Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 40.47 kDa 
• Atom Count: 3011 
• Modelled Residue Count: 336 
• Deposited Residue Count: 347 
• Unique protein chains: 1

1I9Z

CRYSTAL STRUCTURE OF INOSITOL POLYPHOSPHATE 5-PHOSPHATASE DOMAIN (IPP5C) OF SPSYNAPTOJANIN IN COMPLEX WITH INOSITOL (1,4)-BISPHOSPHATE AND CALCIUM ION

• PDB DOI: 10.2210/pdb1I9Z/pdb

• Classification: HYDROLASE
• Organism(s): Schizosaccharomyces pombe
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2001-03-21 Released: 2001-05-16 
• Deposition Author(s): Tsujishita, Y., Guo, S., Stolz, L., York, J.D., Hurley, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.218 
• R-Value Work: 0.191 

Literature

Specificity determinants in phosphoinositide dephosphorylation: crystal structure of an archetypal inositol polyphosphate 5-phosphatase.

Tsujishita, Y., Guo, S., Stolz, L.E., York, J.D., Hurley, J.H.

(2001) Cell 105: 379-389

• PubMed: 11348594 
• DOI: 10.1016/s0092-8674(01)00326-9
• Primary Citation of Related Structures:  
  1I9Y, 1I9Z


• PubMed Abstract: 
  

Inositol polyphosphate 5-phosphatases are central to intracellular processes ranging from membrane trafficking to Ca(2+) signaling, and defects in this activity result in the human disease Lowe syndrome. The 1.8 resolution structure of the inositol polyphosphate 5-phosphatase domain of SPsynaptojanin bound to Ca(2+) and inositol (1,4)-bisphosphate reveals a fold and an active site His and Asp pair resembling those of several Mg(2+)-dependent nucleases. Additional loops mediate specific inositol polyphosphate contacts. The 4-phosphate of inositol (1,4)-bisphosphate is misoriented by 4.6 compared to the reactive geometry observed in the apurinic/apyrimidinic endonuclease 1, explaining the dephosphorylation site selectivity of the 5-phosphatases. Based on the structure, a series of mutants are described that exhibit altered substrate specificity providing general determinants for substrate recognition.

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Organizational Affiliation: 

Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, , Bethesda, MD 20892, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHATIDYLINOSITOL PHOSPHATE PHOSPHATASE	A	347	Schizosaccharomyces pombe	Mutation(s): 0  EC: 3.1.3.36
UniProt
Find proteins for O43001 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore O43001  Go to UniProtKB:  O43001

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2IP	C [auth A]	D-MYO-INOSITOL-1,4-BISPHOSPHATE C6 H14 O12 P2 PELZSPZCXGTUMR-GTTIYYRPSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.218 
• R-Value Work: 0.191 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 148.999	α = 90
b = 67.705	β = 106.152
c = 51.995	γ = 90

Software Package:

Software Name	Purpose
SHARP	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-03-21 
• Released Date: 2001-05-16 
Deposition Author(s): Tsujishita, Y., Guo, S., Stolz, L., York, J.D., Hurley, J.H.

Revision History  

• Version 1.0: 2001-05-16
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance