5HRU

Crystal structure of Plasmodium vivax LDH in complex with a DNA aptamer called pL1

5HRU の概要

• エントリーDOI: 10.2210/pdb5hru/pdb
• 関連するPDBエントリー: 5HS4 5HTO
• 分子名称: L-lactate dehydrogenase, DNA (32-MER), MAGNESIUM ION, ... (4 entities in total)
• 機能のキーワード: dna aptamer, plasmodium ldh, malaria, dna structural element, oxidoreductase-dna complex, oxidoreductase/dna
• 由来する生物種: Plasmodium vivax; 詳細
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 85287.99

構造登録者

Choi, S.J.,Ban, C. (登録日: 2016-01-24, 公開日: 2016-10-19, 最終更新日: 2023-11-08)

主引用文献

Choi, S.J.,Ban, C.
Crystal structure of a DNA aptamer bound to PvLDH elucidates novel single-stranded DNA structural elements for folding and recognition
Sci Rep, 6:34998-34998, 2016

PubMed Abstract: Structural elements are key elements for understanding single-stranded nucleic acid folding. Although various RNA structural elements have been documented, structural elements of single-stranded DNA (ssDNA) have rarely been reported. Herein, we determined a crystal structure of PvLDH in complex with a DNA aptamer called pL1. This aptamer folds into a hairpin-bulge contact by adopting three novel structural elements, viz, DNA T-loop-like motif, base-phosphate zipper, and DNA G·G metal ion zipper. Moreover, the pL1:PvLDH complex shows unique properties compared with other protein:nucleic acid complexes. Generally, extensive intermolecular hydrogen bonds occur between unpaired nucleotides and proteins for specific recognitions. Although most protein-interacting nucleotides of pL1 are unpaired nucleotides, pL1 recognizes PvLDH by predominant shape complementarity with many bridging water molecules owing to the combination of three novel structural elements making protein-binding unpaired nucleotides stable. Moreover, the additional set of Plasmodium LDH residues which were shown to form extensive hydrogen bonds with unpaired nucleotides of 2008s does not participate in the recognition of pL1. Superimposition of the pL1:PvLDH complex with hLDH reveals steric clashes between pL1 and hLDH in contrast with no steric clashes between 2008s and hLDH. Therefore, specific protein recognition mode of pL1 is totally different from that of 2008s.

PubMed: 27725738
DOI: 10.1038/srep34998

実験手法

X-RAY DIFFRACTION (1.71 Å)