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(-) Description

Title :  CRYSTAL STRUCTURE OF PIP4KIIBETA COMPLEX WITH GMPPNP
 
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 :  2.60
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, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1GNP4Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:139 , VAL A:148 , LYS A:150 , ASN A:203 , VAL A:204 , PHE A:205 , LYS A:214 , THR A:237 , ASP A:369 , HOH A:608 , HOH A:609BINDING SITE FOR RESIDUE GNP A 501
2AC2SOFTWARELYS A:96 , TYR A:98 , SER A:154 , HIS A:161 , ASN A:162 , ARG A:188 , TYR A:197BINDING SITE FOR RESIDUE GNP A 502
3AC3SOFTWAREGLN A:293 , GLU A:297 , LYS B:72 , LYS B:96 , TYR B:98 , SER B:154 , VAL B:157 , ALA B:158 , HIS B:161 , ARG B:188 , TYR B:197BINDING SITE FOR RESIDUE GNP A 503
4AC4SOFTWAREPHE B:139 , VAL B:148 , ASN B:203 , VAL B:204 , PHE B:205 , LYS B:214 , ASP B:369 , HOH B:608BINDING SITE FOR RESIDUE GNP B 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3X04)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3X04)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3X04)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3X04)

(-) Exons   (0, 0)

(no "Exon" information available for 3X04)

(-) 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:314
                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhh......hhhhhh.eeeeeee...........eeeeeeehhhhhhhhhhhh..hhhhhhhhhhh......eee.....eeeeeehhhhhhhhhhhhhhhhhhhhhh........eeeeeeeee..eeeeeeeee..........eeeee.........hhhhhh......hhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeehhhhhhhhhhhhhh.............eee........eeeeeeee....hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3x04 A  33 VKLFRASEPILSVLMWGVNHTINELSNVPVPVMLMPDDFKAYSKIKVDNHLFNKENLPSRFKFKEYCPMVFRNLRERFGIDDQDYQNSVTRSAPINRFLTTYDRRFVIKTVSSEDVAEMHNILKKYHQFIVECHGNTLLPQFLGMYRLTVDGVETYMVVTRNVFSHRLTVHRKYDLKGSTVAREASDKEKAKDLPTFKDNDFLNEGQKLHVGEESKKNFLEKLKRDVEFLAQLKIMDYSLLVGIHDVDRAEQEEMEVEERAGPGEFDPSVDVYAMKSHESSPKKEVYFMAIIDILVNPEQYSKRFNEFMSNILT 416
                                    42        52        62        72        82        92       102       112       122     ||141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301||     346       356       366    || 402       412    
                                                                                                                         128|                                                                                                                                                                 302|                              371|                  
                                                                                                                          138                                                                                                                                                                  338                               398                  


Chain B from PDB  Type:PROTEIN  Length:297
                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhh.......hhhhhh.eeeeeee...........eeeeeeehhhhhhhhhhhh..hhhhhhhhhhh......eee.....eeeeeehhhhhhhhhhhhhhhhhhhhhh........eeeeeeeee..eeeeeeeee..........eeeee........hhhhh...eehhhhhhh........hhhhhhhhhhhhhhhhh.....eeeeeeeehhhhhh.............eee.......eeeeeeee.....hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3x04 B  33 VKLFRASEPILSVLMWGVNHTINELSNVPVPVMLMPDDFKAYSKIKVDNHLFNKENLPSRFKFKEYCPMVFRNLRERFGIDDQDYQNSVTRSAPINRFLTTYDRRFVIKTVSSEDVAEMHNILKKYHQFIVECHGNTLLPQFLGMYRLTVDGVETYMVVTRNVFSHRLTVHRKYDLKVAREASDKEKAKDLPTFKDNDFLNEGQKLHVKKNFLEKLKRDVEFLAQLKIMDYSLLVGIHDVDRAEQFGPGEFDPSVDVYAMKSHESSPKEVYFMAIIDILTPEQYSKRFNEFMSNILT 416
                                    42        52        62        72        82        92       102       112       122     ||141       151       161       171       181       191       201       211      |224       234       244       258       268       278       288    || 341       351      |362       372|      409       
                                                                                                                         128|                                                                             218|                           252|                                 293|                  358|         372|                
                                                                                                                          138                                                                              222                            257                                  337                   360          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 3X04)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3X04)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3X04)

(-) Gene Ontology  (27, 27)

Asymmetric/Biological Unit(hide GO term definitions)

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  3x04
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  PI42B_HUMAN | P78356
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  2.7.1.149
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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 3x03 3x05 3x06 3x07 3x08 3x09 3x0a 3x0b 3x0c

(-) Related Entries Specified in the PDB File

3wzz 3x01 3x02 3x03 3x05 3x06 3x07 3x08 3x09 3x0a 3x0b 3x0c