2WOE

Crystal Structure of the D97N variant of dinitrogenase reductase- activating glycohydrolase (DRAG) from Rhodospirillum rubrum in complex with ADP-ribose

Summary for 2WOE

• Entry DOI: 10.2210/pdb2woe/pdb
• Related: 2WOC 2WOD
• Descriptor: ADP-RIBOSYL-[DINITROGEN REDUCTASE] GLYCOHYDROLASE, MANGANESE (II) ION, [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE, ... (6 entities in total)
• Functional Keywords: hydrolase, dimanganese, nitrogen fixation, adp-ribosylglycohydrolase, mono-adp-ribosylhydrolase
• Biological source: RHODOSPIRILLUM RUBRUM
• Total number of polymer chains: 3
• Total formula weight: 98816.25

Authors

Berthold, C.L.,Wang, H.,Nordlund, S.,Hogbom, M. (deposition date: 2009-07-23, release date: 2009-08-18, Last modification date: 2024-05-08)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (1.9 Å)