3NYE

Crystal Structure of Pseudomonas aeruginosa D-Arginine Dehydrogenase in Complex with Imino-Arginine

3NYE の概要

• エントリーDOI: 10.2210/pdb3nye/pdb
• 関連するPDBエントリー: 3NYC 3NYF
• 分子名称: D-Arginine Dehydrogenase, FLAVIN-ADENINE DINUCLEOTIDE, (2E)-5-[(diaminomethylidene)amino]-2-iminopentanoic acid, ... (4 entities in total)
• 機能のキーワード: d-arginine dehydrogenase, fad, imino-arginine, oxidoreductase
• 由来する生物種: Pseudomonas aeruginosa
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 42363.24

構造登録者

Fu, G.,Weber, I.T. (登録日: 2010-07-14, 公開日: 2010-09-15, 最終更新日: 2023-09-06)

主引用文献

Fu, G.,Yuan, H.,Li, C.,Lu, C.D.,Gadda, G.,Weber, I.T.
Conformational changes and substrate recognition in Pseudomonas aeruginosa D-arginine dehydrogenase.
Biochemistry, 49:8535-8545, 2010

PubMed Abstract: DADH catalyzes the flavin-dependent oxidative deamination of d-amino acids to the corresponding α-keto acids and ammonia. Here we report the first X-ray crystal structures of DADH at 1.06 Å resolution and its complexes with iminoarginine (DADH(red)/iminoarginine) and iminohistidine (DADH(red)/iminohistidine) at 1.30 Å resolution. The DADH crystal structure comprises an unliganded conformation and a product-bound conformation, which is almost identical to the DADH(red)/iminoarginine crystal structure. The active site of DADH was partially occupied with iminoarginine product (30% occupancy) that interacts with Tyr53 in the minor conformation of a surface loop. This flexible loop forms an "active site lid", similar to those seen in other enzymes, and may play an essential role in substrate recognition. The guanidinium side chain of iminoarginine forms a hydrogen bond interaction with the hydroxyl of Thr50 and an ionic interaction with Glu87. In the structure of DADH in complex with iminohistidine, two alternate conformations were observed for iminohistidine where the imidazole groups formed hydrogen bond interactions with the side chains of His48 and Thr50 and either Glu87 or Gln336. The different interactions and very distinct binding modes observed for iminoarginine and iminohistidine are consistent with the 1000-fold difference in k(cat)/K(m) values for d-arginine and d-histidine. Comparison of the kinetic data for the activity of DADH on different d-amino acids and the crystal structures in complex with iminoarginine and iminohistidine establishes that this enzyme is characterized by relatively broad substrate specificity, being able to oxidize positively charged and large hydrophobic d-amino acids bound within a flask-like cavity.

PubMed: 20809650
DOI: 10.1021/bi1005865

実験手法

X-RAY DIFFRACTION (1.3 Å)