1KHZ

Structure of the ADPR-ase in complex with AMPCPR and Mg

Summary for 1KHZ

• Entry DOI: 10.2210/pdb1khz/pdb
• Related: 1G0S 1G9Q 1GA7
• Descriptor: ADP-ribose pyrophosphatase, CHLORIDE ION, MAGNESIUM ION, ... (5 entities in total)
• Functional Keywords: nudix, adp-ribose pyrophosphatase, ampcpr, hydrolase
• Biological source: Escherichia coli
• Total number of polymer chains: 2
• Total formula weight: 48057.27

Authors

Gabelli, S.B.,Bianchet, M.A.,Bessman, M.J.,Amzel, L.M. (deposition date: 2001-12-01, release date: 2002-10-09, Last modification date: 2024-02-14)

Primary citation

Gabelli, S.B.,Bianchet, M.A.,Ohnishi, Y.,Ichikawa, Y.,Bessman, M.J.,Amzel, L.M.
Mechanism of the Escherichia coli ADP-ribose pyrophosphatase, a Nudix hydrolase.
Biochemistry, 41:9279-9285, 2002

PubMed Abstract: Escherichia coli ADP-ribose (ADPR) pyrophosphatase (ADPRase), a Nudix enzyme, catalyzes the Mg(2+)-dependent hydrolysis of ADP-ribose to AMP and ribose 5-phosphate. ADPR hydrolysis experiments conducted in the presence of H(2)(18)O and analyzed by electrospray mass spectrometry showed that the ADPRase-catalyzed reaction takes place through nucleophilic attack at the adenosyl phosphate. The structure of ADPRase in complex with Mg(2+) and a nonhydrolyzable ADPR analogue, alpha,beta-methylene ADP-ribose, reveals an active site water molecule poised for nucleophilic attack on the adenosyl phosphate. This water molecule is activated by two magnesium ions, and its oxygen contacts the target phosphorus (P-O distance of 3.0 A) and forms an angle of 177 degrees with the scissile bond, suggesting an associative mechanism. A third Mg(2+) ion bridges the two phosphates and could stabilize the negative charge of the leaving group, ribose 5-phosphate. The structure of the ternary complex also shows that loop L9 moves fully 10 A from its position in the free enzyme, forming a tighter turn and bringing Glu 162 to its catalytic position. These observations indicate that as part of the catalytic mechanism, the ADPRase cycles between an open (free enzyme) and a closed (substrate-metal complex) conformation. This cycling may be important in preventing nonspecific hydrolysis of other nucleotides.

PubMed: 12135348
DOI: 10.1021/bi0259296

Experimental method

X-RAY DIFFRACTION (2.04 Å)