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(-) Description

Title :  INOSITOL 1,3,4,5,6-PENTAKISPHOSPHATE 2-KINASE IN COMPLEX WITH ADP
 
Authors :  J. I Banos-Sanz, J. Sanz-Aparicio, B. Gonzalez
Date :  12 Jun 12  (Deposition) - 04 Jul 12  (Release) - 05 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Phytic Acid, Protein Kinase, Inositide Signalling, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. I. Banos-Sanz, J. Sanz-Aparicio, H. Whitfield, C. Hamilton, C. A. Brearley, B. Gonzalez
Conformational Changes Undergone By Inositol 1, 3, 4, 5, 6-Pentakisphosphate 2-Kinase Upon Substrate Binding: The Role Of N-Lobe And Enantiomeric Substrate Preference
J. Biol. Chem. V. 287 29237 2012
PubMed-ID: 22745128  |  Reference-DOI: 10.1074/JBC.M112.363671

(-) Compounds

Molecule 1 - INOSITOL-PENTAKISPHOSPHATE 2-KINASE
    Chains: A
    EC Number: 2.7.1.158
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA PLYSS
    Expression System Vector: PKLSLT
    Expression System Vector Type: PLASMID
    Organism Common: THALE CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: INOSITOL-1,3,4,5,6-PENTAKISPHOSPHATE 2-KINASE, INS(1,3,4,5,6)P5 2-KINASE, ATIPK1, INSP5 2-KINASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2SO46Ligand/IonSULFATE ION
3ZN1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:18 , GLY A:19 , GLY A:20 , ALA A:21 , ASN A:22 , VAL A:24 , ARG A:40 , ASN A:147 , ASP A:148 , HIS A:149 , GLU A:166 , PHE A:243 , ASP A:407 , HOH A:2004 , HOH A:2005BINDING SITE FOR RESIDUE ADP A1435
2AC2SOFTWAREHIS A:320 , CYS A:330 , CYS A:333 , HIS A:346BINDING SITE FOR RESIDUE ZN A1436
3AC3SOFTWARELYS A:168 , LYS A:170 , LYS A:200 , ASN A:238 , GLU A:255 , SO4 A:1442 , HOH A:2045BINDING SITE FOR RESIDUE SO4 A1437
4AC4SOFTWAREGLU A:18 , ARG A:130 , ARG A:241 , GLY A:254 , HOH A:2004BINDING SITE FOR RESIDUE SO4 A1438
5AC5SOFTWARELYS A:230 , TYR A:233 , PRO A:262 , LEU A:288BINDING SITE FOR RESIDUE SO4 A1439
6AC6SOFTWAREGLY A:98 , PRO A:99 , LYS A:100 , TYR A:203 , ARG A:303 , LYS A:425 , HOH A:2065BINDING SITE FOR RESIDUE SO4 A1440
7AC7SOFTWAREASN A:53 , SER A:54 , THR A:62 , SER A:63BINDING SITE FOR RESIDUE SO4 A1441
8AC8SOFTWARELYS A:170 , ARG A:192 , HIS A:196 , SO4 A:1437 , HOH A:2066BINDING SITE FOR RESIDUE SO4 A1442

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4AXE)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Arg A:46 -Asn A:47

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4AXE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4AXE)

(-) Exons   (0, 0)

(no "Exon" information available for 4AXE)

(-) 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:428
 aligned with IPPK_ARATH | Q93YN9 from UniProtKB/Swiss-Prot  Length:451

