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(-) Description

Title :  STRUCTURAL STUDIES OF METAL BINDING BY INOSITOL MONOPHOSPHATASE: EVIDENCE FOR TWO-METAL ION CATALYSIS
 
Authors :  R. Bone
Date :  08 Feb 94  (Deposition) - 27 Feb 95  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Bone, L. Frank, J. P. Springer, J. R. Atack
Structural Studies Of Metal Binding By Inositol Monophosphatase: Evidence For Two-Metal Ion Catalysis.
Biochemistry V. 33 9468 1994
PubMed-ID: 8068621  |  Reference-DOI: 10.1021/BI00198A012
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - INOSITOL MONOPHOSPHATASE
    ChainsA, B
    EC Number3.1.3.25
    EngineeredYES
    GeneCDNA
    OrganBRAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2MN6Ligand/IonMANGANESE (II) ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:70 , ASP A:90 , ILE A:92 , CL A:281 , HOH A:287BINDING SITE FOR RESIDUE MN A 278
02AC2SOFTWAREASP A:90 , ASP A:93 , ASP A:220 , CL A:281BINDING SITE FOR RESIDUE MN A 279
03AC3SOFTWAREGLU A:70 , CL A:281 , HOH A:285 , HOH A:286 , HOH A:288BINDING SITE FOR RESIDUE MN A 280
04AC4SOFTWAREGLU A:70 , MN A:278 , MN A:279 , MN A:280BINDING SITE FOR RESIDUE CL A 281
05AC5SOFTWAREGLU B:70 , ASP B:90 , ILE B:92 , THR B:95 , MN B:280 , CL B:281 , HOH B:288BINDING SITE FOR RESIDUE MN B 278
06AC6SOFTWAREASP B:90 , ASP B:93 , ASP B:220 , CL B:281 , HOH B:302BINDING SITE FOR RESIDUE MN B 279
07AC7SOFTWAREGLU B:70 , THR B:95 , MN B:278 , CL B:281 , HOH B:285 , HOH B:286 , HOH B:287BINDING SITE FOR RESIDUE MN B 280
08AC8SOFTWAREMN B:278 , MN B:279 , MN B:280BINDING SITE FOR RESIDUE CL B 281
09M1UNKNOWNGLU A:70 , ASP A:90 , PRO A:91 , ILE A:92 , ASP A:93 , GLY A:94 , THR A:95 , ASP A:220NULL
10M2UNKNOWNGLU B:70 , ASP B:90 , PRO B:91 , ILE B:92 , ASP B:93 , GLY B:94 , THR B:95 , ASP B:220NULL

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:24 -A:125
2B:24 -B:125

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ile A:185 -Pro A:186
2Ile B:185 -Pro B:186

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric/Biological Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_049600I109VIMPA1_HUMANPolymorphism204781A/BI109V

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IMP_1PS00629 Inositol monophosphatase family signature 1.IMPA1_HUMAN87-100
 
  2A:87-100
B:87-100
2IMP_2PS00630 Inositol monophosphatase family signature 2.IMPA1_HUMAN219-233
 
  2A:219-233
B:219-233

(-) Exons   (8, 16)

Asymmetric/Biological Unit (8, 16)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002561081aENSE00002126032chr8:82598928-82598487442IMPA1_HUMAN-00--
1.3aENST000002561083aENSE00002163677chr8:82593819-8259373387IMPA1_HUMAN1-21212A:5-21
B:5-21
17
17
1.4aENST000002561084aENSE00000909941chr8:82593018-82592885134IMPA1_HUMAN22-66452A:22-66
B:22-66
45
45
1.5ENST000002561085ENSE00000909940chr8:82591465-82591361105IMPA1_HUMAN66-101362A:66-101
B:66-101
36
36
1.7aENST000002561087aENSE00000909939chr8:82588514-8258846946IMPA1_HUMAN101-116162A:101-116
B:101-116
16
16
1.9dENST000002561089dENSE00002145495chr8:82586184-82586076109IMPA1_HUMAN117-153372A:117-153
B:117-153
37
37
1.10dENST0000025610810dENSE00002149892chr8:82583282-82583174109IMPA1_HUMAN153-189372A:153-189
B:153-189
37
37
1.11bENST0000025610811bENSE00001682001chr8:82572902-82572751152IMPA1_HUMAN189-240522A:189-240
B:189-240
52
52
1.12cENST0000025610812cENSE00001747149chr8:82571701-825701961506IMPA1_HUMAN240-277382A:240-271
B:240-277
32
38

(-) 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:267
 aligned with IMPA1_HUMAN | P29218 from UniProtKB/Swiss-Prot  Length:277

