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(-) Description

Title :  CRYSTAL STRUCTURE AND ALLOSTERIC ACTIVATION OF PROTEIN KINASE C BETA II
 
Authors :  T. A. Leonard, B. Rozycki, L. F. Saidi, G. Hummer, J. H. Hurley
Date :  28 Oct 10  (Deposition) - 02 Feb 11  (Release) - 02 Feb 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  4.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Kinase, Phosphorylation, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. A. Leonard, B. Rozycki, L. F. Saidi, G. Hummer, J. H. Hurley
Crystal Structure And Allosteric Activation Of Protein Kinase C Beta Ii
Cell(Cambridge, Mass. ) V. 144 55 2011
PubMed-ID: 21215369  |  Reference-DOI: 10.1016/J.CELL.2010.12.013

(-) Compounds

Molecule 1 - PROTEIN KINASE C BETA TYPE
    ChainsA
    EC Number2.7.11.13
    EngineeredYES
    Expression SystemTRICHOPLUSIA NI
    Expression System Taxid7111
    FragmentPKC BETA II
    GenePRKCB, PKCB, PRKCB1
    MutationYES
    Organism CommonBROWN RAT,RAT,RATS
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymPKC-B, PKC-BETA

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 9)

Asymmetric/Biological Unit (5, 9)
No.NameCountTypeFull Name
1ANP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2CA3Ligand/IonCALCIUM ION
3SEP1Mod. Amino AcidPHOSPHOSERINE
4TPO2Mod. Amino AcidPHOSPHOTHREONINE
5ZN2Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:187 , ASP A:193 , ASP A:246 , TRP A:247 , ASP A:248BINDING SITE FOR RESIDUE CA A 674
2AC2SOFTWAREMET A:186 , ASP A:187 , ASP A:246 , ASP A:248 , ASP A:254BINDING SITE FOR RESIDUE CA A 675
3AC3SOFTWAREASP A:248 , SER A:251 , ARG A:252 , ASP A:254BINDING SITE FOR RESIDUE CA A 676
4AC4SOFTWAREHIS A:102 , THR A:134 , CYS A:135BINDING SITE FOR RESIDUE ZN A 750
5AC5SOFTWARECYS A:115 , CYS A:118 , HIS A:140 , CYS A:143BINDING SITE FOR RESIDUE ZN A 751
6AC6SOFTWAREALA A:369 , LYS A:371 , MET A:420 , GLU A:421 , TYR A:422 , VAL A:423 , ASP A:484BINDING SITE FOR RESIDUE ANP A 800

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ile A:201 -Pro A:202

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (6, 6)

Asymmetric/Biological Unit (6, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_DAG_PE_2PS50081 Zinc finger phorbol-ester/DAG-type profile.KPCB_RAT36-86
101-151
  1-
A:101-151
2ZF_DAG_PE_1PS00479 Zinc finger phorbol-ester/DAG-type signature.KPCB_RAT37-86
102-151
  1-
A:102-151
3C2PS50004 C2 domain profile.KPCB_RAT173-260  1A:173-260
4PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.KPCB_RAT348-371  1A:348-371
5PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.KPCB_RAT462-474  1A:462-474
6AGC_KINASE_CTERPS51285 AGC-kinase C-terminal domain profile.KPCB_RAT601-671  1A:601-666

(-) Exons   (0, 0)

(no "Exon" information available for 3PFQ)

(-) 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:523
 aligned with KPCB_RAT | P68403 from UniProtKB/Swiss-Prot  Length:671

