2Q9P - JenaLib

Title :   HUMAN DIPHOSPHOINOSITOL POLYPHOSPHATE PHOSPHOHYDROLASE 1, MG-F COMPLEX

Authors :   A. G. Thorsell, R. Busam, C. H. Arrowsmith, H. Berglund, R. Collins, L. G. Dahlgren, A. Edwards, S. Flodin, A. Flores, S. Graslund, M. Hammarstrom, L. Holmberg-Schiavone, I. Johansson, A. Kallas, T. Karlberg, T. Kotenyova, L. Lehtio, M. Moche, P. Nordlund, T. Nyman, D. Ogg, J. Sagemark, M. Sundstrom, S. Van Den Berg, J. Weigelt, M. Welin, C. Persson, B. M. Hallberg, Structural Genomics Consortium (Sgc)

Date :   13 Jun 07 (Deposition) - 11 Sep 07 (Release) - 25 Aug 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.65

Chains :   Asym./Biol. Unit : A

Keywords :   Diphosphoinositol Polyphosphate Phosphohydrolase, Nudix, Inositol Pyrophosphate Metabolism, Structural Genomics Consortium, Sgc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. G. Thorsell, C. Persson, S. Graslund, M. Hammarstrom, R. D. Busam, B. M. Hallberg
Crystal Structure Of Human Diphosphoinositol Phosphatase 1.
Proteins V. 77 242 2009
PubMed-ID: 19585659 | Reference-DOI: 10.1002/PROT.22489
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 16)

Sites (16, 16)

Asymmetric Unit (16, 16)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU A:66 , GLU A:70 , IHP A:201 , MG A:302 , MG A:303 , MG A:304 , F A:403 , F A:405 , F A:409 , F A:410	BINDING SITE FOR RESIDUE MG A 301
02	AC2	SOFTWARE	GLY A:50 , GLY A:51 , GLU A:70 , IHP A:201 , MG A:301 , MG A:303 , F A:402 , F A:403 , F A:410	BINDING SITE FOR RESIDUE MG A 302
03	AC3	SOFTWARE	IHP A:201 , MG A:301 , MG A:302 , MG A:304 , F A:403 , F A:404 , F A:406 , F A:409 , F A:410 , HOH A:836 , HOH A:837	BINDING SITE FOR RESIDUE MG A 303
04	AC4	SOFTWARE	GLU A:66 , MG A:301 , MG A:303 , F A:404 , F A:406 , F A:407 , F A:408 , F A:409	BINDING SITE FOR RESIDUE MG A 304
05	AC5	SOFTWARE	SER A:28 , SER A:30 , GLU A:31 , GLU A:32 , GLU A:33 , HOH A:846	BINDING SITE FOR RESIDUE CL A 401
06	AC6	SOFTWARE	ILE A:47 , GLY A:50 , GLU A:70 , IHP A:201 , MG A:302 , HOH A:566	BINDING SITE FOR RESIDUE F A 402
07	AC7	SOFTWARE	GLY A:50 , GLY A:51 , GLU A:66 , GLU A:70 , IHP A:201 , MG A:301 , MG A:302 , MG A:303 , F A:404 , F A:409 , F A:410 , HOH A:837	BINDING SITE FOR RESIDUE F A 403
08	AC8	SOFTWARE	GLY A:51 , GLY A:52 , GLU A:66 , IHP A:201 , MG A:303 , MG A:304 , F A:403 , F A:406 , F A:407 , F A:409 , HOH A:821 , HOH A:836	BINDING SITE FOR RESIDUE F A 404
09	AC9	SOFTWARE	GLU A:66 , GLU A:69 , GLU A:70 , MG A:301 , F A:409 , F A:410 , HOH A:725	BINDING SITE FOR RESIDUE F A 405
10	BC1	SOFTWARE	MG A:303 , MG A:304 , F A:404 , F A:407 , F A:408 , F A:409 , HOH A:836	BINDING SITE FOR RESIDUE F A 406
11	BC2	SOFTWARE	GLY A:52 , ARG A:65 , GLU A:66 , MG A:304 , F A:404 , F A:406 , F A:408 , HOH A:637	BINDING SITE FOR RESIDUE F A 407
12	BC3	SOFTWARE	ARG A:65 , GLU A:66 , GLU A:69 , MG A:304 , F A:406 , F A:407 , F A:409 , HOH A:824	BINDING SITE FOR RESIDUE F A 408
13	BC4	SOFTWARE	GLU A:66 , MG A:301 , MG A:303 , MG A:304 , F A:403 , F A:404 , F A:405 , F A:406 , F A:408 , F A:410 , HOH A:612	BINDING SITE FOR RESIDUE F A 409
14	BC5	SOFTWARE	GLU A:70 , ARG A:115 , IHP A:201 , MG A:301 , MG A:302 , MG A:303 , F A:403 , F A:405 , F A:409 , HOH A:589 , HOH A:837	BINDING SITE FOR RESIDUE F A 410
15	BC6	SOFTWARE	ASN A:86 , GLN A:136	BINDING SITE FOR RESIDUE F A 411
16	BC7	SOFTWARE	ARG A:10 , LYS A:18 , ARG A:20 , SER A:39 , SER A:40 , ARG A:41 , ILE A:47 , GLY A:50 , GLY A:51 , GLY A:52 , GLU A:70 , ARG A:89 , HIS A:91 , ARG A:115 , LYS A:133 , MG A:301 , MG A:302 , MG A:303 , F A:402 , F A:403 , F A:404 , F A:410 , HOH A:602 , HOH A:606 , HOH A:738 , HOH A:803 , HOH A:821 , HOH A:836 , HOH A:837	BINDING SITE FOR RESIDUE IHP A 201

