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

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

Date :   21 Mar 01 (Deposition) - 16 May 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym./Biol. Unit : A

Keywords :   Spsynaptojanin, Ipp5C, Ip3, Ip2, , Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Tsujishita, S. Guo, L. E. Stolz, J. D. York, J. H. Hurley
Specificity Determinants In Phosphoinositide Dephosphorylation: Crystal Structure Of An Archetypal Inositol Polyphosphate 5-Phosphatase.
Cell(Cambridge, Mass. ) V. 105 379 2001
PubMed-ID: 11348594 | Reference-DOI: 10.1016/S0092-8674(01)00326-9
(for further references see the PDB file header)

Molecule 1 - PHOSPHATIDYLINOSITOL PHOSPHATE PHOSPHATASE
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET22B
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	IPP5C DOMAIN, RESIDUES 534-880
	Organism Common	:	FISSION YEAST
	Organism Scientific	:	SCHIZOSACCHAROMYCES POMBE
	Organism Taxid	:	4896
	Synonym	:	SYNAPTOJANIN

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 2)

No.	Name	Count	Type	Full Name
1	2IP	1	Ligand/Ion	D-MYO-INOSITOL-1,4-BISPHOSPHATE
2	CA	1	Ligand/Ion	CALCIUM ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:117 , HOH A:198 , HOH A:200 , HOH A:211 , ASN A:568 , GLU A:597	BINDING SITE FOR RESIDUE CA A 301
2	AC2	SOFTWARE	HOH A:126 , HOH A:162 , HOH A:199 , HOH A:200 , GLY A:703 , TYR A:704 , ARG A:744 , TYR A:794 , LYS A:795 , ARG A:810	BINDING SITE FOR RESIDUE 2IP A 302

(no "SS Bond" information available for 1I9Z)

(no "Cis Peptide Bond" information available for 1I9Z)

(no "SAP(SNP)/Variant" information available for 1I9Z)

(no "PROSITE Motif" information available for 1I9Z)

(no "Exon" information available for 1I9Z)

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:336
 aligned with SYJ1_SCHPO | O43001 from UniProtKB/Swiss-Prot  Length:1076

    Alignment length:345
                                   543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       833       843       853       863       873     
           SYJ1_SCHPO   534 YDPIHEYVNHELRKRENEFSEHKNVKIFVASYNLNGCSATTKLENWLFPENTPLADIYVVGFQEIVQLTPQQVISADPAKRREWESCVKRLLNGKCTSGPGYVQLRSGQLVGTALMIFCKESCLPSIKNVEGTVKKTGLGGVSGNKGAVAIRFDYEDTGLCFITSHLAAGYTNYDERDHDYRTIASGLRFRRGRSIFNHDYVVWFGDFNYRISLTYEEVVPCIAQGKLSYLFEYDQLNKQMLTGKVFPFFSELPITFPPTYKFDIGTDIYDTSDKHRVPAWTDRILYRGELVPHSYQSVPLYYSDHRPIYATYEANIVKVDREKKKILFEELYNQRKQEVRDASQ 878
               SCOP domains d1i9za_ A: Synaptojanin, IPP5C domain                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1i9zA00 A:534-878  [code=3.60.10.10, no name defined]                                                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh.eeeeeeeeeeeeee.........hhhhhh........eeeeeee......-----..hhhhhhhhhhhhhhhhhhh......eeeeeeeee..eeeeeeee.hhhh.eeeeeeeeee...----...eeeeeeeee..eeeeeeeee......hhhhhhhhhhhhhhhh.hhhhh......eeeeeee.......hhhhhhhhhhh.hhhhhhh.hhhhhhhhh.......................................eeeeee...eeeeeee..........eeeeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1i9z A 534 YDPIHEYVNHELRKRENEFSEHKNVKIFVASYNLNGCSATTKLENWLFPENTPLADIYVVGFQEIVQLT-----SADPAKRREWESCVKRLLNGKCTSGPGYVQLRSGQLVGTALMIFCKESCLPSIKNVEGTVKKTGL----GNKGAVAIRFDYEDTGLCFITSHLAAGYTNYDERDHDYRTIASGLRFRRGRSIFNHDYVVWFGDFNYRISLTYEEVVPCIAQGKLSYLFEYDQLNKQMLTGKVFPFFSELPITFPPTYKFDIGTDIYDTSDKHRVPAWTDRILYRGELVPHSYQSVPLYYSDHRPIYATYEANIVKVDREKKKILFEELYNQRKQEVRDASQ 878
                                   543       553       563       573       583       593        |-    |  613       623       633       643       653       663        |-   |   683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       833       843       853       863       873     
                                                                                              602   608                                                             672  677

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: Alpha and beta proteins (a+b) (23004)

Fold: DNase I-like (70)

Superfamily: DNase I-like (70)

Family: Inositol polyphosphate 5-phosphatase (IPP5) (7)

