2B4P

Structure of the D223N mutant of Selenomonas ruminantium PTP-like phytase

Summary for 2B4P

• Entry DOI: 10.2210/pdb2b4p/pdb
• Related: 1U24 1U25 1U26 2B40 2B4U
• Descriptor: myo-inositol hexaphosphate phosphohydrolase, MALONATE ION, CHLORIDE ION, ... (4 entities in total)
• Functional Keywords: ptp-like, ionic strength, hydrolase
• Biological source: Selenomonas ruminantium
• Total number of polymer chains: 2
• Total formula weight: 76997.47

Authors

Gruninger, R.J.,Selinger, L.B.,Mosimann, S.C. (deposition date: 2005-09-26, release date: 2006-11-07, Last modification date: 2024-02-14)

Primary citation

Puhl, A.A.,Gruninger, R.J.,Greiner, R.,Janzen, T.W.,Mosimann, S.C.,Selinger, L.B.
Kinetic and structural analysis of a bacterial protein tyrosine phosphatase-like myo-inositol polyphosphatase.
Protein Sci., 16:1368-1378, 2007

PubMed Abstract: PhyA from Selenomonas ruminantium (PhyAsr), is a bacterial protein tyrosine phosphatase (PTP)-like inositol polyphosphate phosphatase (IPPase) that is distantly related to known PTPs. PhyAsr has a second substrate binding site referred to as a standby site and the P-loop (HCX5R) has been observed in both open (inactive) and closed (active) conformations. Site-directed mutagenesis and kinetic and structural studies indicate PhyAsr follows a classical PTP mechanism of hydrolysis and has a broad specificity toward polyphosphorylated myo-inositol substrates, including phosphoinositides. Kinetic and molecular docking experiments demonstrate PhyAsr preferentially cleaves the 3-phosphate position of Ins P6 and will produce Ins(2)P via a highly ordered series of sequential dephosphorylations: D-Ins(1,2,4,5,6)P5, Ins(2,4,5,6)P4, D-Ins(2,4,5)P3, and D-Ins(2,4)P2. The data support a distributive enzyme mechanism and suggest the PhyAsr standby site is involved in the recruitment of substrate. Structural studies at physiological pH and high salt concentrations demonstrate the "closed" or active P-loop conformation can be induced in the absence of substrate. These results suggest PhyAsr should be reclassified as a D-3 myo-inositol hexakisphosphate phosphohydrolase and suggest the PhyAsr reaction mechanism is more similar to that of PTPs than previously suspected.

PubMed: 17567745
DOI: 10.1110/ps.062738307

Experimental method

X-RAY DIFFRACTION (1.81 Å)