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(-) Description

Title :  CRYSTAL STRUCTURE OF RAT CK2-BETA SUBUNIT
 
Authors :  Y. Shen
Date :  06 Sep 07  (Deposition) - 23 Sep 08  (Release) - 17 Mar 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A (1x),B (1x)
Keywords :  Zinc Binding, Regulatory Subunit, Phosphorylation, Wnt Signaling Pathway, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  W. Zhou, X. Qin, X. Yan, X. Xie, L. Li, S. Fang, J. Long, J. Adelman, W. -J. Tang, Y. Shen
Crystal Structures Of Catalytic And Regulatory Subunits Of Rat Protein Kinase Ck2
Chin. Sci. Bull. V. 54 220 2009
PubMed: search  |  Reference-DOI: 10.1007/S11434-008-0580-2
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CASEIN KINASE II SUBUNIT BETA
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPUBS520
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism CommonRAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymREGULATORY SUBUNIT OF PROTEIN KINASE CK2, CK II BETA, PHOSVITIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:109 , CYS A:114 , CYS A:137 , CYS A:140BINDING SITE FOR RESIDUE ZN A 216
2AC2SOFTWARECYS B:109 , CYS B:114 , CYS B:137 , CYS B:140BINDING SITE FOR RESIDUE ZN B 216

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2R6M)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1His B:193 -Pro B:194

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2R6M)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CK2_BETAPS01101 Casein kinase II regulatory subunit signature.CSK2B_RAT109-140
 
  2A:109-140
B:109-140
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CK2_BETAPS01101 Casein kinase II regulatory subunit signature.CSK2B_RAT109-140
 
  2A:109-140
B:109-140

(-) Exons   (0, 0)

(no "Exon" information available for 2R6M)

(-) Sequences/Alignments

Asymmetric 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:176
 aligned with CSK2B_RAT | P67874 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:186
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186      
            CSK2B_RAT     7 VSWISWFCGLRGNEFFCEVDEDYIQDKFNLTGLNEQVPHYRQALDMILDLEPDEELEDNPNQSDLIEQAAEMLYGLIHARYILTNRGIAQMLEKYQQGDFGYCPRVYCENQPMLPIGLSDIPGEAMVKLYCPKCMDVYTPKSSRHHHTDGAYFGTGFPHMLFMVHPEYRPKRPANQFVPRLYGFKI 192
               SCOP domains d2r6ma_ A: Casein kinase II beta subunit                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhh.........hhhhhhhhhhh........hhhhhhhhhh...----------.....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.......hhhhh....eee...........eeee....eee..........hhhhh..hhhhhhhh.hhhhh................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------CK2_BETA  PDB: A:109-140        ---------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2r6m A   7 VSWISWFCGLRGNEFFCEVDEDYIQDKFNLTGLNEQVPHYRQALDMILDLE----------QSDLIEQAAEMLYGLIHARYILTNRGIAQMLEKYQQGDFGYCPRVYCENQPMLPIGLSDIPGEAMVKLYCPKCMDVYTPKSSRHHHTDGAYFGTGFPHMLFMVHPEYRPKRPANQFVPRLYGFKI 192
                                    16        26        36        46        56|        - |      76        86        96       106       116       126       136       146       156       166       176       186      
                                                                             57         68                                                                                                                            

