5XFH

Crystal structure of Orysata lectin in complex with biantennary N-glycan

Summary for 5XFH

• Entry DOI: 10.2210/pdb5xfh/pdb
• Related: 5XFI
• Descriptor: Salt stress-induced protein, beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose (3 entities in total)
• Functional Keywords: lectin, jacalin-related lectin, n-glycan, glycobiology, sugar binding protein
• Biological source: Oryza sativa Japonica Group (Rice)
• Total number of polymer chains: 2
• Total formula weight: 31500.98

Authors

Nagae, M.,Yamaguchi, Y. (deposition date: 2017-04-10, release date: 2017-10-18, Last modification date: 2023-11-22)

Primary citation

Nagae, M.,Mishra, S.K.,Hanashima, S.,Tateno, H.,Yamaguchi, Y.
Distinct roles for each N-glycan branch interacting with mannose-binding type Jacalin-related lectins Orysata and Calsepa.
Glycobiology, 27:1120-1133, 2017

PubMed Abstract: Mannose-binding type Jacalin-related lectins (mJRLs) bind to branched N-glycans via conserved sugar-binding sites. Despite, significant 3D structural similarities, each mJRL is known to have a unique binding preference toward various N-glycans. However, the molecular basis of varying binding preference is substantially unknown. Here, we report a detailed comparison of N-glycan-binding preference for two mJRLs, Orysata and Calsepa using frontal affinity chromatography (FAC), X-ray and molecular modeling. The FAC analysis using a panel of N-glycans shows difference in N-glycan-binding preference between the lectins. Orysata shows broader specificity toward most high-mannose-type glycans as well as biantennary complex-type glycans bearing an extension on the Manα1-6 branch. Whereas, Calsepa shows narrow specificity to complex-type glycans with bisecting GlcNAc. The X-ray crystallographic structure reveals that two Orysata lectins bind to one biantennary N-glycan (2:1 binding) where one lectin binds to mannose of the α1-3 branch, while the other interacts with an N-acetylglucosamine of the α1-6 branch. In contrast, Calsepa shows 1:1 binding where α1-3 branch and core chitobiose region N-glycan interacts with lectin, while α1-6 branch is flipped-back to the chitobiose core. Molecular dynamics study of Orysata bound to N-glycans substantiate possibility of two-binding modes for each N-glycan. Binding free energies calculated separately for α1-3 and α1-6 branches of each N-glycan suggest both branches can bind to Orysata. Overall these results suggest that each branch of N-glycan has a distinct role in binding to mJRLs and the nonbinding branch can contribute significantly to the binding affinity and hence to the specificity.

PubMed: 28973127
DOI: 10.1093/glycob/cwx081

Experimental method

X-RAY DIFFRACTION (1.903 Å)