2F5X

Structure of periplasmic binding protein BugD

2F5X の概要

• エントリーDOI: 10.2210/pdb2f5x/pdb
• 分子名称: BugD, ASPARTIC ACID (3 entities in total)
• 機能のキーワード: periplasmic binding protein, transport protein
• 由来する生物種: Bordetella pertussis Tohama I
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 102490.35

構造登録者

Huvent, I.,Belrhali, H.,Antoine, R.,Bompard, C.,Jacob-Dubuisson, F.,Villeret, V. (登録日: 2005-11-28, 公開日: 2006-01-24, 最終更新日: 2024-11-20)

主引用文献

Huvent, I.,Belrhali, H.,Antoine, R.,Bompard, C.,Locht, C.,Jacob-Dubuisson, F.,Villeret, V.
Crystal Structure of Bordetella pertussis BugD Solute Receptor Unveils the Basis of Ligand Binding in a New Family of Periplasmic Binding Proteins
J.Mol.Biol., 356:1014-1026, 2006

PubMed Abstract: Periplasmic binding proteins of a new family particularly well represented in Bordetella pertussis have been called Bug receptors. One B.pertussis Bug protein is part of a tripartite tricarboxylate transporter while the functions of the other 77 are unknown. We report the first structure of a Bug receptor, BugD. It adopts the characteristic Venus flytrap motif observed in other periplasmic binding proteins, with two globular domains bisected by a deep cleft. BugD displays a closed conformation resulting from the fortuitous capture of a ligand, identified from the electron density as an aspartate. The structure reveals a distinctive alpha carboxylate-binding motif, involving two water molecules that bridge the carboxylate oxygen atoms to the protein. Both water molecules are hydrogen bonded to a common carbonyl group from Ala14, and each forms a hydrogen bond with one carboxylate oxygen atom of the ligand. Additional hydrogen bonds are found between the ligand alpha carboxylate oxygen atoms and protein backbone amide groups and with a threonine hydroxyl group. This specific ligand-binding motif is highly conserved in Bug proteins, indicating that they may all be receptors of amino acids or other carboxylated solutes, with a similar binding mode. The present structure thus unveils the bases of ligand binding in this large family of periplasmic binding proteins, several hundred members of which have been identified in various bacterial species.

PubMed: 16403514
DOI: 10.1016/j.jmb.2005.11.096

実験手法

X-RAY DIFFRACTION (1.72 Å)