Chain B from PDB  Type:PROTEIN  Length:181
 aligned with CSK2B_RAT | P67874 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:188
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186        
            CSK2B_RAT     7 VSWISWFCGLRGNEFFCEVDEDYIQDKFNLTGLNEQVPHYRQALDMILDLEPDEELEDNPNQSDLIEQAAEMLYGLIHARYILTNRGIAQMLEKYQQGDFGYCPRVYCENQPMLPIGLSDIPGEAMVKLYCPKCMDVYTPKSSRHHHTDGAYFGTGFPHMLFMVHPEYRPKRPANQFVPRLYGFKIHP 194
               SCOP domains d2r6mb_ B: Casein kinase II beta subunit                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -CK_II_beta-2r6mB01 B:8-191                                                                                                                                                              --- Pfam domains (1)
           Pfam domains (2) -CK_II_beta-2r6mB02 B:8-191                                                                                                                                                              --- Pfam domains (2)
         Sec.struct. author .hhhhhhhhh.........hhhhhhhhhhh........hhhhhhhhhh.....-------...hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.......hhhhh....eee...........eee......ee..........hhhhh..hhhhhhhh.hhhhh................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------CK2_BETA  PDB: B:109-140        ------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r6m B   7 VSWISWFCGLRGNEFFCEVDEDYIQDKFNLTGLNEQVPHYRQALDMILDLEPD-------NQSDLIEQAAEMLYGLIHARYILTNRGIAQMLEKYQQGDFGYCPRVYCENQPMLPIGLSDIPGEAMVKLYCPKCMDVYTPKSSRHHHTDGAYFGTGFPHMLFMVHPEYRPKRPANQFVPRLYGFKIHP 194
                                    16        26        36        46        56  |      -|       76        86        96       106       116       126       136       146       156       166       176       186        
                                                                               59      67                                                                                                                               

   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 Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2R6M)

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (22, 22)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (CSK2B_RAT | P67874)
molecular function
    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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
    GO:0019887    protein kinase regulator activity    Modulates the activity of a protein kinase, an enzyme which phosphorylates a protein.
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    GO:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
biological process
    GO:0007249    I-kappaB kinase/NF-kappaB signaling    The process in which a signal is passed on to downstream components within the cell through the I-kappaB-kinase (IKK)-dependent activation of NF-kappaB. The cascade begins with activation of a trimeric IKK complex (consisting of catalytic kinase subunits IKKalpha and/or IKKbeta, and the regulatory scaffold protein NEMO) and ends with the regulation of transcription of target genes by NF-kappaB. In a resting state, NF-kappaB dimers are bound to I-kappaB proteins, sequestering NF-kappaB in the cytoplasm. Phosphorylation of I-kappaB targets I-kappaB for ubiquitination and proteasomal degradation, thus releasing the NF-kappaB dimers, which can translocate to the nucleus to bind DNA and regulate transcription.
    GO:0016055    Wnt signaling pathway    The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in cell state.
    GO:0033211    adiponectin-activated signaling pathway    A series of molecular signals initiated by the binding of adiponectin to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0061154    endothelial tube morphogenesis    The process in which the anatomical structures of a tube are generated and organized from an endothelium. Endothelium refers to the layer of cells lining blood vessels, lymphatics, the heart, and serous cavities, and is derived from bone marrow or mesoderm. Corneal endothelium is a special case, derived from neural crest cells.
    GO:0043537    negative regulation of blood vessel endothelial cell migration    Any process that stops, prevents, or reduces the frequency, rate or extent of the migration of the endothelial cells of blood vessels.
    GO:0030177    positive regulation of Wnt signaling pathway    Any process that activates or increases the frequency, rate or extent of Wnt signal transduction.
    GO:0032927    positive regulation of activin receptor signaling pathway    Any process that activates or increases the frequency, rate or extent of the activity of any activin receptor signaling pathway.
    GO:0010862    positive regulation of pathway-restricted SMAD protein phosphorylation    Any process that increases the rate, frequency or extent of pathway-restricted SMAD protein phosphorylation. Pathway-restricted SMAD proteins and common-partner SMAD proteins are involved in the transforming growth factor beta receptor signaling pathways.
    GO:0045859    regulation of protein kinase activity    Any process that modulates the frequency, rate or extent of protein kinase activity.
cellular component
    GO:0031519    PcG protein complex    A chromatin-associated multiprotein complex containing Polycomb Group proteins. In Drosophila, Polycomb group proteins are involved in the long-term maintenance of gene repression, and PcG protein complexes associate with Polycomb group response elements (PREs) in target genes to regulate higher-order chromatin structure.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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.
    GO:0005956    protein kinase CK2 complex    A protein complex that possesses protein serine/threonine kinase activity, and contains two catalytic alpha subunits and two regulatory beta subunits. Protein kinase CK2 complexes are found in nearly every subcellular compartment, and can phosphorylate many protein substrates in addition to casein.

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2r7i