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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PHOSPHATIDYLINOSITOL-5-PHOSPHATE 4-KINASE TYPE-2 ALPHA
 
Authors :  L. Tresaugues, M. Moche, C. H. Arrowsmith, H. Berglund, C. Bountra, R. C A. M. Edwards, T. Ekblad, S. Flodin, S. Graslund, T. Karlberg, T. Koten E. Kouznetsova, T. Nyman, C. Persson, H. Schuler, M. I. Siponen, A. G. T E. Wahlberg, J. Weigelt, P. Nordlund
Date :  30 Mar 11  (Deposition) - 25 Jan 12  (Release) - 25 Jan 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.56
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transferase, Kinase, Signalling (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Tresaugues, M. Moche, C. H. Arrowsmith, H. Berglund, C. Bountra, R. Collins, A. M. Edwards, T. Ekblad, S. Flodin, S. Graslund, T. Karlberg, T. Kotenyova, E. Kouznetsova, T. Nyman, C. Persson, H. Schuler, M. I. Siponen, A. G. Thorsell, E. Wahlberg, J. Weigelt, P. Nordlund
Crystal Structure Of Human Phosphatidylinositol-5- Phosphate 4-Kinase Type-2 Alpha
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PHOSPHATIDYLINOSITOL-5-PHOSPHATE 4-KINASE TYPE-2 ALPHA
    ChainsA, B
    EC Number2.7.1.149
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC28-BSA4
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantR3 PRARE
    Expression System Vector TypePLASMID
    FragmentRESIDUES 35-405
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsPHOSPHORYL-ASPARTATE INTERMEDIATE IN POSITION 359
    Other Details - SourceMAMMALIAN GENE COLLECTION (MGC)
    Synonym1-PHOSPHATIDYLINOSITOL-5-PHOSPHATE 4-KINASE 2-ALPHA, DIPHOSPHOINOSITIDE KINASE 2-ALPHA, PIP5KIII, PHOSPHATIDYLINOSITOL-5-PHOSPHATE 4-KINASE TYPE II ALPHA, PI(5)P 4-KINASE TYPE II ALPHA, PIP4KII-ALPHA, PTDINS(4)P-5-KINASE B ISOFORM, PTDINS(4)P-5-KINASE C ISOFORM, PTDINS(5)P-4-KINASE ISOFORM 2-ALPHA

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1PHD2Mod. Amino AcidASPARTYL PHOSPHATE
2PO41Ligand/IonPHOSPHATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:213 , ARG A:219 , LYS A:234 , PHD A:359BINDING SITE FOR RESIDUE PO4 A1406

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2YBX)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Thr A:216 -Val A:217

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 3)

Asymmetric/Biological Unit (2, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_059764L7IPI42A_HUMANPolymorphism11813789AL29I
2UniProtVAR_024565N251SPI42A_HUMANPolymorphism10828317A/BN251S

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PIPKPS51455 Phosphatidylinositol phosphate kinase (PIPK) domain profile.PI42A_HUMAN33-405
 
  2A:35-405
B:35-405

(-) Exons   (0, 0)

(no "Exon" information available for 2YBX)

(-) 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:322
 aligned with PI42A_HUMAN | P48426 from UniProtKB/Swiss-Prot  Length:406

