2WOD

Crystal Structure of the dinitrogenase reductase-activating glycohydrolase (DRAG) from Rhodospirillum rubrum in complex with ADP- ribsoyllysine

2WOD の概要

• エントリーDOI: 10.2210/pdb2wod/pdb
• 関連するPDBエントリー: 2WOC 2WOE
• 分子名称: ADP-RIBOSYL-[DINITROGEN REDUCTASE] GLYCOHYDROLASE, MANGANESE (II) ION, [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [[(2R,3R)-2,3-DIHYDROXY-4-OXO-PENTOXY]-OXIDO-PHOSPHORYL] PHOSPHATE, ... (6 entities in total)
• 機能のキーワード: hydrolase, nitrogen fixation, dimanganese-dependent, adp-ribosylglycohydrolase, mono-adp-ribosylhydrolase
• 由来する生物種: RHODOSPIRILLUM RUBRUM
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 65901.62

構造登録者

Berthold, C.L.,Wang, H.,Nordlund, S.,Hogbom, M. (登録日: 2009-07-23, 公開日: 2009-08-11, 最終更新日: 2018-01-17)

主引用文献

Berthold, C.L.,Wang, H.,Nordlund, S.,Hogbom, M.
Mechanism of Adp-Ribosylation Removal Revealed by the Structure and Ligand Complexes of the Dimanganese Mono-Adp-Ribosylhydrolase Drag.
Proc.Natl.Acad.Sci.USA, 106:14247-, 2009

PubMed Abstract: ADP-ribosylation is a ubiquitous regulatory posttranslational modification involved in numerous key processes such as DNA repair, transcription, cell differentiation, apoptosis, and the pathogenic mechanism of certain bacterial toxins. Despite the importance of this reversible process, very little is known about the structure and mechanism of the hydrolases that catalyze removal of the ADP-ribose moiety. In the phototrophic bacterium Rhodospirillum rubrum, dinitrogenase reductase-activating glycohydrolase (DraG), a dimanganese enzyme that reversibly associates with the cell membrane, is a key player in the regulation of nitrogenase activity. DraG has long served as a model protein for ADP-ribosylhydrolases. Here, we present the crystal structure of DraG in the holo and ADP-ribose bound forms. We also present the structure of a reaction intermediate analogue and propose a detailed catalytic mechanism for protein de-ADP-ribosylation involving ring opening of the substrate ribose. In addition, the particular manganese coordination in DraG suggests a rationale for the enzyme's preference for manganese over magnesium, although not requiring a redox active metal for the reaction.

PubMed: 19706507
DOI: 10.1073/PNAS.0905906106

実験手法

X-RAY DIFFRACTION (2.25 Å)