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(-) Description

Title :  CRYSTAL STRUCTURE OF MS0616
 
Authors :  T. Hosaka, A. Nishino, K. -T. Uchikubo, S. Kishishita, K. Murayama, M. Shirouzu, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  24 Jul 06  (Deposition) - 24 Jan 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.62
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Hosaka, A. Nishino, K. -T. Uchikubo, S. Kishishita, K. Murayama, M. Shirouzu, S. Yokoyama
Crystal Structure Of Ms0616
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MS0616
    Chains: A, B
    EC Number: 3.6.1.52, 3.6.1.-
    Engineered: YES
    Expression System Plasmid: PX051128-08
    Expression System Vector Type: PLASMID
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: CELL-FREE PROTEIN SYNTHESIS
    Synonym: DIPHOSPHOINOSITOL POLYPHOSPHATE PHOSPHOHYDROLASE 2, DIPP-2, DIADENOSINE 5',5'''-P1,P6-HEXAPHOSPHATE HYDROLASE 2, NUCLEOSIDE DIPHOSPHATE-LINKED MOIETY X MOTIF 4, NUDIX MOTIF 4

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2DUK)

(-) Sites  (0, 0)

(no "Site" information available for 2DUK)

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:123 -B:123

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DUK)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NUDIXPS51462 Nudix hydrolase domain profile.NUDT4_MOUSE17-143
 		  2A:10-136
B:10-136
2NUDIX_BOXPS00893 Nudix box signature.NUDT4_MOUSE50-71
 		  2A:43-64
B:43-64
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NUDIXPS51462 Nudix hydrolase domain profile.NUDT4_MOUSE17-143
 		  1A:10-136
-
2NUDIX_BOXPS00893 Nudix box signature.NUDT4_MOUSE50-71
 		  1A:43-64
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NUDIXPS51462 Nudix hydrolase domain profile.NUDT4_MOUSE17-143
 		  1-
B:10-136
2NUDIX_BOXPS00893 Nudix box signature.NUDT4_MOUSE50-71
 		  1-
B:43-64

(-) Exons   (0, 0)

(no "Exon" information available for 2DUK)

(-) Sequences/Alignments

Asymmetric 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:138
 aligned with NUDT4_MOUSE | Q8R2U6 from UniProtKB/Swiss-Prot  Length:179

    Alignment length:138
                                    17        27        37        47        57        67        77        87        97       107       117       127       137        
          NUDT4_MOUSE     8 TRTYDREGFKKRAACLCFRSEQEDEVLLVSSSRYPDQWIVPGGGMEPEEEPGGAAVREVYEEAGVKGKLGRLLGIFENQDRKHRTYVYVLTVTEILEDWEDSVNIGRKREWFKVEDAIKVLQCHKPVHAEYLEKLKLG 145
               SCOP domains d2duka_ A: automated matches                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eeeeeeeee......eeeeee.......ee..eee.....hhhhhhhhhhhhhh.eeeeeeeeeeeeee....eeeeeeeeeeeee.....hhhhhh..eeeeehhhhhhhhhh.hhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ---------NUDIX  PDB: A:10-136 UniProt: 17-143                                                                                           -- PROSITE (1)
                PROSITE (2) ------------------------------------------NUDIX_BOX  PDB: A:43-6-------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2duk A   1 TRTYDREGFKKRAACLCFRSEQEDEVLLVSSSRYPDQWIVPGGGMEPEEEPGGAAVREVYEEAGVKGKLGRLLGIFENQDRKHRTYVYVLTVTEILEDWEDSVNIGRKREWFKVEDAIKVLQCHKPVHAEYLEKLKLG 138
                                    10        20        30        40        50        60        70        80        90       100       110       120       130        


Chain B from PDB  Type:PROTEIN  Length:132
 aligned with NUDT4_MOUSE | Q8R2U6 from UniProtKB/Swiss-Prot  Length:179

    Alignment length:138
                                    17        27        37        47        57        67        77        87        97       107       117       127       137        
          NUDT4_MOUSE     8 TRTYDREGFKKRAACLCFRSEQEDEVLLVSSSRYPDQWIVPGGGMEPEEEPGGAAVREVYEEAGVKGKLGRLLGIFENQDRKHRTYVYVLTVTEILEDWEDSVNIGRKREWFKVEDAIKVLQCHKPVHAEYLEKLKLG 145
               SCOP domains d2dukb_ B: automated matches                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eeeeeeeee......eeeeee.......ee..eee.....hhhhhhhhhhhhh..eeeeeeeeeeeeee....eeeeeeeeeeeee....------...eeeeehhhhhhhhh....hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ---------NUDIX  PDB: B:10-136 UniProt: 17-143                                                                                           -- PROSITE (1)
                PROSITE (2) ------------------------------------------NUDIX_BOX  PDB: B:43-6-------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2duk B   1 TRTYDREGFKKRAACLCFRSEQEDEVLLVSSSRYPDQWIVPGGGMEPEEEPGGAAVREVYEEAGVKGKLGRLLGIFENQDRKHRTYVYVLTVTEILEDW------GRKREWFKVEDAIKVLQCHKPVHAEYLEKLKLG 138
                                    10        20        30        40        50        60        70        80        90        |-     | 110       120       130        
                                                                                                                             99    106
   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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2DUK)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 19)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (NUDT4_MOUSE | Q8R2U6)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    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:0050072    m7G(5')pppN diphosphatase activity    Catalysis of the reaction: 7-methylguanosine 5'-triphospho-5'-polynucleotide + H2O = 7-methylguanosine 5'-phosphate + polynucleotide.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0030515    snoRNA binding    Interacting selectively and non-covalently with small nucleolar RNA.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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