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(-) Description

Title :  CRYSTAL STRUCTURE OF PIP4KIIBETA COMPLEX WITH AMPPNP
 
Authors :  K. Takeuchi, Y. H. Lo, K. Sumita, M. Senda, J. Terakawa, A. Dimitoris, J. W. Locasale, M. Sasaki, H. Yoshino, Y. Zhang, E. R. Kahoud, T. Takano T. Yokota, B. Emerling, J. A. Asara, T. Ishida, I. Shimada, T. Daikoku, L. C. Cantley, T. Senda, A. T. Sasaki
Date :  09 Oct 14  (Deposition) - 14 Oct 15  (Release) - 03 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Lipid Kinase, Phosphoinositide Signaling, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Sumita, Y. H. Lo, K. Takeuchi, M. Senda, S. Kofuji, Y. Ikeda, J. Terakawa, M. Sasaki, H. Yoshino, N. Majd, Y. Zheng, E. R. Kahoud, T. Yokota, B. M. Emerling, J. M. Asara, T. Ishida, J. W. Locasale, T. Daikoku, D. Anastasiou, T. Senda, A. T. Sasaki
The Lipid Kinase Pi5P4K Beta Is An Intracellular Gtp Sensor For Metabolism And Tumorigenesis
Mol. Cell V. 61 187 2016
PubMed-ID: 26774281  |  Reference-DOI: 10.1016/J.MOLCEL.2015.12.011

(-) Compounds

Molecule 1 - PHOSPHATIDYLINOSITOL 5-PHOSPHATE 4-KINASE TYPE-2 BETA
    Chains: A, B
    EC Number: 2.7.1.149
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 31-416
    Gene: PIP4K2B
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: 1-PHOSPHATIDYLINOSITOL 5-PHOSPHATE 4-KINASE 2-BETA, DIPHOSPHOINOSITIDE KINASE 2-BETA, PHOSPHATIDYLINOSITOL 5-PHOSPHATE 4- KINASE TYPE II BETA, PI(5)P 4-KINASE TYPE II BETA, PIP4KII-BETA, PTDINS(5)P-4-KINASE ISOFORM 2-BETA

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1ANP3Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:139 , VAL A:148 , ARG A:202 , ASN A:203 , VAL A:204 , LYS A:214BINDING SITE FOR RESIDUE ANP A 501
2AC2SOFTWARELYS A:96 , TYR A:98 , SER A:154 , ALA A:158 , HIS A:161 , ARG A:188 , GLU A:195 , TYR A:197BINDING SITE FOR RESIDUE ANP A 502
3AC3SOFTWAREPHE B:139 , VAL B:148 , ARG B:202 , ASN B:203 , VAL B:204 , LEU B:282BINDING SITE FOR RESIDUE ANP B 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3X03)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Thr A:137 -Arg A:138

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3X03)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3X03)

(-) Exons   (0, 0)

(no "Exon" information available for 3X03)

(-) 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:320
                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhh........hhhhhh.eeeeeee...........eeeeeeehhhhhhhhhhhh..hhhhhhhhhhh...ee...eee.....eeeeeehhhhhhhhhhhhhhhhhhhhhh........eeeeeeeee..eeeeeeeee..........eeeee.........hhhhhhh...eehhhhhhhh...ee.hhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeehhhhhhhhhhhhhhhh.............eee........eeeeeeee.....hhhhhhhhhhhhhhhhee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3x03 A  32 KVKLFRASEPILSVLMWGVNHTINELSNVPVPVMLMPDDFKAYSKIKVDNHLFNKENLPSRFKFKEYCPMVFRNLRERFGIDDQDYQNSVTRSAPINSTRFLTTYDRRFVIKTVSSEDVAEMHNILKKYHQFIVECHGNTLLPQFLGMYRLTVDGVETYMVVTRNVFSHRLTVHRKYDLKGSTVAREASDKEKAKDLPTFKDNDFLNEGQKLHVGEESKKNFLEKLKRDVEFLAQLKIMDYSLLVGIHDVDRAEQEEMEVEERAEDGPGEFDPSVDVYAMKSHESSPKKEVYFMAIIDILTVNPEQYSKRFNEFMSNILT 416
                                    41        51        61        71        81        91       101       111       121       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298     ||341       351       361       371|      406       416
                                                                                                                           129|                                                                                                                                                                    304|                              371|                   
                                                                                                                            137                                                                                                                                                                     338                               397                   


Chain B from PDB  Type:PROTEIN  Length:302
                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhh........hhhhhh.eeeeeeeee.........eeeeeeehhhhhhhhhhhh..hhhhhhhhhhh......eee.....eeeeeehhhhhhhhhhhhhhhhhhhhhh........eeeeeeeee..eeeeeeeee..........eeeee.................eehhhhhhhh......hhhhhhhhhhhhhhhhhh......eeeeeeeehhhhhh...............eee........eeeeeeee.....hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3x03 B  33 VKLFRASEPILSVLMWGVNHTINELSNVPVPVMLMPDDFKAYSKIKVDNHLFNKENLPSRFKFKEYCPMVFRNLRERFGIDDQDYQNSVTRSAPINRFLTTYDRRFVIKTVSSEDVAEMHNILKKYHQFIVECHGNTLLPQFLGMYRLTVDGVETYMVVTRNVFSHRLTVHRKYDLKGVAREASDKEKAKDLPTFKDNDFLNELHVGEESKKNFLEKLKRDVEFLAQLKIMDYSLLVGIHDVDRAEQRFFGPGEFDPSVDVYAMKSHESSPKKEVYFMAIIDILTPEQYSKRFNEFMSNILT 416
                                    42        52        62        72        82        92       102       112       122     ||141       151       161       171       181       191       201       211       223       233       243  ||   256       266       276       286      |337       347       357       367    || 404       414  
                                                                                                                         128|                                                                              219|                     246|                                        293|                                  372|                
                                                                                                                          138                                                                               222                      250                                         335                                   400
   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 3X03)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3X03)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3X03)

(-) Gene Ontology  (27, 27)

Asymmetric/Biological Unit(hide GO term definitions)

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    Thr A:137 - Arg A:138   [ RasMol ]  
 

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  3x03
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  PI42B_HUMAN | P78356
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 Related Entries

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

UniProtKB/Swiss-Prot
        PI42B_HUMAN | P78356: 1bo1 3wzz 3x01 3x02 3x04 3x05 3x06 3x07 3x08 3x09 3x0a 3x0b 3x0c

(-) Related Entries Specified in the PDB File

3wzz 3x01 3x02 3x04 3x05 3x06 3x07 3x08 3x09 3x0a 3x0b 3x0c