Protein domain: Synaptojanin, IPP5C domain (2)

Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] (2)

d1i9za_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

Architecture: 4-Layer Sandwich (459)

Topology: Deoxyribonuclease I; Chain A (35)

Homologous Superfamily: [code=3.60.10.10, no name defined] (35)

Fission yeast (Schizosaccharomyces pombe) (2)

1i9zA00

A:534-878

(no "Pfam Domain" information available for 1I9Z)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (SYJ1_SCHPO | O43001)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:1990651	inositol-1,2,4,5,6-pentakisphosphate 5-phosphatase activity	Catalysis of the reaction: 1D-myo-inositol 1,2,4,5,6-pentakisphosphate + H2O = 1D-myo-inositol 1,2,4,6-tetrakisphosphate + phosphate.
	GO:1990649	inositol-1,2,4,5-tetrakisphosphate 5-phosphatase activity	Catalysis of the reaction: 1D-myo-inositol 1,2,4,5-tetrakisphosphate + H2O = 1D-myo-inositol 1,2,4-trisphosphate + phosphate.
	GO:0052659	inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity	Catalysis of the reaction: 1D-myo-inositol 1,3,4,5-tetrakisphosphate + H2O = 1D-myo-inositol 1,3,4-trisphosphate + phosphate.
	GO:0052658	inositol-1,4,5-trisphosphate 5-phosphatase activity	Catalysis of the reaction: 1D-myo-inositol 1,4,5-trisphosphate + H2O = 1D-myo-inositol 1,4-bisphosphate + phosphate.
	GO:1990650	inositol-2,4,5,6-tetrakisphosphate 5-phosphatase activity	Catalysis of the reaction: 1D-myo-inositol 2,4,5,6-tetrakisphosphate + H2O = 1D-myo-inositol 2,4,6-trisphosphate + phosphate.
	GO:1990640	inositol-2,4,5-triphosphate 5-phosphatase activity	Catalysis of the reaction: 1D-myo-inositol 2,4,5-trisphosphate + H2O = 1D-myo-inositol 2,4-bisphosphate + phosphate.
	GO:1990648	inositol-4,5,6-triphosphate 5-phosphatase activity	Catalysis of the reaction: 1D-myo-inositol 4,5,6-trisphosphate + H2O = 1D-myo-inositol 4,6-bisphosphate + phosphate.
	GO:0030487	inositol-4,5-bisphosphate 5-phosphatase activity	Catalysis of the reaction: 1D-myo-inositol 4,5-bisphosphate + H2O = 1D-myo-inositol 4-phosphate + phosphate.
	GO:0034485	phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity	Catalysis of the reaction: phosphatidylinositol-3,4,5-trisphosphate + H2O = phosphatidylinositol-3,4-bisphosphate + phosphate.
	GO:0043813	phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity	Catalysis of the reaction: phosphatidylinositol-3,5-bisphosphate + H2O = phosphatidylinositol-3-phosphate + orthophosphate.
	GO:0004439	phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity	Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 4-phosphate + phosphate.
	GO:0042578	phosphoric ester hydrolase activity	Catalysis of the reaction: RPO-R' + H2O = RPOOH + R'H. This reaction is the hydrolysis of any phosphoric ester bond, any ester formed from orthophosphoric acid, O=P(OH)3.
biological process
	GO:0006897	endocytosis	A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.
	GO:0048017	inositol lipid-mediated signaling	A series of molecular signals in which a cell uses an inositol-containing lipid to convert a signal into a response. Inositol lipids include the phosphoinositides (phosphatidylinositol and its phosphorylated derivatives), ceramides containing inositol, and inositol glycolipids.
	GO:0006629	lipid metabolic process	The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
	GO:0046856	phosphatidylinositol dephosphorylation	The process of removing one or more phosphate groups from a phosphatidylinositol.
	GO:0036092	phosphatidylinositol-3-phosphate biosynthetic process	The chemical reactions and pathways resulting in the formation of phosphatidylinositol-3-phosphate, a phosphatidylinositol monophosphate carrying the phosphate group at the 3-position.
	GO:0015031	protein transport	The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0032153	cell division site	The eventual plane of cell division (also known as cell cleavage or cytokinesis) in a dividing cell. In Eukaryotes, the cleavage apparatus, composed of septin structures and the actomyosin contractile ring, forms along this plane, and the mitotic, or meiotic, spindle is aligned perpendicular to the division plane. In bacteria, the cell division site is generally located at mid-cell and is the site at which the cytoskeletal structure, the Z-ring, assembles.
	GO:0051286	cell tip	The region at the end of the longest axis of a cylindrical or elongated cell.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric/Biological Unit
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	SYJ1_SCHPO \| O43001	:	1i9y

1i9y	CRYSTAL STRUCTURE OF INOSITOL POLYPHOSPHATE 5-PHOSPHATASE DOMAIN (IPP5C) OF SPSYNAPTOJANIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

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