    Alignment length:400
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405
          PI42A_HUMAN     6 NLGSSVLASKTKTKKKHFVAQKVKLFRASDPLLSVLMWGVNHSINELSHVQIPVMLMPDDFKAYSKIKVDNHLFNKENMPSHFKFKEYCPMVFRNLRERFGIDDQDFQNSLTRSAPLPNDSQARSGARFHTSYDKRYIIKTITSEDVAEMHNILKKYHQYIVECHGITLLPQFLGMYRLNVDGVEIYVIVTRNVFSHRLSVYRKYDLKGSTVAREASDKEKAKELPTLKDNDFINEGQKIYIDDNNKKVFLEKLKKDVEFLAQLKLMDYSLLVGIHDVERAEQEEVECEENDGEEEGESDGTHPVGTPPDSPGNTLNSSPPLAPGEFDPNIDVYGIKCHENSPRKEVYFMAIIDILTHYDAKKKAAHAAKTVKHGAGAEISTVNPEQYSKRFLDFIGHIL 405
               SCOP domains d2                      ybxa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..----------------------.....hhhhhhhhhhhhhhhhhhh........hhhhhh.eeeeeeeee.........eeeeeeehhhhhhhhhhhh..hhhhhhhhhhh...ee..-----...eee.....eeeeeehhhhhhhhhhhhhhhhhhhhhh........eeeeeeeee..eeeeeeeee..........eeeee.........hhhhhh....eehhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.ee..eeeeeeeehhhhhhhhhh.--------------------------------..............eee........eeeeeeee...ee...-------------------...hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -I---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------S---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------PIPK  PDB: A:35-405 UniProt: 33-405                                                                                                                                                                                                                                                                                                                                                   PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ybx A  28 NL----------------------YFQSMDPLLSVLMWGVNHSINELSHVQIPVMLMPDDFKAYSKIKVDNHLFNKENMPSHFKFKEYCPMVFRNLRERFGIDDQDFQNSLTRSAPLPND-----GARFHTSYDKRYIIKTITSEDVAEMHNILKKYHQYIVECHGITLLPQFLGMYRLNVDGVEIYVIVTRNVFSHRLSVYRKYDLKGSTVAREASDKEKAKELPTLKDNDFINEGQKIYIDDNNKKVFLEKLKKDVEFLAQLKLMDYSLLVGIHDVERAEQEEVEC--------------------------------PLAPGEFDPNIDVYGIKCHENSPRKEVYFMAIIdILTHYDA-------------------STVNPEQYSKRFLDFIGHIL 405
                             |       -         -    |   35        45        55        65        75        85        95       105       115       125     | 135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       | -         -         -         -|      335       345       355   |   365|        -         -|      395       405
                             |                     30                                                                                            125   131                                                                                                                                                               293                              326                              359-PHD366                 386                   
                            29                                                                                                                                                                                                                                                                                                                                                                                                              

Chain B from PDB  Type:PROTEIN  Length:312
 aligned with PI42A_HUMAN | P48426 from UniProtKB/Swiss-Prot  Length:406

    Alignment length:377
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       
          PI42A_HUMAN    29 KLFRASDPLLSVLMWGVNHSINELSHVQIPVMLMPDDFKAYSKIKVDNHLFNKENMPSHFKFKEYCPMVFRNLRERFGIDDQDFQNSLTRSAPLPNDSQARSGARFHTSYDKRYIIKTITSEDVAEMHNILKKYHQYIVECHGITLLPQFLGMYRLNVDGVEIYVIVTRNVFSHRLSVYRKYDLKGSTVAREASDKEKAKELPTLKDNDFINEGQKIYIDDNNKKVFLEKLKKDVEFLAQLKLMDYSLLVGIHDVERAEQEEVECEENDGEEEGESDGTHPVGTPPDSPGNTLNSSPPLAPGEFDPNIDVYGIKCHENSPRKEVYFMAIIDILTHYDAKKKAAHAAKTVKHGAGAEISTVNPEQYSKRFLDFIGHIL 405
               SCOP domains d2ybxb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhh......hhhhhh.eeeeeeeee.........eeeeeeehhhhhhhhhhhh..hhhhhhhhhhh...ee...---....eee.....eeeeeehhhhhhhhhhhhhhhhhhhhhh........eeeeeeeee..eeeeeeeee..........eeeee.........hhhhhhh...eeehhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.....eeeeeeee....-----------------------------------------............eee........eeeeeeee........---------------------.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------S---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----PIPK  PDB: B:35-405 UniProt: 33-405                                                                                                                                                                                                                                                                                                                                                   PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ybx B  29 LYFQSMDPLLSVLMWGVNHSINELSHVQIPVMLMPDDFKAYSKIKVDNHLFNKENMPSHFKFKEYCPMVFRNLRERFGIDDQDFQNSLTRSAPLPNDS---SGARFHTSYDKRYIIKTITSEDVAEMHNILKKYHQYIVECHGITLLPQFLGMYRLNVDGVEIYVIVTRNVFSHRLSVYRKYDLKGSTVAREASDKEKAKELPTLKDNDFINEGQKIYIDDNNKKVFLEKLKKDVEFLAQLKLMDYSLLVGIHDVERA-----------------------------------------APGEFDPNIDVYGIKCHENSPRKEVYFMAIIdILTHYDA---------------------VNPEQYSKRFLDFIGHIL 405
                                    38        48        58        68        78        88        98       108       118       | - |     138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       | -         -         -         -       328       338       348       358|      | -         -       388       398       
                                                                                                                           126 130                                                                                                                                                         286                                       328                            359-PHD366                   388                 

