6BYF

Crystal structure of the core catalytic domain of PP-IP phosphatase SIW14 from S. cerevisiae in complex with citrate

Summary for 6BYF

• Entry DOI: 10.2210/pdb6byf/pdb
• Descriptor: Tyrosine-protein phosphatase SIW14, CITRIC ACID, 1,2-ETHANEDIOL, ... (5 entities in total)
• Functional Keywords: protein tyrosine phosphatase, phosphatase, inositol, inositol polyphosphate, inositol pyrophosphate, substrate specificity, transferase
• Biological source: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
• Cellular location: Cytoplasm : P53965
• Total number of polymer chains: 9
• Total formula weight: 181406.55

Authors

Wang, H.,Shears, S.B. (deposition date: 2017-12-20, release date: 2018-03-21, Last modification date: 2022-03-16)

Primary citation

Wang, H.,Gu, C.,Rolfes, R.J.,Jessen, H.J.,Shears, S.B.
Structural and biochemical characterization of Siw14: A protein-tyrosine phosphatase fold that metabolizes inositol pyrophosphates.
J. Biol. Chem., 293:6905-6914, 2018

PubMed Abstract: Inositol pyrophosphates (PP-InsPs) are "energetic" intracellular signals that are ubiquitous in animals, plants, and fungi; structural and biochemical characterization of PP-InsP metabolic enzymes provides insight into their evolution, reaction mechanisms, and regulation. Here, we describe the 2.35-Å-resolution structure of the catalytic core of Siw14, a 5-PP-InsP phosphatase from and a member of the protein tyrosine-phosphatase (PTP) superfamily. Conclusions that we derive from structural data are supported by extensive site-directed mutagenesis and kinetic analyses, thereby attributing new functional significance to several key residues. We demonstrate the high activity and exquisite specificity of Siw14 for the 5-diphosphate group of PP-InsPs. The three structural elements that demarcate a 9.2-Å-deep substrate-binding pocket each have spatial equivalents in PTPs, but we identify how these are specialized for Siw14 to bind and hydrolyze the intensely negatively charged PP-InsPs. () The catalytic P-loop with the CR(S/T) PTP motif contains additional, positively charged residues. () A loop between the α5 and α6 helices, corresponding to the Q-loop in PTPs, contains a lysine and an arginine that extend into the catalytic pocket due to displacement of the α5 helix orientation through intramolecular crowding caused by three bulky, hydrophobic residues. () The general-acid loop in PTPs is replaced in Siw14 with a flexible loop that does not use an aspartate or glutamate as a general acid. We propose that an acidic residue is not required for phosphoanhydride hydrolysis.

PubMed: 29540476
DOI: 10.1074/jbc.RA117.001670

Experimental method

X-RAY DIFFRACTION (2.35 Å)