6AHG

Trimeric structure of concanavalin A from Canavalia ensiformis

Summary for 6AHG

• Entry DOI: 10.2210/pdb6ahg/pdb
• Descriptor: Concanavalin-A,Concanavalin-A, CALCIUM ION, CADMIUM ION, ... (4 entities in total)
• Functional Keywords: concanavalin a, sugar binding protein
• Biological source: Canavalia ensiformis (Jack bean); More
• Total number of polymer chains: 3
• Total formula weight: 77661.85

Authors

Park, J.H.,Kim, D.S.,Park, Y.R.,Lee, S.J. (deposition date: 2018-08-18, release date: 2018-11-21, Last modification date: 2025-03-12)

Primary citation

Park, Y.R.,Kim, D.S.,Lee, D.H.,Kang, H.G.,Park, J.H.,Lee, S.J.
Cadmium-substituted concanavalin A and its trimeric complexation
J. Microbiol. Biotechnol., 28(12):2106-2112, 2018

PubMed Abstract: Concanavalin A (ConA) interacts with carbohydrates as a lectin, and recent reports proposed its application for detecting a diversity of viruses and pathogens. Structural studies have detailed the interaction between ConA and carbohydrates and the metal coordination environment with manganese and calcium ions (Mn-Ca-ConA). In this study, ConA was crystallized with a cadmium-containing precipitant, and the refined structure indicates that Mn²⁺ was replaced by Cd²⁺ (Cd-Ca-ConA). The structural comparison with ConA demonstrates that the metal-coordinated residues of Cd-Ca-ConA, that is Glu8, Asp10, Asn14, Asp19, and His24, do not have conformational shifts, but residues for sugar binding, including Arg228, Tyr100, and Leu99, reorient their side chains, slightly. Previous studies demonstrated that excess cadmium ions can coordinate with other residues, including Glu87 and Glu183, which were not coordinated with Cd²⁺ in this study. The trimeric ConA in this study coordinated Cd²⁺ with other residues, including Asp80 and Asp82, for the complex generation. The monomers does not have specific interaction near interface regions with the other monomer, but secondary cadmium coordinated with two aspartates (Asp80 and Asp82) from monomer 1 and one aspartate (Asp16) from monomer 2. This study demonstrated that complex generation was induced via coordination with secondary Cd²⁺ and showed the application potential regarding the design of complex formation for specific interactions with target saccharides.

PubMed: 30380822
DOI: 10.4014/jmb.1809.09027

Experimental method

X-RAY DIFFRACTION (2.83 Å)