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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CATALYTIC SUBUNIT OF HUMAN PROTEIN KINASE CK2
 
Authors :  E. Pechkova, G. Zanotti, C. Nicolini
Date :  27 Nov 02  (Deposition) - 26 Aug 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Ck2, Protein Kinase, Microcrystals, Thin-Film Nanotechnology, Microfocus Esrf, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Pechkova, G. Zanotti, C. Nicolini
Three-Dimensional Atomic Structure Of A Catalytic Subunit Mutant Of Human Protein Kinase Ck2.
Acta Crystallogr. , Sect. D V. 59 2133 2003
PubMed-ID: 14646071  |  Reference-DOI: 10.1107/S0907444903018900
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CASEIN KINASE II, ALPHA CHAIN
    ChainsA
    EC Number2.7.1.37
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System StrainBL21
    Expression System Taxid511693
    FragmentCATALYTIC SUBUNIT
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCK II

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1NA7)

(-) Sites  (0, 0)

(no "Site" information available for 1NA7)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1NA7)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:230 -Pro A:231

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 4)

Asymmetric/Biological Unit (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_077045R47QCSK21_HUMANDisease (OCNDS)869312845AR47Q
2UniProtVAR_077046Y50SCSK21_HUMANDisease (OCNDS)869312849AY50S
3UniProtVAR_077047D175GCSK21_HUMANDisease (OCNDS)869312848AD175G
4UniProtVAR_077048K198RCSK21_HUMANDisease (OCNDS)869312840AK198R

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.CSK21_HUMAN45-68  1A:45-68
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.CSK21_HUMAN152-164  1A:152-164

(-) Exons   (11, 11)

Asymmetric/Biological Unit (11, 11)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003497361bENSE00001937660chr20:524465-524316150CSK21_HUMAN-00--
1.3ENST000003497363ENSE00001709328chr20:489304-489095210CSK21_HUMAN1-34341A:4-3431
1.4ENST000003497364ENSE00001688643chr20:485873-485762112CSK21_HUMAN34-71381A:34-7138
1.5ENST000003497365ENSE00001705871chr20:480578-480477102CSK21_HUMAN72-105341A:72-10534
1.6ENST000003497366ENSE00001598088chr20:479949-47989951CSK21_HUMAN106-122171A:106-12217
1.7ENST000003497367ENSE00001618963chr20:478424-47836560CSK21_HUMAN123-142201A:123-14220
1.8ENST000003497368ENSE00000655095chr20:476446-47636384CSK21_HUMAN143-170281A:143-17028
1.9ENST000003497369ENSE00000655092chr20:473008-472898111CSK21_HUMAN171-207371A:171-20737
1.10ENST0000034973610ENSE00001666435chr20:470525-470424102CSK21_HUMAN208-241341A:208-24134
1.11bENST0000034973611bENSE00000655089chr20:469422-469322101CSK21_HUMAN242-275341A:242-27534
1.12ENST0000034973612ENSE00000655088chr20:468219-468071149CSK21_HUMAN275-325511A:275-32551
1.13ENST0000034973613ENSE00000655087chr20:467106-46702087CSK21_HUMAN325-354301A:325-3295
1.14cENST0000034973614cENSE00001891680chr20:464720-4617412980CSK21_HUMAN354-391380--

(-) 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:326
 aligned with CSK21_HUMAN | P68400 from UniProtKB/Swiss-Prot  Length:391

    Alignment length:326
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323      
          CSK21_HUMAN     4 PVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVK 329
               SCOP domains d1na7a_ A: Protein kinase CK2, alpha subunit                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---1na7A02           1na7A01 A:25-115 Phosphorylase Kinase; domain 1                                            1na7A02 A:7-24,A:116-329 Transferase(Phosphotransferase) domain 1                                                                                                                                                      CATH domains
               Pfam domains -----------------------------------Pkinase-1na7A01 A:39-324                                                                                                                                                                                                                                                                      ----- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhh.....hhh.eeeeeeeee...eeeeeeee.....eeeeeee...hhhhhhhhhhhhhhh........eeeeee......eeeee......hhhhhh...hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eeee....eeee......ee............hhhhhhhhhhh......hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhh.................hhhhhhhhhhhhhhhhh........hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------Q--S----------------------------------------------------------------------------------------------------------------------------G----------------------R----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------PROTEIN_KINASE_ATP      -----------------------------------------------------------------------------------PROTEIN_KINAS--------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: A:4-34          -------------------------------------Exon 1.5  PDB: A:72-105           Exon 1.6         Exon 1.7            Exon 1.8  PDB: A:143-170    Exon 1.9  PDB: A:171-207             Exon 1.10  PDB: A:208-241         Exon 1.11b  PDB: A:242-275        -------------------------------------------------1.13  Transcript 1 (1)
           Transcript 1 (2) ------------------------------Exon 1.4  PDB: A:34-71 UniProt: 34-71 -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.12  PDB: A:275-325 UniProt: 275-325         ---- Transcript 1 (2)
                 1na7 A   4 PVPSRARVYTDVNTHRPREYWDYASHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKNKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVK 329
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323      