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

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:132
 aligned with NUDT3_HUMAN | O95989 from UniProtKB/Swiss-Prot  Length:172

    Alignment length:132
                                    19        29        39        49        59        69        79        89        99       109       119       129       139  
          NUDT3_HUMAN    10 RTYDGDGYKKRAACLCFRSESEEEVLLVSSSRHPDRWIVPGGGMEPEEEPSVAAVREVCEEAGVKGTLGRLVGIFENQERKHRTYVYVLIVTEVLEDWEDSVNIGRKREWFKIEDAIKVLQYHKPVQASYFE 141
               SCOP domains d2q9pa_ A: Diphosphoinositol polyphosphate phosphohydrolase                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeeeeeeee......eeeeee.......ee..eee.....hhhhhhhhhhhhhhheeeeeeeeeeeeee....eeeeeeeeeeeee...hhhhhhhh..eeeeehhhhhhhhh..hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -------NUDIX  PDB: A:17-141 UniProt: 17-142                                                                                          PROSITE (1)
                PROSITE (2) -----------------------------------------NUDIX_BOX  PDB: A:51-7--------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2q9p A  10 RTYDGDGYKKRAACLCFRSESEEEVLLVSSSRHPDRWIVPGGGMEPEEEPSVAAVREVCEEAGVKGTLGRLVGIFENQERKHRTYVYVLIVTEVLEDWEDSVNIGRKREWFKIEDAIKVLQYHKPVQASYFE 141
                                    19        29        39        49        59        69        79        89        99       109       119       129       139

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (20, 20)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (NUDT3_HUMAN | O95989)

molecular function
	GO:0008486	diphosphoinositol-polyphosphate diphosphatase activity	Catalysis of the reaction: diphospho-myo-inositol polyphosphate + H2O = myo-inositol polyphosphate + phosphate.
	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:0052841	inositol bisdiphosphate tetrakisphosphate diphosphatase activity	Catalysis of the reaction: inositol bisdiphosphate tetrakisphosphate + H2O = inositol diphosphate pentakisphosphate + phosphate.
	GO:0052842	inositol diphosphate pentakisphosphate diphosphatase activity	Catalysis of the reaction: inositol diphosphate pentakisphosphate + H2O = inositol hexakisphosphate + phosphate.
	GO:0052840	inositol diphosphate tetrakisphosphate diphosphatase activity	Catalysis of the reaction: inositol diphosphate tetrakisphosphate + H2O = inositol 1,3,4,5,6-pentakisphosphate + phosphate.
	GO:0052846	inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 1-diphosphatase activity	Catalysis of the reaction: 1,5-bisdiphosphoinositol-1D-myo-inositol 2,3,4,6-tetrakisphosphate + H2O = 1-diphospho-1D-myo-inositol 1,2,3,4,6-pentakisphosphate + phosphate + H+.
	GO:0052847	inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity	Catalysis of the reaction: 1,5-bisdiphosphoinositol-1D-myo-inositol 2,3,4,6-tetrakisphosphate + H2O = 1-diphospho-1D-myo-inositol 2,3,4,5,6-pentakisphosphate + phosphate + H+.
	GO:0052843	inositol-1-diphosphate-2,3,4,5,6-pentakisphosphate diphosphatase activity	Catalysis of the reaction: inositol 1-diphosphate 2,3,4,5,6-pentakisphosphate + H2O = inositol 1,2,3,4,5,6-hexakisphosphate + phosphate + 2 H+.
	GO:0052848	inositol-3,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity	Catalysis of the reaction: 3,5-bisdiphosphoinositol-1D-myo-inositol 2,3,4,6-tetrakisphosphate + H2O = 3-diphospho-1D-myo-inositol 1,2,4,5,6-pentakisphosphate + phosphate + H+.
	GO:0052844	inositol-3-diphosphate-1,2,4,5,6-pentakisphosphate diphosphatase activity	Catalysis of the reaction: inositol 3-diphosphate 1,2,4,5,6-pentakisphosphate + H2O = inositol 1,2,3,4,5,6-hexakisphosphate + phosphate + 2 H+.
	GO:0052845	inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity	Catalysis of the reaction: inositol 5-diphosphate 1,2,3,4,6-pentakisphosphate + H2O = inositol 1,2,3,4,5,6-hexakisphosphate + phosphate + 2 H+.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0007267	cell-cell signaling	Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions.
	GO:0015961	diadenosine polyphosphate catabolic process	The chemical reactions and pathways resulting in the breakdown of diadenosine polyphosphate, a derivative of the nucleoside adenosine with phosphate groups attached.
	GO:0071544	diphosphoinositol polyphosphate catabolic process	The chemical reactions and pathways resulting in the breakdown of a diphosphoinositol polyphosphate, 1,2,3,4,5,6-cyclohexanehexol with one or more diphosphate groups and multiple monophosphate groups attached.
	GO:0043647	inositol phosphate metabolic process	The chemical reactions and pathways involving inositol phosphate, 1,2,3,4,5,6-cyclohexanehexol, with one or more phosphate groups attached.
cellular component
	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.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.

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