpuratus revealed by the GlcNAc-complex crystal in the presence of Ca2.
Acta Crystallogr.,Sect.F 76 271 277 (2020)
PMID: 32510468 DOI: 10.1107/S2053230X20007256

Abstact

The C-type lectins SPL-1 and SPL-2 from the bivalve Saxidomus purpuratus are composed of A and B chains and of two B chains, respectively. They bind specific carbohydrates containing acetamido groups, such as N-acetylglucosamine (GlcNAc) and N-acetylgalactosamine (GalNAc), in a Ca2+-independent manner. Unlike ordinary C-type lectins, which require Ca2+ ions for carbohydrate recognition, these lectins recognize specific carbohydrates mainly through interactions with the acetamido group without Ca2+ ions, even though Ca2+ enhances the binding affinity of these lectins, especially SPL-1. In the present study, the crystal structure of the SPL-1-GlcNAc complex in the presence of Ca2+ revealed that the binding of SPL-1 to GlcNAc is stabilized by hydrogen bonds to the water molecule(s) coordinating Ca2+, whereas in ordinary C-type lectins Ca2+ directly forms coordinate bonds to the hydroxy groups of carbohydrates. These differences may also allow SPL-1 and SPL-2 to recognize both GlcNAc and GalNAc, which have different orientations of the 4-hydroxy group.

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