2CZH - JenaLib

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Title :   CRYSTAL STRUCTURE OF HUMAN MYO-INOSITOL MONOPHOSPHATASE 2 (IMPA2) WITH PHOSPHATE ION (ORTHORHOMBIC FORM)

Authors :   K. Ito, R. Arai, T. Kamo-Uchikubo, T. Ohnishi, H. Ohba, T. Yoshikawa, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   13 Jul 05 (Deposition) - 25 Jul 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

Chains :   Asym./Biol. Unit : A,B

Keywords :   Myo-Inositol Monophosphatase (Impa), Bipolar Disorder, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Arai, K. Ito, T. Ohnishi, H. Ohba, R. Akasaka, Y. Bessho, K. Hanawa-Suetsugu, T. Yoshikawa, M. Shirouzu, S. Yokoyama
Crystal Structure Of Human Myo-Inositol Monophosphatase 2, The Product Of The Putative Susceptibility Gene For Bipolar Disorder, Schizophrenia, And Febrile Seizures
Proteins V. 67 732 2007
PubMed-ID: 17340635 | Reference-DOI: 10.1002/PROT.21299
(for further references see the PDB file header)

Molecule 1 - INOSITOL MONOPHOSPHATASE 2
	Chains	:	A, B
	EC Number	:	3.1.3.25
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET44A
	Expression System Strain	:	BL21(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	IMPA2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	IMPASE 2, IMP 2, INOSITOL-1(OR 4)-MONOPHOSPHATASE 2, MYO-INOSITOL MONOPHOSPHATASE A2

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	PO4	2	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:104 , SER A:206 , SER A:207 , GLN A:224	BINDING SITE FOR RESIDUE PO4 A 289
2	AC2	SOFTWARE	ASP B:104 , SER B:206 , SER B:207	BINDING SITE FOR RESIDUE PO4 B 289

Asymmetric/Biological Unit

No.	Residues
1	A:90	-	A:229
2	B:90	-	B:229

(no "Cis Peptide Bond" information available for 2CZH)

Asymmetric/Biological Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_049601	A	88	T	IMPA2_HUMAN	Polymorphism	16976948	A	A	88	T

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IMP_1	PS00629	Inositol monophosphatase family signature 1.	IMPA2_HUMAN	98-111	2	A:98-111 B:98-111
2	IMP_2	PS00630	Inositol monophosphatase family signature 2.	IMPA2_HUMAN	230-244	2	A:230-244 B:230-244

Asymmetric/Biological Unit (8, 16)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000269159	1a	ENSE00001818223	chr18:11981427-11981764	338	IMPA2_HUMAN	1-32	32	2	A:15-32 B:15-32	18 18
1.2	ENST00000269159	2	ENSE00001268518	chr18:11999053-11999186	134	IMPA2_HUMAN	33-77	45	2	A:33-77 (gaps) B:33-77 (gaps)	45 45
1.4	ENST00000269159	4	ENSE00001268511	chr18:12009882-12009986	105	IMPA2_HUMAN	77-112	36	2	A:77-112 B:77-112 (gaps)	36 36
1.5	ENST00000269159	5	ENSE00000948305	chr18:12012169-12012214	46	IMPA2_HUMAN	112-127	16	2	A:112-127 B:112-127	16 16
1.6	ENST00000269159	6	ENSE00000948306	chr18:12014264-12014372	109	IMPA2_HUMAN	128-164	37	2	A:128-164 B:128-164	37 37
1.7	ENST00000269159	7	ENSE00000948307	chr18:12028042-12028150	109	IMPA2_HUMAN	164-200	37	2	A:164-200 B:164-200	37 37
1.8	ENST00000269159	8	ENSE00000948308	chr18:12028841-12028992	152	IMPA2_HUMAN	200-251	52	2	A:200-251 B:200-251	52 52
1.9	ENST00000269159	9	ENSE00001268526	chr18:12030342-12030876	535	IMPA2_HUMAN	251-288	38	2	A:251-277 B:251-279	27 29

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:254
 aligned with IMPA2_HUMAN | O14732 from UniProtKB/Swiss-Prot  Length:288