    Alignment length:570
                                   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       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670
             KPCB_RAT   101 KHKFKIHTYSSPTFCDHCGSLLYGLIHQGMKCDTCMMNVHKRCVMNVPSLCGTDHTERRGRIYIQAHIDREVLIVVVRDAKNLVPMDPNGLSDPYVKLKLIPDPKSESKQKTKTIKCSLNPEWNETFRFQLKESDKDRRLSVEIWDWDLTSRNDFMGSLSFGISELQKAGVDGWFKLLSQEEGEYFNVPVPPEGSEGNEELRQKFERAKIGQGTKAPEEKTANTISKFDNNGNRDRMKLTDFNFLMVLGKGSFGKVMLSERKGTDELYAVKILKKDVVIQDDDVECTMVEKRVLALPGKPPFLTQLHSCFQTMDRLYFVMEYVNGGDLMYHIQQVGRFKEPHAVFYAAEIAIGLFFLQSKGIIYRDLKLDNVMLDSEGHIKIADFGMCKENIWDGVTTKTFCGTPDYIAPEIIAYQPYGKSVDWWAFGVLLYEMLAGQAPFEGEDEDELFQSIMEHNVAYPKSMSKEAVAICKGLMTKHPGKRLGCGPEGERDIKEHAFFRYIDWEKLERKEIQPPYKPKARDKRDTSNFDKEFTRQPVELTPTDKLFIMNLDQNEFAGFSYTNPEFVIN 670
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -C1_1-3pfqA01 A:102-154                               ------------------C2-3pfqA02 A:173-260                                                                    ---------------------------------------------------------------------------------Pkinase-3pfqA03 A:342-600                                                                                                                                                                                                                                          -------------------Pkin-ase_C-3pfqA04 A:620-660              --------- Pfam domains
         Sec.struct. author .....ee.....................ee..............................eeeeeeee...eeeeeeeeee............eeeeeeee........ee..........eeeeeeeee........eeeeeeee.......ee........hhhhhh.eeeeee....hhhhh..ee...----------------------------------------------...eeeeee........eeeeee.....eeeeeeeehhhhhhh..hhhhhhhhhhhh..........eeee.....eeeeeee.....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee........eee.....eee......ee..................hhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh.........hhhhhhhhhhhh............hhhhhhhhhhhhh..hhhhhh............hh-hhhhhhh.............hhhhhhhhhhhhhh...ee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ZF_DAG_PE_2  PDB: A:101-151 UniProt: 101-151       ---------------------C2  PDB: A:173-260 UniProt: 173-260                                                     ---------------------------------------------------------------------------------------PROTEIN_KINASE_ATP      ------------------------------------------------------------------------------------------PROTEIN_KINAS------------------------------------------------------------------------------------------------------------------------------AGC_KINASE_CTER  PDB: A:601-666 UniProt: 601-671                       PROSITE (1)
                PROSITE (2) -ZF_DAG_PE_1  PDB: A:102-151 UniProt: 102-151      --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3pfq A 101 KHKFKIHTYSSPTFCDHCGSLLYGLIHQGMKCDTCMMNVHKRCVMNVPSLCGTDHTERRGRIYIQAHIDREVLIVVVRDAKNLVPMDPNGLSDPYVKLKLIPDPKSESKQKTKTIKSSLNPEWNETFRFQLKESDKDRRLSVEIWDWDLTSRNDFMGSLSFGISELQKAGVDGWFKLLSQEEGEYFNVPVPP----------------------------------------------LTDFNFLMVLGKGSFGKVMLSERKGTDELYAVKILKKDVVIQDDDVECTMVEKRVLALPGKPPFLTQLHSCFQTMDRLYFVMEYVNGGDLMYHIQQVGRFKEPHAVFYAAEIAIGLFFLQSKGIIYRDLKLDNVMLDSEGHIKIADFGMCKENIWDGVTTKtFCGTPDYIAPEIIAYQPYGKSVDWWAFGVLLYEMLAGQAPFEGEDEDELFQSIMEHNVAYPKSMSKEAVAICKGLMTKHPGKRLGCGPEGERDIKEHAFFRYIDWEKLERKEIQPPYKPKASG-RNAENFDRFFTRHPPVLtPPDQEVIRNIDQSEFEGFsFVNSEFLKP 669
                                   110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290 |       -         -         -         -       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620  | |  629       639 |     649       659|      669
                                                                                                                                                                                                                         292                                            339                                                                                                                                                              500-TPO                                                                                                                    623 |              641-TPO            660-SEP     
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      624                                             

   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 3PFQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (4, 4)

Asymmetric/Biological Unit
(-)
Clan: C1 (13)
(-)
Clan: C2 (71)
(-)
Clan: PKinase (934)