   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/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (23, 23)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PI42A_HUMAN | P48426)
molecular function
    GO:0052811    1-phosphatidylinositol-3-phosphate 4-kinase activity    Catalysis of the reaction: a 1-phosphatidyl-1D-myo-inositol 4-phosphate + ATP = a 1-phosphatidyl-1D-myo-inositol 3,4-bisphosphate + ADP + 2 H(+).
    GO:0016308    1-phosphatidylinositol-4-phosphate 5-kinase activity    Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 4-phosphate + ATP = 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate + ADP + 2 H(+).
    GO:0016309    1-phosphatidylinositol-5-phosphate 4-kinase activity    Catalysis of the reaction: ATP + 1-phosphatidyl-1D-myo-inositol 5-phosphate = ADP + 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate.
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    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:0016307    phosphatidylinositol phosphate kinase activity    Catalysis of the reaction: ATP + a phosphatidylinositol phosphate = ADP + a phosphatidylinositol bisphosphate.
    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:0035855    megakaryocyte development    The process whose specific outcome is the progression of a megakaryocyte cell over time, from its formation to the mature structure. Megakaryocyte development does not include the steps involved in committing a cell to a megakaryocyte fate. A megakaryocyte is a giant cell 50 to 100 micron in diameter, with a greatly lobulated nucleus, found in the bone marrow.
    GO:0006661    phosphatidylinositol biosynthetic process    The chemical reactions and pathways resulting in the formation of phosphatidylinositol, any glycophospholipid in which the sn-glycerol 3-phosphate residue is esterified to the 1-hydroxyl group of 1D-myo-inositol.
    GO:0046488    phosphatidylinositol metabolic process    The chemical reactions and pathways involving phosphatidylinositol, any glycophospholipid in which a sn-glycerol 3-phosphate residue is esterified to the 1-hydroxyl group of 1D-myo-inositol.
    GO:0046854    phosphatidylinositol phosphorylation    The process of introducing one or more phosphate groups into a phosphatidylinositol, any glycerophosphoinositol having one phosphatidyl group esterified to one of the hydroxy groups of inositol.
    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.
    GO:2000786    positive regulation of autophagosome assembly    Any process that activates or increases the frequency, rate or extent of autophagic vacuole assembly.
    GO:0010506    regulation of autophagy    Any process that modulates the frequency, rate or extent of autophagy. Autophagy is the process in which cells digest parts of their own cytoplasm.
    GO:0014066    regulation of phosphatidylinositol 3-kinase signaling    Any process that modulates the frequency, rate or extent of signal transduction mediated by the phosphatidylinositol 3-kinase cascade.
cellular component
    GO:0005776    autophagosome    A double-membrane-bounded compartment that engulfs endogenous cellular material as well as invading microorganisms to target them to the vacuole/lysosome for degradation as part of macroautophagy.
    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.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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