4Z72

Crystal structure of inorganic pyrophosphatase from Mycobacterium tuberculosis in complex with two phosphate ions

4Z72 の概要

• エントリーDOI: 10.2210/pdb4z72/pdb
• 関連するPDBエントリー: 4Z70 4Z71
• 分子名称: Inorganic pyrophosphatase, PHOSPHATE ION, CALCIUM ION, ... (4 entities in total)
• 機能のキーワード: pyrophosphatase, phosphatase, hydrolase, inorganic pyrophosphate
• 由来する生物種: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
• 細胞内の位置: Cytoplasm : P9WI55
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 19765.04

構造登録者

Pratt, A.C.,Biswas, T.,Barnard-Britson, S.,Tsodikov, O.V. (登録日: 2015-04-06, 公開日: 2015-08-26, 最終更新日: 2023-09-27)

主引用文献

Pratt, A.C.,Dewage, S.W.,Pang, A.H.,Biswas, T.,Barnard-Britson, S.,Cisneros, G.A.,Tsodikov, O.V.
Structural and computational dissection of the catalytic mechanism of the inorganic pyrophosphatase from Mycobacterium tuberculosis.
J.Struct.Biol., 192:76-87, 2015

PubMed Abstract: Family I inorganic pyrophosphatases (PPiases) are ubiquitous enzymes that are critical for phosphate metabolism in all domains of life. The detailed catalytic mechanism of these enzymes, including the identity of the general base, is not fully understood. We determined a series of crystal structures of the PPiase from Mycobacterium tuberculosis (Mtb PPiase) bound to catalytic metals, inorganic pyrophosphate (PPi; the reaction substrate) and to one or two inorganic phosphate ions (Pi; the reaction product), ranging in resolution from 1.85 to 3.30Å. These structures represent a set of major kinetic intermediates in the catalytic turnover pathway for this enzyme and suggest an order of association and dissociation of the divalent metals, the substrate and the two products during the catalytic turnover. The active site of Mtb PPiase exhibits significant structural differences from the well characterized Escherichia coli PPiase in the vicinity of the bound PPi substrate. Prompted by these differences, quantum mechanics/molecular mechanics (QM/MM) analysis yielded an atomic description of the hydrolysis step for Mtb PPiase and, unexpectedly, indicated that Asp89, rather than Asp54 that was proposed for E. coli PPiase, can abstract a proton from a water molecule to activate it for a nucleophilic attack on the PPi substrate. Mutagenesis studies of the key Asp residues of Mtb PPiase supported this mechanism. This combination of structural and computational analyses clarifies our understanding of the mechanism of family I PPiases and has potential utility for rational development of drugs targeting this enzyme.

PubMed: 26296329
DOI: 10.1016/j.jsb.2015.08.010

実験手法

X-RAY DIFFRACTION (2.352 Å)