    Alignment length:434
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430    
           IPPK_ARATH     1 MEMILEEKDASDWIYRGEGGANLVLAYAGSSPLFVGKVIRIQKARRNDKAIKNANGVVSVLTSDEQHLWRENNELISSPNKEVLEQRYVKNVIIPLLGPKHVDAGVRVSVSKEFLECVDKKVTKQRPLWRVNAANVDTSHDSALILNDHSLFSQGISSGGDCISVEIKPKCGFLPTSRFIGKENMLKTSVSRFKMHQLLKLEYNEISEESEYDPLDLFSGSKESVLEAIKALYSTPQNNFRVFLNGSLILGGSGESTGRTSPEIGYAFEDALKGFIQSEDGHRTECFLQLVSDAVYGSGVLDRLLEIQKLDKLDIEGAIHSYYDLINQPCPICKEGKPLEAELSLHALPLDESLKIVKEYLIAATAKDCSIMISFQSRNAWDSEPSGDYVSLKPTNQTFDYKVHFIDLSLKPLKRMESYYKLDKKIISFYNRKQ 434
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee..hhhh.eeeeee...eeeeee.........eeeeee.....hhhhh.........hhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhh.......eeeeehhhhhhhhhhhhhhhhhhhhh..........eeeeee..........--..eeeeee.............hhhhhhhhh.hhhhhhhhhhhhh.........hhhhhh..hhhhhhhhhhhhhhh....eeeee..eeee..hhhhh...hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh.......---..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeee........-..eeee....eeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4axe A   1 MEMILEEKDASDWIYRGEGGANLVLAYAGSSPLFVGKVIRIQKARRNDKAIKNSNGVVSVLTSDEQHLWRENNELISSPNKEVLEQRYVQNVIIPLLGPKHVDAGVRVSVSKEFLECVDKKVTKQRPLWRVNAANVDTSHDSALILNDHSLFSQGIT--GDCISVEIKPKCGFLPTSRFIGKENMLKTSVSRFKMHQLLKLEYIEISEESEYDPLDLFSGSKERVLEAIKALYSTPQNNFRVFLNGSLILGGSGESTGRTSPEIGYAFEDALKGFIQSEDGHRTECFLQLVSDAVYGSGVLDRLLEIQKLDKLDIEGAIHCYYDIINQPCPIC---RPLEAELSLHALPLDESLKIVKEYLIAATAKDCSIMISFQSRNAWDSEP-GDYVSLKPTNQTFDYKVHFIDLSLKPLKRMESYYKLDKKIISFYNRKQ 434
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150      |160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330  |   |340       350       360       370       380    | |390       400       410       420       430    
                                                                                                                                                                                      157  |                                                                                                                                                                          333 337                                             385 |                                               
                                                                                                                                                                                         160                                                                                                                                                                                                                                387
   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 4AXE)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4AXE)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4AXE)

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (IPPK_ARATH | Q93YN9)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0035299    inositol pentakisphosphate 2-kinase activity    Catalysis of the reaction: 1D-myo-inositol 1,3,4,5,6-pentakisphosphate + ATP = 1D-myo-inositol hexakisphosphate + ADP + 2 H(+).
    GO:0032942    inositol tetrakisphosphate 2-kinase activity    Catalysis of the reaction: 1D-myo-inositol tetrakisphosphate + ATP = 1D-myo-inositol pentakisphosphate (containing 2-phosphate) + ADP.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    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:0030643    cellular phosphate ion homeostasis    Any process involved in the maintenance of an internal steady state of phosphate ions at the level of a cell.
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
    GO:0050832    defense response to fungus    Reactions triggered in response to the presence of a fungus that act to protect the cell or organism.
    GO:0051607    defense response to virus    Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
    GO:0040007    growth    The increase in size or mass of an entire organism, a part of an organism or a cell.
    GO:0048527    lateral root development    The process whose specific outcome is the progression of the lateral root over time, from its formation to the mature structure. A lateral root is one formed from pericycle cells located on the xylem radius of the root, as opposed to the initiation of the main root from the embryo proper.
    GO:0010264    myo-inositol hexakisphosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of phytic acid, myo-inositol hexakisphosphate, a regulator of intracellular signaling, a highly abundant animal anti-nutrient and a phosphate and mineral storage compound in plant seeds.
    GO:0055062    phosphate ion homeostasis    Any process involved in the maintenance of an internal steady state of phosphate ions within an organism or cell.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        IPPK_ARATH | Q93YN9: 2xal 2xam 2xan 2xao 2xar 3uds 3udt 3udz 4aqk 4axc 4axd 4axf 4lv7

(-) Related Entries Specified in the PDB File

2xal LEAD DERIVATIVE OF INOSITOL 1,3,4,5,6- PENTAKISPHOSPHATE 2-KINASE FROM A. THALIANA IN COMPLEX WITH ADP AND IP6.
2xam INOSITOL 1,3,4,5,6-PENTAKISPHOSPHATE 2-KINASE FROM A. THALIANA IN COMPLEX WITH ADP AND IP6.
2xan INOSITOL 1,3,4,5,6-PENTAKISPHOSPHATE 2-KINASE FROM A. THALIANA IN COMPLEX WITH AMP PNP AND IP5
2xao INOSITOL 1,3,4,5,6-PENTAKISPHOSPHATE 2-KINASE FROM A. THALIANA IN COMPLEX WITH IP5
2xar INOSITOL 1,3,4,5,6-PENTAKISPHOSPHATE 2-KINASE FROM A. THALIANA IN COMPLEX WITH IP6.
4aqk INOSITOL 1,3,4,5,6-PENTAKISPHOSPHATE 2-KINASE IN COMPLEX WITH ADP AND IP6
4axc INOSITOL 1,3,4,5,6-PENTAKISPHOSPHATE 2-KINASE APO FORM
4axd INOSITOL 1,3,4,5,6-PENTAKISPHOSPHATE 2-KINASE IN COMPLEX WITH AMPPNP
4axf INSP5 2-K IN COMPLEX WITH INS(3,4,5,6)P4 PLUS AMPPNP