    Alignment length:267
                                    14        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       
          IMPA1_HUMAN     5 WQECMDYAVTLARQAGEVVCEAIKNEMNVMLKSSPVDLVTATDQKVEKMLISSIKEKYPSHSFIGEESVAAGEKSILTDNPTWIIDPIDGTTNFVHRFPFVAVSIGFAVNKKIEFGVVYSCVEGKMYTARKGKGAFCNGQKLQVSQQEDITKSLLVTELGSSRTPETVRMVLSNMEKLFCIPVHGIRSVGTAAVNMCLVATGGADAYYEMGIHCWDVAGAGIIVTEAGGVLMDVTGGPFDLMSRRVIAANNRILAERIAKEIQVIPL 271
               SCOP domains d1imca_ A: Inositol monophosphatase                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1imcA01 A:5-146 Fructose-1,6-Bisphosphatase, subunit A, domain 1                                                                              1imcA02 A:147-270  [code=3.40.190.80, no name defined]                                                                      - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhh....eeeehhhhhh..........eeeee....hhhhhh.....eeeeeee.....eeeeeeee...eeeeee...eeeee..............eeeee.......hhhhhhhhhhhhhhhh...eeee....hhhhhhhhhh....eeeee...hhhhhhhhhhhhhh..eeee...........eeeeee.hhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------V------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------IMP_1         ----------------------------------------------------------------------------------------------------------------------IMP_2          -------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3a        Exon 1.4a  PDB: A:22-66 UniProt: 22-66       ----------------------------------Exon 1.7a       ------------------------------------Exon 1.10d  PDB: A:153-189           --------------------------------------------------Exon 1.12c  PDB: A:240-271       Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------Exon 1.5  PDB: A:66-101             ---------------Exon 1.9d  PDB: A:117-153            -----------------------------------Exon 1.11b  PDB: A:189-240 UniProt: 189-240         ------------------------------- Transcript 1 (2)
                 1imc A   5 WQECMDYAVTLARQAGEVVCEAIKNEMNVMLKSSPVDLVTATDQKVEKMLISSIKEKYPSHSFIGEESVAAGEKSILTDNPTWIIDPIDGTTNFVHRFPFVAVSIGFAVNKKIEFGVVYSCVEGKMYTARKGKGAFCNGQKLQVSQQEDITKSLLVTELGSSRTPETVRMVLSNMEKLFCIPVHGIRSVGTAAVNMCLVATGGADAYYEMGIHCWDVAGAGIIVTEAGGVLMDVTGGPFDLMSRRVIAANNRILAERIAKEIQVIPL 271
                                    14        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       

Chain B from PDB  Type:PROTEIN  Length:273
 aligned with IMPA1_HUMAN | P29218 from UniProtKB/Swiss-Prot  Length:277

    Alignment length:273
                                    14        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   
          IMPA1_HUMAN     5 WQECMDYAVTLARQAGEVVCEAIKNEMNVMLKSSPVDLVTATDQKVEKMLISSIKEKYPSHSFIGEESVAAGEKSILTDNPTWIIDPIDGTTNFVHRFPFVAVSIGFAVNKKIEFGVVYSCVEGKMYTARKGKGAFCNGQKLQVSQQEDITKSLLVTELGSSRTPETVRMVLSNMEKLFCIPVHGIRSVGTAAVNMCLVATGGADAYYEMGIHCWDVAGAGIIVTEAGGVLMDVTGGPFDLMSRRVIAANNRILAERIAKEIQVIPLQRDDED 277
               SCOP domains d1imcb_ B: Inositol monophosphatase                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1imcB01 B:5-146 Fructose-1,6-Bisphosphatase, subunit A, domain 1                                                                              1imcB02 B:147-276  [code=3.40.190.80, no name defined]                                                                            - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhh....eeeehhhhhh..........eeeee....hhhhhh.....eeeeeee.....eeeeeeee...eeeeee...eeeee..............eeeee.......hhhhhhhhhhhhhhhh...eeee....hhhhhhhhhh....eeeee...hhhhhhhhhhhhhh..eeee...........eeeeee.hhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------V------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------IMP_1         ----------------------------------------------------------------------------------------------------------------------IMP_2          -------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3a        Exon 1.4a  PDB: B:22-66 UniProt: 22-66       ----------------------------------Exon 1.7a       ------------------------------------Exon 1.10d  PDB: B:153-189           --------------------------------------------------Exon 1.12c  PDB: B:240-277             Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------Exon 1.5  PDB: B:66-101             ---------------Exon 1.9d  PDB: B:117-153            -----------------------------------Exon 1.11b  PDB: B:189-240 UniProt: 189-240         ------------------------------------- Transcript 1 (2)
                 1imc B   5 WQECMDYAVTLARQAGEVVCEAIKNEMNVMLKSSPVDLVTATDQKVEKMLISSIKEKYPSHSFIGEESVAAGEKSILTDNPTWIIDPIDGTTNFVHRFPFVAVSIGFAVNKKIEFGVVYSCVEGKMYTARKGKGAFCNGQKLQVSQQEDITKSLLVTELGSSRTPETVRMVLSNMEKLFCIPVHGIRSVGTAAVNMCLVATGGADAYYEMGIHCWDVAGAGIIVTEAGGVLMDVTGGPFDLMSRRVIAANNRILAERIAKEIQVIPLQRDDED 277
                                    14        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   

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (23, 23)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (IMPA1_HUMAN | P29218)
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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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:0031403    lithium ion binding    Interacting selectively and non-covalently with lithium ions (Li+).
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) 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:0006661    phosphatidylinositol biosynthetic process    The chemical reactions and pathways resulting in the formation of phosphatidylinositol, any glycophospholipid in which the sn-glycerol 3-phosphate residue is esterified to the 1-hydroxyl group of 1D-myo-inositol.
    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.
    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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 Related Entries

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        IMPA1_HUMAN | P292181awb 1ima 1imb 1imd 1ime 1imf 2hhm 4as4

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