5U38

Crystal structure of native lectin from Platypodium elegans seeds (PELa) complexed with Man1-3Man-OMe.

5U38 の概要

• エントリーDOI: 10.2210/pdb5u38/pdb
• 分子名称: Lectin, alpha-D-mannopyranose-(1-3)-methyl alpha-D-mannopyranoside, 2-acetamido-2-deoxy-beta-D-glucopyranose, ... (6 entities in total)
• 機能のキーワード: platypodium elegans, lectin, man1-3man-ome, sugar binding protein
• 由来する生物種: Platypodium elegans
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 27403.07

構造登録者

Silva, I.B.,Araripe, D.A.,Neco, A.H.B.,Pinto-Junior, V.R.,Osterne, V.J.S.,Santiago, M.Q.,Silva-Filho, J.C.,Leal, R.B.,Rocha, C.R.C.,Nascimento, K.S.,Cavada, B.S. (登録日: 2016-12-01, 公開日: 2017-10-04, 最終更新日: 2024-11-13)

主引用文献

Cavada, B.S.,Araripe, D.A.,Silva, I.B.,Pinto-Junior, V.R.,Osterne, V.J.S.,Neco, A.H.B.,Laranjeira, E.P.P.,Lossio, C.F.,Correia, J.L.A.,Pires, A.F.,Assreuy, A.M.S.,Nascimento, K.S.
Structural studies and nociceptive activity of a native lectin from Platypodium elegans seeds (nPELa).
Int. J. Biol. Macromol., 107:236-246, 2018

PubMed Abstract: A native lectin (nPELa), purified from seeds of the species Platypodium elegans, Dalbergieae tribe, was crystallized and structurally characterized by X-ray diffraction crystallography and bioinformatics tools. The obtained crystals diffracted to 1.6Å resolution, and nPELa structure were solved through molecular substitution. In addition, nPELa has a metal binding site and a conserved carbohydrate recognition domain (CRD) similar to other Dalbergieae tribe lectins, such as PAL (Pterocarpus angolensis) and CTL (Centrolobium tomentosum). Molecular docking analysis indicated high affinity of this lectin for different mannosides, mainly trimannosides, formed by α-1,3 or α-1,6 glycosidic bond, as evidenced by the obtained scores. In addition, molecular dynamics simulations were performed to demonstrate the structural behavior of nPELa in aqueous solution. In solution, nPELa was highly stable, and structural modifications in its carbohydrate recognition site allowed interaction between the lectin and the different ligands. Different modifications were observed during simulations for each one of the glycans, which included different hydrogen bonds and hydrophobic interactions through changes in the relevant residues. In addition, nPELa was evaluated for its nociceptive activity in mice and was reported to be the first lectin of the Dalbergieae tribe to show CRD-dependent hypernociceptive activity.

PubMed: 28867234
DOI: 10.1016/j.ijbiomac.2017.08.174

実験手法

X-RAY DIFFRACTION (1.6 Å)