    Alignment length:263
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274   
          IMPA2_HUMAN    15 PWEECFQAAVQLALRAGQIIRKALTEEKRVSTKTSAADLVTETDHLVEDLIISELRERFPSHRFIAEEAAASGAKCVLTHSPTWIIDPIDGTCNFVHRFPTVAVSIGFAVRQELEFGVIYHCTEERLYTGRRGRGAFCNGQRLRVSGETDLSKALVLTEIGPKRDPATLKLFLSNMERLLHAKAHGVRVIGSSTLALCHLASGAADAYYQFGLHCWDLAAATVIIREAGGIVIDTSGGPLDLMACRVVAASTREMAMLIAQAL 277
               SCOP domains d2czha_ A: automated matches                                                                                                                                                                                                                                            SCOP domains
               CATH domains 2czhA01 A:15-157 Fructose-1,         6-Bisphosphatase, subunit A, domain 1                                                                     2czhA02 A:158-277  [code=3.40.190.80, no name defined]                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh....---------hhhhhhhhhhhhhhhhhhhhhh...eeee................eeeeeeeehhhhhhh.....eeeeeeee..eeeeeeeee....eeeeee...eeee...........hhhh.eeee......hhhhhhhhhhhhhhhhhh...eee...hhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhh...eee............eeeee.hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------T--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------IMP_1         ----------------------------------------------------------------------------------------------------------------------IMP_2          --------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a         Exon 1.2  PDB: A:33-77 (gaps) UniProt: 33-77 ----------------------------------Exon 1.5        Exon 1.6  PDB: A:128-164             -----------------------------------Exon 1.8  PDB: A:200-251 UniProt: 200-251           -------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------Exon 1.4  PDB: A:77-112             ---------------------------------------------------Exon 1.7  PDB: A:164-200             --------------------------------------------------Exon 1.9  PDB: A:251-277    Transcript 1 (2)
                 2czh A  15 PWEECFQAAVQLALRAGQIIRKALTEEK---------DLVTETDHLVEDLIISELRERFPSHRFIAEEAAASGAKCVLTHSPTWIIDPIDGTCNFVHRFPTVAVSIGFAVRQELEFGVIYHCTEERLYTGRRGRGAFCNGQRLRVSGETDLSKALVLTEIGPKRDPATLKLFLSNMERLLHAKAHGVRVIGSSTLALCHLASGAADAYYQFGLHCWDLAAATVIIREAGGIVIDTSGGPLDLMACRVVAASTREMAMLIAQAL 277
                                    24        34       | -       |54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274   
                                                      42        52

Chain B from PDB  Type:PROTEIN  Length:246
 aligned with IMPA2_HUMAN | O14732 from UniProtKB/Swiss-Prot  Length:288

    Alignment length:265
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274     
          IMPA2_HUMAN    15 PWEECFQAAVQLALRAGQIIRKALTEEKRVSTKTSAADLVTETDHLVEDLIISELRERFPSHRFIAEEAAASGAKCVLTHSPTWIIDPIDGTCNFVHRFPTVAVSIGFAVRQELEFGVIYHCTEERLYTGRRGRGAFCNGQRLRVSGETDLSKALVLTEIGPKRDPATLKLFLSNMERLLHAKAHGVRVIGSSTLALCHLASGAADAYYQFGLHCWDLAAATVIIREAGGIVIDTSGGPLDLMACRVVAASTREMAMLIAQALQT 279
               SCOP domains d2czhb_ B: automated match            es                                                                                                                                                                                                                                  SCOP domains
               CATH domains 2czhB01 B:15-157 Fructose-            1,6-Bisphosphatase, subunit A       , domain 1                                                           2czhB02 B:158-279  [code=3.40.190.80, no name defined]                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh..------------..hhhhhhhhhhhhhhhhhhh...eeee.-------........eeeeeeeehhhhhhhh....eeeeeeee..eeeeeeeee....eeeeee...eeee..ee.......hhhh.eeee......hhhhhhhhhhhhhhhhhh...eee...hhhhhhhhhhh....eeeee..hhhhhhhhhhhhhhh..eee............eeeee.hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------IMP_1         ----------------------------------------------------------------------------------------------------------------------IMP_2          ----------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a         Exon 1.2  PDB: B:33-77 (gaps) UniProt: 33-77 ----------------------------------Exon 1.5        Exon 1.6  PDB: B:128-164             -----------------------------------Exon 1.8  PDB: B:200-251 UniProt: 200-251           ---------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------Exon 1.4  PDB: B:77-112 (gaps)      ---------------------------------------------------Exon 1.7  PDB: B:164-200             --------------------------------------------------Exon 1.9  PDB: B:251-279      Transcript 1 (2)
                 2czh B  15 PWEECFQAAVQLALRAGQIIRKALTE------------LVTETDHLVEDLIISELRERFPSHRFIAE-------KCVLTHSPTWIIDPIDGTCNFVHRFPTVAVSIGFAVRQELEFGVIYHCTEERLYTGRRGRGAFCNGQRLRVSGETDLSKALVLTEIGPKRDPATLKLFLSNMERLLHAKAHGVRVIGSSTLALCHLASGAADAYYQFGLHCWDLAAATVIIREAGGIVIDTSGGPLDLMACRVVAASTREMAMLIAQALQT 279
                                    24        34     |   -        54        64        74      |  -    |   94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274     
                                                    40           53                          81      89

