PDBsum entry 1v8l

Hydrolase

PDB id: 1v8l

Contents

Protein chain

157 a.a. *

Ligands

APR

Waters ×49

* Residue conservation analysis

PDB id:

1v8l

Name:

Hydrolase

Title:

Structure analysis of the adp-ribose pyrophosphatase complexed with adp-ribose

Structure:

Adp-ribose pyrophosphatase. Chain: a. Engineered: yes

Source:

Thermus thermophilus. Organism_taxid: 274. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PDB file)

Resolution:

2.10Å R-factor: 0.217 R-free: 0.240

Authors:

S.Yoshiba,T.Ooga,N.Nakagawa,T.Shibata,Y.Inoue,S.Yokoyama,S.Kuramitsu, R.Masui,Riken Structural Genomics/proteomics Initiative (Rsgi)

Key ref:

S.Yoshiba et al. (2004). Structural insights into the Thermus thermophilus ADP-ribose pyrophosphatase mechanism via crystal structures with the bound substrate and metal. J Biol Chem, 279, 37163-37174. PubMed id: 15210687 DOI: 10.1074/jbc.M403817200

Date:

10-Jan-04 Release date: 19-Oct-04

Protein chain

Q84CU3  (Q84CU3_THETH) -  ADP-ribose pyrophosphatase from Thermus thermophilus

Seq: 170 a.a.

Struc: 157 a.a.

Enzyme reactions

• Enzyme class: E.C.3.6.1.13 - ADP-ribose diphosphatase.
• Reaction: ADP-D-ribose + H2O = D-ribose 5-phosphate + AMP + 2 H⁺

ADP-D-ribose (Bound ligand (Het Group name = APR) corresponds exactly) + H2O = D-ribose 5-phosphate + AMP + 2 × H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1074/jbc.M403817200

J Biol Chem 279:37163-37174 (2004)

PubMed id: 15210687

Structural insights into the Thermus thermophilus ADP-ribose pyrophosphatase mechanism via crystal structures with the bound substrate and metal.

S.Yoshiba, T.Ooga, N.Nakagawa, T.Shibata, Y.Inoue, S.Yokoyama, S.Kuramitsu, R.Masui.

ABSTRACT

ADP-ribose pyrophosphatase (ADPRase) catalyzes the divalent metal ion-dependent hydrolysis of ADP-ribose to ribose 5'-phosphate and AMP. This enzyme plays a key role in regulating the intracellular ADP-ribose levels, and prevents nonenzymatic ADP-ribosylation. To elucidate the pyrophosphatase hydrolysis mechanism employed by this enzyme, structural changes occurring on binding of substrate, metal and product were investigated using crystal structures of ADPRase from an extreme thermophile, Thermus thermophilus HB8. Seven structures were determined, including that of the free enzyme, the Zn(2+)-bound enzyme, the binary complex with ADP-ribose, the ternary complexes with ADP-ribose and Zn(2+) or Gd(3+), and the product complexes with AMP and Mg(2+) or with ribose 5'-phosphate and Zn(2+). The structural and functional studies suggested that the ADP-ribose hydrolysis pathway consists of four reaction states: bound with metal (I), metal and substrate (II), metal and substrate in the transition state (III), and products (IV). In reaction state II, Glu-82 and Glu-70 abstract a proton from a water molecule. This water molecule is situated at an ideal position to carry out nucleophilic attack on the adenosyl phosphate, as it is 3.6 A away from the target phosphorus and almost in line with the scissile bond.

Selected figure(s)

Figure 4.
FIG. 4. Metal binding site. The electron densities of Zn2+ ions (A and B) and Gd^3+ ions (C) derived from the anomalous difference Fourier maps at peak wavelength are superimposed on the models. Metal ions are shown as green balls (Zn) or light green balls (Gd). Water molecules are represented by WA to WD. The geometries of metal coordination are drawn with blue lines, and the distances to the metal ion are shown in Table V.

Figure 8.
FIG. 8. Schematic representation of the reaction mechanism of ADPR hydrolysis. The reaction scheme was proposed based on the active site architecture according to the structural and functional analyses of TtADPRase. Reaction state I is the metal-bound state, II is the ternary complex with substrate and metal, III is the transition state, and IV is the product release state. The nucleophilic attack and proton abstraction events are shown by pink arrows.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 37163-37174) copyright 2004.

Figures were selected by an automated process.