PDBsum entry 2b4o

Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
Protein chains
313 a.a. *
GOL ×2
_CL ×6
Waters ×591
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Structure of the r258k mutant of selenomonas ruminantium ptp phytase
Structure: Myo-inositol hexaphosphate phosphohydrolase. Chain: a, b. Engineered: yes. Mutation: yes
Source: Selenomonas ruminantium. Organism_taxid: 971. Gene: phyasr_r252k. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
2.30Å     R-factor:   0.191     R-free:   0.226
Authors: R.J.Gruninger,L.B.Selinger,S.C.Mosimann
Key ref:
A.A.Puhl et al. (2007). Kinetic and structural analysis of a bacterial protein tyrosine phosphatase-like myo-inositol polyphosphatase. Protein Sci, 16, 1368-1378. PubMed id: 17567745 DOI: 10.1110/ps.062738307
26-Sep-05     Release date:   07-Nov-06    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q7WUJ1  (Q7WUJ1_SELRU) -  Myo-inositol hexaphosphate phosphohydrolase
346 a.a.
313 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     peptidyl-tyrosine dephosphorylation   2 terms 
  Biochemical function     hydrolase activity     2 terms  


DOI no: 10.1110/ps.062738307 Protein Sci 16:1368-1378 (2007)
PubMed id: 17567745  
Kinetic and structural analysis of a bacterial protein tyrosine phosphatase-like myo-inositol polyphosphatase.
A.A.Puhl, R.J.Gruninger, R.Greiner, T.W.Janzen, S.C.Mosimann, L.B.Selinger.
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.
  Selected figure(s)  
Figure 6.
Figure 6. The effect of binding an axial vs. an equatorial ligand in the
  The above figure is reprinted by permission from the Protein Society: Protein Sci (2007, 16, 1368-1378) copyright 2007.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18853154 A.A.Puhl, R.Greiner, and L.B.Selinger (2009).
Stereospecificity of myo-inositol hexakisphosphate hydrolysis by a protein tyrosine phosphatase-like inositol polyphosphatase from Megasphaera elsdenii.
  Appl Microbiol Biotechnol, 82, 95.  
18358762 A.A.Puhl, R.Greiner, and L.B.Selinger (2008).
A protein tyrosine phosphatase-like inositol polyphosphatase from Selenomonas ruminantium subsp. lactilytica has specificity for the 5-phosphate of myo-inositol hexakisphosphate.
  Int J Biochem Cell Biol, 40, 2053-2064.  
18756327 A.A.Puhl, R.Greiner, and L.B.Selinger (2008).
Kinetics, substrate specificity, and stereospecificity of two new protein tyrosine phosphatase-like inositol polyphosphatases from Selenomonas lacticifex.
  Biochem Cell Biol, 86, 322-330.  
18573100 R.J.Gruninger, L.Brent Selinger, and S.C.Mosimann (2008).
Effect of ionic strength and oxidation on the P-loop conformation of the protein tyrosine phosphatase-like phytase, PhyAsr.
  FEBS J, 275, 3783-3792.
PDB codes: 2psz 2pt0 3d1h 3d1o 3d1q
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.