4YLH

Crystal structure of DpgC with bound substrate analog and Xe on oxygen diffusion pathway

4YLH の概要

• エントリーDOI: 10.2210/pdb4ylh/pdb
• 関連するPDBエントリー: 2NP9 2PG8
• 分子名称: DpgC, XENON, [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL (3R)-4-({3-[(2-{[(3,5-DIHYDROXYPHENYL)ACETYL]AMINO}ETHYL)AMINO]-3-OXOPROPYL}AMINO)-3-HYDROXY-2,2-DIMETHYL-4-OXOBUTYL DIHYDROGEN DIPHOSPHATE, ... (4 entities in total)
• 機能のキーワード: dioxygenase, xe complex, hydrolase
• 由来する生物種: Streptomyces toyocaensis
• タンパク質・核酸の鎖数: 12
• 化学式量合計: 592814.04

構造登録者

Li, K.,Di Russo, N.V.,Condurso, H.L.,Roitberg, A.E.,Bruner, S.D. (登録日: 2015-03-05, 公開日: 2015-08-05, 最終更新日: 2023-09-27)

主引用文献

Di Russo, N.V.,Condurso, H.L.,Li, K.,Bruner, S.D.,Roitberg, A.E.
Oxygen diffusion pathways in a cofactor-independent dioxygenase.
Chem Sci, 6:6341-6348, 2015

PubMed Abstract: Molecular oxygen plays an important role in a wide variety of enzymatic reactions. Through recent research efforts combining computational and experimental methods a new view of O diffusion is emerging, where specific channels guide O to the active site. The focus of this work is DpgC, a cofactor-independent oxygenase. Molecular dynamics simulations, together with mutagenesis experiments and xenon-binding data, reveal that O reaches the active site of this enzyme using three main pathways and four different access points. These pathways connect a series of dynamic hydrophobic pockets, concentrating O at a specific face of the enzyme substrate. Extensive molecular dynamics simulations provide information about which pathways are more frequently used. This data is consistent with the results of kinetic measurements on mutants and is difficult to obtain using computational cavity-location methods. Taken together, our results reveal that although DpgC is rare in its ability of activating O in the absence of cofactors or metals, the way O reaches the active site is similar to that reported for other O-using proteins: multiple access channels are available, and the architecture of the pathway network can provide regio- and stereoselectivity. Our results point to the existence of common themes in O access that are conserved among very different types of proteins.

PubMed: 26508997
DOI: 10.1039/C5SC01638J

実験手法

X-RAY DIFFRACTION (2.58 Å)