3I9O

Crystal structure of ADP ribosyl cyclase complexed with ribo-2'F-ADP ribose

Summary for 3I9O

• Entry DOI: 10.2210/pdb3i9o/pdb
• Descriptor: ADP-ribosyl cyclase, [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3R,4S)-4-fluoro-3-hydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (2 entities in total)
• Functional Keywords: homodimer, enzyme-reaction-intermediate complex, adp-ribosyl cyclase, disulfide bond, fertilization, hydrolase, nad
• Biological source: Aplysia californica (California sea hare)
• Cellular location: Cytoplasmic vesicle: P29241
• Total number of polymer chains: 2
• Total formula weight: 60250.50

Authors

Graeff, R.,Liu, Q.,Kriksunov, I.A.,Kotaka, M.,Oppenheimer, N.,Hao, Q.,Lee, H.C. (deposition date: 2009-07-12, release date: 2009-07-28, Last modification date: 2023-11-01)

Primary citation

Graeff, R.,Liu, Q.,Kriksunov, I.A.,Kotaka, M.,Oppenheimer, N.,Hao, Q.,Lee, H.C.
Mechanism of cyclizing NAD to cyclic ADP-ribose by ADP-ribosyl cyclase and CD38
J.Biol.Chem., 284:27629-27636, 2009

PubMed Abstract: Mammalian CD38 and its Aplysia homolog, ADP-ribosyl cyclase (cyclase), are two prominent enzymes that catalyze the synthesis and hydrolysis of cyclic ADP-ribose (cADPR), a Ca(2+) messenger molecule responsible for regulating a wide range of cellular functions. Although both use NAD as a substrate, the cyclase produces cADPR, whereas CD38 produces mainly ADP-ribose (ADPR). To elucidate the catalytic differences and the mechanism of cyclizing NAD, the crystal structure of a stable complex of the cyclase with an NAD analog, ribosyl-2'F-2'deoxynicotinamide adenine dinucleotide (ribo-2'-F-NAD), was determined. The results show that the analog was a substrate of the cyclase and that during the reaction, the nicotinamide group was released and a stable intermediate was formed. The terminal ribosyl unit at one end of the intermediate formed a close linkage with the catalytic residue (Glu-179), whereas the adenine ring at the other end stacked closely with Phe-174, suggesting that the latter residue is likely to be responsible for folding the linear substrate so that the two ends can be cyclized. Mutating Phe-174 indeed reduced cADPR production but enhanced ADPR production, converting the cyclase to be more CD38-like. Changing the equivalent residue in CD38, Thr-221 to Phe, correspondingly enhanced cADPR production, and the double mutation, Thr-221 to Phe and Glu-146 to Ala, effectively converted CD38 to a cyclase. This study provides the first detailed evidence of the cyclization process and demonstrates the feasibility of engineering the reactivity of the enzymes by mutation, setting the stage for the development of tools to manipulate cADPR metabolism in vivo.

PubMed: 19640843
DOI: 10.1074/jbc.M109.030965

Experimental method

X-RAY DIFFRACTION (3 Å)