(-) Gene Ontology  (50, 50)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (KPCB_RAT | P68403)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0050681    androgen receptor binding    Interacting selectively and non-covalently with an androgen receptor.
    GO:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    GO:0042393    histone binding    Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity.
    GO:0035403    histone kinase activity (H3-T6 specific)    Catalysis of the transfer of a phosphate group to the threonine-6 residue of the N-terminal tail of histone H3.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0030374    ligand-dependent nuclear receptor transcription coactivator activity    The function of a transcription cofactor that activates transcription in conjuction with a ligand-dependent nuclear receptor from a RNA polymerase II promoter; does not bind DNA itself.
    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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0004697    protein kinase C activity    Catalysis of the reaction: ATP + a protein = ADP + a phosphoprotein. This reaction requires diacylglycerol.
    GO:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    GO:0004674    protein serine/threonine kinase activity    Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
    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.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0042113    B cell activation    The change in morphology and behavior of a mature or immature B cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.
    GO:0050853    B cell receptor signaling pathway    A series of molecular signals initiated by the cross-linking of an antigen receptor on a B cell.
    GO:0002250    adaptive immune response    An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory).
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0018894    dibenzo-p-dioxin metabolic process    The chemical reactions and pathways involving dibenzo-p-dioxin, a substance composed of two benzene rings linked by two ether bonds. Dibenzo-p-dioxins are generated as by-products in the manufacturing of herbicides, insecticides, fungicides, paper pulp bleaching, and in incineration, and can accumulate in milk and throughout the food chain, creating significant health concern.
    GO:0035408    histone H3-T6 phosphorylation    The modification of histone H3 by the addition of an phosphate group to a threonine residue at position 6 of the histone.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0035556    intracellular signal transduction    The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
    GO:0010829    negative regulation of glucose transport    Any process that decreases the frequency, rate or extent of glucose transport. Glucose transport is the directed movement of the hexose monosaccharide glucose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0046627    negative regulation of insulin receptor signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of insulin receptor signaling.
    GO:0018105    peptidyl-serine phosphorylation    The phosphorylation of peptidyl-serine to form peptidyl-O-phospho-L-serine.
    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:0050861    positive regulation of B cell receptor signaling pathway    Any process that activates or increases the frequency, rate or extent of signaling pathways initiated by the cross-linking of an antigen receptor on a B cell.
    GO:0043123    positive regulation of I-kappaB kinase/NF-kappaB signaling    Any process that activates or increases the frequency, rate or extent of I-kappaB kinase/NF-kappaB signaling.
    GO:0051092    positive regulation of NF-kappaB transcription factor activity    Any process that activates or increases the frequency, rate or extent of activity of the transcription factor NF-kappaB.
    GO:0045766    positive regulation of angiogenesis    Any process that activates or increases angiogenesis.
    GO:0042488    positive regulation of odontogenesis of dentin-containing tooth    Any process that activates or increases the frequency, rate or extent of the formation and development of teeth, the hard, bony appendages that are borne on the jaws, or on other bones in the walls of the mouth or pharynx of most vertebrates.
    GO:0030949    positive regulation of vascular endothelial growth factor receptor signaling pathway    Any process that activates or increases the frequency, rate or extent of vascular endothelial growth factor receptor signaling pathway activity.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0014059    regulation of dopamine secretion    Any process that modulates the frequency, rate or extent of the regulated release of dopamine.
    GO:0040008    regulation of growth    Any process that modulates the frequency, rate or extent of the growth of all or part of an organism so that it occurs at its proper speed, either globally or in a specific part of the organism's development.
    GO:0006357    regulation of transcription from RNA polymerase II promoter    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0042493    response to drug    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0045471    response to ethanol    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ethanol stimulus.
    GO:0009749    response to glucose    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucose stimulus.
    GO:0033280    response to vitamin D    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a vitamin D stimulus.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0031526    brush border membrane    The portion of the plasma membrane surrounding the brush border.
    GO:0005813    centrosome    A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        KPCB_RAT | P684031a25

(-) Related Entries Specified in the PDB File

1a25 C2 DOMAIN FROM PROTEIN KINASE C (BETA)
2i0e STRUCTURE OF CATALYTIC DOMAIN OF HUMAN PROTEIN KINASE C BETA II COMPLEXED WITH A BISINDOLYLMALEIMIDE INHIBITOR