3ZVX

STRUCTURE OF THE LECTIN FROM PLATYPODIUM ELEGANS IN COMPLEX WITH A TRIMANNOSIDE

Summary for 3ZVX

• Entry DOI: 10.2210/pdb3zvx/pdb
• Related: 3ZYR
• Descriptor: LECTIN, alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose, MANGANESE (II) ION, ... (7 entities in total)
• Functional Keywords: sugar binding protein, plant lectin, n-glycan
• Biological source: PLATYPODIUM ELEGANS
• Total number of polymer chains: 2
• Total formula weight: 59699.67

Authors

Benevides, R.G.,Ganne, G.,Unverzagt, C.,Cavada, B.S.,Breton, C.,Varrot, A.,Imberty, A. (deposition date: 2011-07-28, release date: 2012-01-11, Last modification date: 2023-12-20)

Primary citation

Benevides, R.G.,Ganne, G.,Simoes, R.D.C.,Schubert, V.,Niemietz, M.,Unverzagt, C.,Chazalet, V.,Breton, C.,Varrot, A.,Cavada, B.S.,Imberty, A.
A Lectin from Platypodium Elegans with Unusual Specificity and Affinity for Asymmetric Complex N-Glycans.
J.Biol.Chem., 287:26352-, 2012

PubMed Abstract: Lectin activity with specificity for mannose and glucose has been detected in the seed of Platypodium elegans, a legume plant from the Dalbergieae tribe. The gene of Platypodium elegans lectin A has been cloned, and the resulting 261-amino acid protein belongs to the legume lectin family with similarity with Pterocarpus angolensis agglutinin from the same tribe. The recombinant lectin has been expressed in Escherichia coli and refolded from inclusion bodies. Analysis of specificity by glycan array evidenced a very unusual preference for complex type N-glycans with asymmetrical branches. A short branch consisting of one mannose residue is preferred on the 6-arm of the N-glycan, whereas extensions by GlcNAc, Gal, and NeuAc are favorable on the 3-arm. Affinities have been obtained by microcalorimetry using symmetrical and asymmetrical Asn-linked heptasaccharides prepared by the semi-synthetic method. Strong affinity with K(d) of 4.5 μm was obtained for both ligands. Crystal structures of Platypodium elegans lectin A complexed with branched trimannose and symmetrical complex-type Asn-linked heptasaccharide have been solved at 2.1 and 1.65 Å resolution, respectively. The lectin adopts the canonical dimeric organization of legume lectins. The trimannose bridges the binding sites of two neighboring dimers, resulting in the formation of infinite chains in the crystal. The Asn-linked heptasaccharide binds with the 6-arm in the primary binding site with extensive additional contacts on both arms. The GlcNAc on the 6-arm is bound in a constrained conformation that may rationalize the higher affinity observed on the glycan array for N-glycans with only a mannose on the 6-arm.

PubMed: 22692206
DOI: 10.1074/JBC.M112.375816

Experimental method

X-RAY DIFFRACTION (2.1 Å)