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: Multi-domain proteins (alpha and beta) (2421)

Fold: Carbohydrate phosphatase (140)

Superfamily: Carbohydrate phosphatase (140)

Family: automated matches (14)

Protein domain: automated matches (14)

Human (Homo sapiens) [TaxId: 9606] (5)

1a	d2czha_	A:
1b	d2czhb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Fructose-1,6-Bisphosphatase; Chain A, domain 1 (114)

Homologous Superfamily: Fructose-1,6-Bisphosphatase, subunit A, domain 1 (114)

Human (Homo sapiens) (25)

1a	2czhA01	A:15-157
1b	2czhB01	B:15-157

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: D-Maltodextrin-Binding Protein; domain 2 (600)

Homologous Superfamily: [code=3.40.190.80, no name defined] (109)

Human (Homo sapiens) (25)

2a	2czhB02	B:158-279
2b	2czhA02	A:158-277

(no "Pfam Domain" information available for 2CZH)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (IMPA2_HUMAN | O14732)

molecular function
	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:0008934	inositol monophosphate 1-phosphatase activity	Catalysis of the reaction: myo-inositol 1-phosphate + H2O = myo-inositol + phosphate.
	GO:0052832	inositol monophosphate 3-phosphatase activity	Catalysis of the reaction: myo-inositol 3-phosphate + H2O = myo-inositol + phosphate.
	GO:0052833	inositol monophosphate 4-phosphatase activity	Catalysis of the reaction: myo-inositol 4-phosphate + H2O = myo-inositol + phosphate.
	GO:0052834	inositol monophosphate phosphatase activity	Catalysis of the reaction: myo-inositol phosphate + H2O = myo-inositol + phosphate.
	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.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
	GO:0006021	inositol biosynthetic process	The chemical reactions and pathways resulting in the formation of inositol, 1,2,3,4,5,6-cyclohexanehexol, a growth factor for animals and microorganisms.
	GO:0006020	inositol metabolic process	The chemical reactions and pathways involving inositol, 1,2,3,4,5,6-cyclohexanehexol, a growth factor for animals and microorganisms.
	GO:0046855	inositol phosphate dephosphorylation	The process of removing a phosphate group from any mono- or polyphosphorylated inositol.
	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.
	GO:0006796	phosphate-containing compound metabolic process	The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid.
	GO:0046854	phosphatidylinositol phosphorylation	The process of introducing one or more phosphate groups into a phosphatidylinositol, any glycerophosphoinositol having one phosphatidyl group esterified to one of the hydroxy groups of inositol.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
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.

Asymmetric/Biological Unit
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	2czh
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	3.1.3.25
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	IMPA2_HUMAN \| O14732	:	2czi 2czk 2ddk 2fvz

2czi	CRYSTAL STRUCTURE OF THE TRIGONAL FORM OF IMPA2 WITH CALCIUM AND PHOSPHATE
2czk	CRYSTAL STRUCTURE OF THE TRIGONAL FORM OF IMPA2
2ddk	CRYSTAL STRUCTURE OF THE ORTHORHOMBIC FORM OF IMPA2

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Ligands, Modified Residues, Ions (1, 2)

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Cis Peptide Bonds (0, 0)

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