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: PKinase (934)

(-) Gene Ontology  (37, 37)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CSK21_HUMAN | P68400)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0051879    Hsp90 protein binding    Interacting selectively and non-covalently with Hsp90 proteins, any of a group of heat shock proteins around 90kDa in size.
    GO:0008013    beta-catenin binding    Interacting selectively and non-covalently with the beta subunit of the catenin complex.
    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:0047485    protein N-terminus binding    Interacting selectively and non-covalently with a protein N-terminus, the end of any peptide chain at which the 2-amino (or 2-imino) function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    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: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:0019888    protein phosphatase regulator activity    Modulates the activity of a protein phosphatase, an enzyme which catalyzes of the removal of a phosphate group from a protein substrate molecule.
    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.
biological process
    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: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:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0061077    chaperone-mediated protein folding    The process of inhibiting aggregation and assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure that is dependent on interaction with a chaperone.
    GO:0071174    mitotic spindle checkpoint    A mitotic cell cycle checkpoint that originates from the spindle and delays the metaphase/anaphase transition of a mitotic nuclear division until the spindle is correctly assembled and oriented, the completion of anaphase until chromosomes are attached to the spindle, or mitotic exit and cytokinesis when the spindle does not form.
    GO:0043154    negative regulation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of a cysteine-type endopeptidase activity involved in the apoptotic process.
    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:0030177    positive regulation of Wnt signaling pathway    Any process that activates or increases the frequency, rate or extent of Wnt signal transduction.
    GO:0030307    positive regulation of cell growth    Any process that activates or increases the frequency, rate, extent or direction of cell growth.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0045732    positive regulation of protein catabolic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
    GO:0046777    protein autophosphorylation    The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).
    GO:0006457    protein folding    The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:1901796    regulation of signal transduction by p53 class mediator    Any process that modulates the frequency, rate or extent of signal transduction by p53 class mediator.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0048511    rhythmic process    Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0016581    NuRD complex    An approximately 2 MDa multi-subunit complex that exhibits ATP-dependent chromatin remodeling activity in addition to histone deacetylase (HDAC) activity, and has been shown to establish transcriptional repression of a number of target genes in vertebrates, invertebrates and fungi. Amongst its subunits, the NuRD complex contains histone deacetylases, histone binding proteins and Mi-2-like proteins.
    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:0016580    Sin3 complex    A multiprotein complex that functions broadly in eukaryotic organisms as a transcriptional repressor of protein-coding genes, through the gene-specific deacetylation of histones. Amongst its subunits, the Sin3 complex contains Sin3-like proteins, and a number of core proteins that are shared with the NuRD complex (including histone deacetylases and histone binding proteins). The Sin3 complex does not directly bind DNA itself, but is targeted to specific genes through protein-protein interactions with DNA-binding proteins.
    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:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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
        CSK21_HUMAN | P684001jwh 1pjk 2pvr 2zjw 3amy 3at2 3at3 3at4 3axw 3bqc 3c13 3fwq 3h30 3juh 3mb6 3mb7 3nga 3nsz 3owj 3owk 3owl 3pe1 3pe2 3pe4 3q04 3q9w 3q9x 3q9y 3q9z 3qa0 3r0t 3rps 3tax 3u4u 3u87 3u9c 3w8l 3war 3wik 3wil 3wow 4dgl 4fbx 4grb 4gub 4gyw 4gyy 4gz3 4ib5 4kwp 4md7 4md8 4md9 4nh1 4rll 4ub7 4uba 5b0x 5clp 5cqu 5cqw 5cs6 5csh 5csp 5csv 5ct0 5ctp 5cu0 5cu2 5cu3 5cu4 5cu6 5cvf 5cvg 5cvh 5cx9 5h8b 5h8e 5h8g 5hgv 5m44 5m4c 5m4f 5m4i 5mmf 5mmr 5mo5 5mo6 5mo7 5mo8 5mod 5moe 5moh 5mot 5mov 5mow 5mp8 5mpj 5n1v 5nqc

(-) Related Entries Specified in the PDB File

1a6o PROTEIN KINASE CK2 (CATALYTIC SUBUNIT) FROM ZEA MAYS
1f0q ALPHA SUBUNIT OF PROTEIN KINASE CK2 IN COMPLEX WITH THE NUCLEOTIDE COMPETITIVE INHIBITOR EMODIN
1m2q 1,8-DI-HYDROXY-4-NITRO-XANTEN-9-TITONE/CK2 KINASE COMPLEX
1m2r 5,8-DI-AMINO-1,4-DI-HYDROXY- ANTHRAQUINONE/CK2 KINASE COMPLEX