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(-) Description

Title :  INOSITOL 1,3,4-TRISPHOSPHATE 5/6-KINASE IN COMPLEX WITH MG2+/ADP/INS(1,3,4,6)P4
 
Authors :  G. J. Miller, M. P. Wilson, P. W. Majerus, J. H. Hurley
Date :  08 Mar 05  (Deposition) - 19 Apr 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.24
Chains :  Asym./Biol. Unit :  X
Keywords :  Inositol Phosphate Kinase, Atp-Grasp, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. J. Miller, M. P. Wilson, P. W. Majerus, J. H. Hurley
Specificity Determinants In Inositol Polyphosphate Synthesis: Crystal Structure Of Inositol 1, 3, 4-Trisphosphat 5/6-Kinase.
Mol. Cell V. 18 201 2005
PubMed-ID: 15837423  |  Reference-DOI: 10.1016/J.MOLCEL.2005.03.016

(-) Compounds

Molecule 1 - INOSITOL 1,3,4-TRISPHOSPHATE 5/6-KINASE
    Chains: X
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-6P3
    Expression System Strain: ROSETTA(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: INOSITOL PHOSPHATE KINASE, ATP-GRASP
    Organism Scientific: ENTAMOEBA HISTOLYTICA
    Organism Taxid: 294381

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : X

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2I4P1Ligand/Ion(1S,3R,4R,6S)-1,3,4,6-TETRAPKISPHOSPHATE
3MG2Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP X:275 , ASP X:289 , ADP X:871 , I4P X:2699 , HOH X:2700BINDING SITE FOR RESIDUE MG X 1295
2AC2SOFTWAREASP X:289 , ASN X:291 , ADP X:871 , HOH X:2702 , HOH X:2703BINDING SITE FOR RESIDUE MG X 1296
3AC3SOFTWAREARG X:94 , PRO X:109 , LYS X:136 , HIS X:147 , MET X:149 , GLN X:168 , HIS X:169 , TYR X:170 , ILE X:171 , HIS X:173 , ILE X:177 , SER X:194 , LEU X:195 , ASN X:210 , ASP X:275 , VAL X:288 , ASP X:289 , MG X:1295 , MG X:1296 , I4P X:2699 , HOH X:2700 , HOH X:2702 , HOH X:2703 , HOH X:2714 , HOH X:2770 , HOH X:2919 , HOH X:3186 , HOH X:3205BINDING SITE FOR RESIDUE ADP X 871
4AC4SOFTWARELYS X:17 , THR X:20 , LYS X:57 , GLN X:141 , GLY X:142 , HIS X:147 , LYS X:179 , PHE X:181 , ASP X:275 , ASP X:289 , ASN X:291 , PRO X:294 , SER X:295 , TYR X:296 , ADP X:871 , MG X:1295 , HOH X:2700 , HOH X:2702 , HOH X:2715 , HOH X:2781 , HOH X:2840 , HOH X:2856 , HOH X:2919 , HOH X:2922 , HOH X:2927 , HOH X:2930 , HOH X:2980 , HOH X:3044 , HOH X:3074 , HOH X:3119 , HOH X:3165 , HOH X:3172 , HOH X:3201BINDING SITE FOR RESIDUE I4P X 2699

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Z2O)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Leu X:82 -Glu X:83
2Leu X:131 -Pro X:132
3Phe X:163 -Pro X:164

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Z2O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Z2O)

(-) Exons   (0, 0)

(no "Exon" information available for 1Z2O)

(-) 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 X from PDB  Type:PROTEIN  Length:311
 aligned with ITPK1_ENTHI | Q9XYQ1 from UniProtKB/Swiss-Prot  Length:319

    Alignment length:311
                                    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       284       294       304       314 
          ITPK1_ENTHI     5 QTVSLFIWLPESKQKTLFISTKNHTQFELNNIIFDVTLSTELPDKEPNAIITKRTHPVGKMADEMRKYEKDHPKVLFLESSAIHDMMSSREEINALLIKNNIPIPNSFSVKSKEEVIQLLQSKQLILPFIVKPENAQGTFNAHQMKIVLEQEGIDDIHFPCLCQHYINHNNKIVKVFCIGNTLKWQTRTSLPNVHRCGIKSVDFNNQHLEDILSWPEGVIDKQDIIENSANRFGSKILEDPILLNLTSEAEMRDLAYKVRCALGVQLCGIDFIKENEQGNPLVVDVNVFPSYGGKVDFDWFVEKVALCYTE 315
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Ins134_P3_kin-1z2oX01 X:5-309                                                                                                                                                                                                                                                                                    ------ Pfam domains
         Sec.struct. author .eeeeeee.hhhhhhhhh.....eeeeee..eeeeeeee.........eeee......hhhhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhhhhh......eeee.hhhhhhhhhhh......eeeee.....hhhh.eeeee.hhhhhh.....eeeee.......eeeeeee..eeeeeee............eeeee..hhhhhhhh.....hhhhhhhhhh.................hhhhhhhhhhhhhhhhh..eeeeeeehhhhh...eeeeeee........hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z2o X   5 QTVSLFIWLPESKQKTLFISTKNHTQFELNNIIFDVTLSTELPDKEPNAIITKRTHPVGKMADEMRKYEKDHPKVLFLESSAIHDMMSSREEINALLIKNNIPIPNSFSVKSKEEVIQLLQSKQLILPFIVKPENAQGTFNAHQMKIVLEQEGIDDIHFPCLCQHYINHNNKIVKVFCIGNTLKWQTRTSLPNVHRCGIKSVDFNNQHLEDILSWPEGVIDKQDIIENSANRFGSKILEDPILLNLTSEAEMRDLAYKVRCALGVQLCGIDFIKENEQGNPLVVDVNVFPSYGGKVDFDWFVEKVALCYTE 315
                                    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       284       294       304       314
   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  (0, 0)

(no "SCOP Domain" information available for 1Z2O)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1Z2O)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: ATP-grasp (83)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain X   (ITPK1_ENTHI | Q9XYQ1)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0047325    inositol tetrakisphosphate 1-kinase activity    Catalysis of the reaction: 1D-myo-inositol 3,4,5,6-tetrakisphosphate + ATP = 1D-myo-inositol 1,3,4,5,6-pentakisphosphate + ADP.
    GO:0052726    inositol-1,3,4-trisphosphate 5-kinase activity    Catalysis of the reaction: 1D-myo-inositol 1,3,4-trisphosphate + ATP = 1D-myo-inositol 1,3,4,5-tetrakisphosphate + ADP + 2 H(+).
    GO:0052725    inositol-1,3,4-trisphosphate 6-kinase activity    Catalysis of the reaction: 1D-myo-inositol 1,3,4-trisphosphate + ATP = 1D-myo-inositol 1,3,4,6-tetrakisphosphate + ADP + 2 H(+).
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    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:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0032957    inositol trisphosphate metabolic process    The chemical reactions and pathways involving myo-inositol phosphate, 1,2,3,4,5,6-cyclohexanehexol, with three phosphate groups attached.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
cellular component
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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        ITPK1_ENTHI | Q9XYQ1: 1z2n 1z2p

(-) Related Entries Specified in the PDB File

1z2n INOSITOL 1,3,4-TRISPHOSPHATE 5/6-KINASE COMPLEXED MG2+/ADP
1z2p INOSITOL 1,3,4-TRISPHOSPHATE 5/6-KINASE IN COMPLEX WITH MG2+/AMP-PCP/INS(1,3,4)P3