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(-) Description

Title :  STRUCTURE OF N-TERMINAL DOMAIN OF RSK2 KINASE IN COMPLEX WITH FLAVONOID GLYCOSIDE SL0101
 
Authors :  D. Utepbergenov, U. Derewenda, Z. S. Derewenda
Date :  24 Oct 11  (Deposition) - 05 Sep 12  (Release) - 05 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.53
Chains :  Asym./Biol. Unit :  A
Keywords :  Kinase-Inhibitor Complex, Induced Fit, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Utepbergenov, U. Derewenda, N. Olekhnovich, G. Szukalska, B. Banerjee, M. K. Hilinski, D. A. Lannigan, P. T. Stukenberg, Z. S. Derewenda
Insights Into The Inhibition Of The P90 Ribosomal S6 Kinase (Rsk) By The Flavonol Glycoside Sl0101 From The 1. 5 A Crystal Structure Of The N-Terminal Domain Of Rsk2 With Bound Inhibitor.
Biochemistry V. 51 6499 2012
PubMed-ID: 22846040  |  Reference-DOI: 10.1021/BI300620C

(-) Compounds

Molecule 1 - RIBOSOMAL PROTEIN S6 KINASE ALPHA-3
    ChainsA
    EC Number2.7.11.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPHISPARALLEL2
    Expression System StrainBL21(DE3) RIPL
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentN-TERMINAL KINASE DOMAIN, UNP RESIDUES 45-346
    GeneMAPKAPK1B, RPS6KA-RS1, RPS6KA3, RSK2
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymS6K-ALPHA-3, 90 KDA RIBOSOMAL PROTEIN S6 KINASE 3, P90-RSK 3, P90RSK3, MAP KINASE-ACTIVATED PROTEIN KINASE 1B, MAPK-ACTIVATED PROTEIN KINASE 1B, MAPKAP KINASE 1B, MAPKAPK-1B, RIBOSOMAL S6 KINASE 2, RSK-2, PP90RSK2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1SL01Ligand/Ion5,7-DIHYDROXY-2-(4-HYDROXYPHENYL)-4-OXO-4H-CHROMEN-3-YL3,4-DI-O-ACETYL-6-DEOXY-ALPHA-L-MANNOPYRANOSIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:50 , SER A:78 , PHE A:79 , ALA A:98 , LYS A:100 , VAL A:131 , LEU A:147 , ASP A:148 , GLU A:197 , LEU A:200 , HOH A:530 , HOH A:598 , HOH A:648BINDING SITE FOR RESIDUE SL0 A 400

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.KS6A3_MOUSE74-100
428-451
  1A:74-100
-
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.KS6A3_MOUSE189-201
535-547
  1A:189-201
-
3AGC_KINASE_CTERPS51285 AGC-kinase C-terminal domain profile.KS6A3_MOUSE328-397  1A:328-346

(-) Exons   (0, 0)

(no "Exon" information available for 3UBD)

(-) 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:287
 aligned with KS6A3_MOUSE | P18654 from UniProtKB/Swiss-Prot  Length:740

    Alignment length:298
                                    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        
          KS6A3_MOUSE    49 EIAITHHVKEGHEKADPSQFELLKVLGQGSFGKVFLVKKISGSDARQLYAMKVLKKATLKVRDRVRTKMERDILVEVNHPFIVKLHYAFQTEGKLYLILDFLRGGDLFTRLSKEVMFTEEDVKFYLAELALALDHLHSLGIIYRDLKPENILLDEEGHIKLTDFGLSKESIDHEKKAYSFCGTVEYMAPEVVNRRGHTQSADWWSFGVLMFEMLTGTLPFQGKDRKETMTMILKAKLGMPQFLSPEAQSLLRMLFKRNPANRLGAGPDGVEEIKRHSFFSTIDWNKLYRREIHPPFKP 346
               SCOP domains d3ubda_ A: automated matches                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.......hhh.eeeeeeee.hhh.eeeeeee........eeeeeeee.eeeeeee..------..........ee.eeeeeee..eeeeee......eehhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eeee..eeee.-----........hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh........hhhhhhhhhhhh..hhhhh......hhhhhhhhhhhh..hhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------PROTEIN_KINASE_ATP         ----------------------------------------------------------------------------------------PROTEIN_KINAS------------------------------------------------------------------------------------------------------------------------------AGC_KINASE_CTER     PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ubd A  49 EIAITHHVKEGHEKADPSQFELLKVLGQGSFGKVFLVKKISGSDARQLYAMKVLKKATLKVRDRV------DILVEVNHPFIVKLHYAFQTEGKLYLILDFLRGGDLFTRLSKEVMFTEEDVKFYLAELALALDHLHSLGIIYRDLKPENILLDEEGHIKLTDFGLSKE-----KKAYSFCGTVEYMAPEVVNRRGHTQSADWWSFGVLMFEMLTGTLPFQGKDRKETMTMILKAKLGMPQFLSPEAQSLLRMLFKRNPANRLGAGPDGVEEIKRHSFFSTIDWNKLYRREIHPPFKP 346
                                    58        68        78        88        98       108    |    - |     128       138       148       158       168       178       188       198       208        |-    |  228       238       248       258       268       278       288       298       308       318       328       338        
                                                                                          113    120                                                                                              217   223                                                                                                                           

   Legend:   → Mismatch (orange background)
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    → 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  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (KS6A3_MOUSE | P18654)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0043027    cysteine-type endopeptidase inhibitor activity involved in apoptotic process    Stops, prevents or reduces the activity of a cysteine-type endopeptidase involved in the apoptotic process.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    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: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:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
    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: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: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: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:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0032496    response to lipopolysaccharide    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0002224    toll-like receptor signaling pathway    Any series of molecular signals generated as a consequence of binding to a toll-like receptor. Toll-like receptors directly bind pattern motifs from a variety of microbial sources to initiate innate immune response.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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.

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 Related Entries

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        KS6A3_MOUSE | P186542qr7 2qr8 3g51 4el9 4gue 4m8t 4mao

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