3X0J: Adp Ribose Pyrophosphatase From Thermus Thermophilus Hb8 In Apo State At 0.92 Angstrom Resolution

Adenosine diphosphate ribose pyrophosphatase (ADPRase), a member of the Nudix family proteins, catalyzes the metal-induced and concerted general acid-base hydrolysis of ADP ribose (ADPR) into AMP and ribose-5'-phosphate (R5P). The ADPR-hydrolysis reaction of ADPRase from Thermus thermophilus HB8 (TtADPRase) requires divalent metal cations such as Mn(2+), Zn(2+), or Mg(2+) as cofactors. Here, we report the reaction pathway observed in the catalytic center of TtADPRase, based on cryo-trapping X-ray crystallography at atomic resolutions around 1.0 A using Mn(2+) as the reaction trigger, which was soaked into TtADPRase-ADPR binary complex crystals. Integrating 11 structures along the reaction timeline, five reaction states of TtADPRase were assigned, which were ADPRase alone (E), the ADPRase-ADPR binary complex (ES), two ADPRase-ADPR-Mn(2+) reaction intermediates (ESM, ESMM), and the postreaction state (E'). Two Mn(2+) ions were inserted consecutively into the catalytic center of the ES-state and ligated by Glu86 and Glu82, which are highly conserved among the Nudix family, in the ESM- and ESMM-states. The ADPR-hydrolysis reaction was characterized by electrostatic, proximity, and orientation effects, and by preferential binding for the transition state. A new reaction mechanism is proposed, which differs from previous ones suggested from structure analyses with nonhydrolyzable substrate analogues or point-mutated ADPRases.
PDB ID: 3X0JDownload
MMDB ID: 138466
PDB Deposition Date: 2014/10/16
Updated in MMDB: 2016/05
Experimental Method:
x-ray diffraction
Resolution: 0.92  Å
Source Organism:
Similar Structures:
Biological Unit for 3X0J: dimeric; determined by author and by software (PISA)
Molecular Components in 3X0J
Label Count Molecule
Proteins (2 molecules)
Adp-ribose Pyrophosphatase
Molecule annotation
Chemicals (8 molecules)
* Click molecule labels to explore molecular sequence information.

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