5T7P

Crystal structure of Pisum arvense lectin (PAL) complexed with X-Man

Summary for 5T7P

• Entry DOI: 10.2210/pdb5t7p/pdb
• Descriptor: Lectin, MANGANESE (II) ION, CALCIUM ION, ... (5 entities in total)
• Functional Keywords: pisum arvense, lectin, pal, x-man., sugar binding protein
• Biological source: Pisum sativum (Garden pea)
• Total number of polymer chains: 2
• Total formula weight: 53046.52

Authors

Pinto-Junior, V.R.,Santiago, M.Q.,Osterne, V.J.S.,Silva-Filho, J.C.,Rocha, B.A.M.,Delatorre, P.,Nascimento, K.S.,Cavada, B.S. (deposition date: 2016-09-05, release date: 2017-08-09, Last modification date: 2023-10-04)

Primary citation

Pinto-Junior, V.R.,Santiago, M.Q.,Nobre, C.B.,Osterne, V.J.S.,Leal, R.B.,Cajazeiras, J.B.,Lossio, C.F.,Rocha, B.A.M.,Martins, M.G.Q.,Nobre, C.A.S.,Silva, M.T.L.,Nascimento, K.S.,Cavada, B.S.
Crystal structure of Pisum arvense seed lectin (PAL) and characterization of its interaction with carbohydrates by molecular docking and dynamics.
Arch. Biochem. Biophys., 630:27-37, 2017

PubMed Abstract: The Pisum arvense lectin (PAL), a legume protein belonging to the Vicieae tribe, is capable of specific recognition of mannose, glucose and its derivatives without altering its structure. In this work, the three-dimensional structure of PAL was determined by X-ray crystallography and studied in detail by a combination of molecular docking and molecular dynamics (MD). Crystals belonging to monoclinic space group P2 were grown by the vapor diffusion method at 293 K. The structure was solved at 2.16 Å and was similar to that of other Vicieae lectins. The structure presented R and R of 17.04% and 22.08%, respectively, with all acceptable geometric parameters. Molecular docking was performed to analyze interactions of the lectin with monosaccharides, disaccharides and high-mannose N-glycans. PAL demonstrated different affinities on carbohydrates, depending on bond orientation and glycosidic linkage present in ligands. Furthermore, the lectin interacted with representative N-glycans in a manner consistent with the biological effects described for Vicieae lectins. Carbohydrate-recognition domain (CRD) in-depth analysis was performed by MD, describing the behavior of CRD residues in complex with ligand, stability, flexibility of the protein over time, CRD volume and topology. This is a first report of its kind for a lectin of the Vicieae tribe.

PubMed: 28754321
DOI: 10.1016/j.abb.2017.07.013

Experimental method

X-RAY DIFFRACTION (2.16 Å)