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(-) Description

Title :  2.0A X-RAY STRUCTURE OF C-TERMINAL KINASE DOMAIN OF P90 RIBOSOMAL S6 KINASE 2: SE-MET DERIVATIVE
 
Authors :  M. Malakhova, V. Tereshko, Z. Dong
Date :  27 Jul 07  (Deposition) - 11 Dec 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Kinase Domain, Rsk2, Autoinhibitory, Atp-Binding, Nucleotide-Binding, Phosphorylation, Serine/Threonine-Protein Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Malakhova, V. Tereshko, S. Y. Lee, K. Yao, Y. -Y. Cho, A. Bode, Z. Dong
Structural Basis For Activation Of The Autoinhibitory C-Terminal Kinase Domain Of P90 Rsk2.
Nat. Struct. Mol. Biol. V. 15 112 2008
PubMed-ID: 18084304  |  Reference-DOI: 10.1038/NSMB1347

(-) Compounds

Molecule 1 - RIBOSOMAL PROTEIN S6 KINASE ALPHA-3
    ChainsA
    EC Number2.7.11.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-46 EK/LIC
    Expression System StrainBL21-CODON PLUS (DE3)-RILP
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneRPS6KA3, RPS6KA-RS1, RSK2
    MutationYES
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymS6K-ALPHA 3, 90 KDA RIBOSOMAL PROTEIN S6 KINASE 3, P90-RSK 3, RIBOSOMAL S6 KINASE 2, RSK-2, PP90RSK2, MAP KINASE-ACTIVATED PROTEIN KINASE 1B, MAPKAPK1B

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2NA1Ligand/IonSODIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:471 , HIS A:473 , ILE A:476 , THR A:478 , HOH A:1001 , HOH A:1002BINDING SITE FOR RESIDUE NA A 1000

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:579 -A:579

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2QR7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2QR7)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.KS6A3_MOUSE74-100
428-451
  1-
A:428-451
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.KS6A3_MOUSE189-201
535-547
  1-
A:535-547

(-) Exons   (0, 0)

(no "Exon" information available for 2QR7)

(-) 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:298
 aligned with KS6A3_MOUSE | P18654 from UniProtKB/Swiss-Prot  Length:740

    Alignment length:298
                                   426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706        
          KS6A3_MOUSE   417 QFTDGYEVKEDIGVGSYSVCKRCIHKATNMEFAVKIIDKSKRDPTEEIEILLRYGQHPNIITLKDVYDDGKYVYVVTELMKGGELLDKILRQKFFSEREASAVLFTITKTVEYLHAQGVVHRDLKPSNILYVDESGNPESIRICDFGFAKQLRAENGLLMTPCYTANFVAPEVLKRQGYDAACDIWSLGVLLYTMLTGYTPFANGPDDTPEEILARIGSGKFSLSGGYWNSVSDTAKDLVSKMLHVDPHQRLTAALVLRHPWIVHWDQLPQYQLNRQDAPHLVKGAMAATYSALNRNQ 714
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------2qr7A02            -------------------2qr7A02 A:459-477,A:497-714 Transferase(Phosphotransferase) domain 1                                                                                                                                                       CATH domains
               Pfam domains -----Pkinase-2qr7A01 A:422-679                                                                                                                                                                                                                                         ----------------------------------- Pfam domains
         Sec.struct. author hhhhheeeeeeeee...eeeeeeee.....eeeeeeee.....hhhhhhhhhhhh.......eeeeee...eeeeee......hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....hhh.eee......ee..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhh............hhhhhhhhhhhh........hhhhhh.hhhhhhhhhh.........hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------PROTEIN_KINASE_ATP      -----------------------------------------------------------------------------------PROTEIN_KINAS----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qr7 A 417 QFTDGYEVKEDIGVGSYSVCKRCIHKATNmEFAVKIIDKSKRDPTEEIEILLRYGQHPNIITLKDVYDDGKYVYVVTELmKGGELLDKILRQKFFSEREASAVLFTITKTVEYLHAQGVVHRDLKPSNILYVDESGNPESIRICDFGFAKQLRAENGLLmTPCYTANFVAPEVLERQGYDAACDIWSLGVLLYTmLTGYTPFANGPDDTPEEILARIGSGKFSLSGGYWNSVSDTAKDLVSKmLHVDPHQRLTAALVLRHPWIVHWDQLPQYQLNRQDAPHLVKGAmAATYSALNRNQ 714
                                   426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606    |  616       626       636       646       656  |    666       676       686       696      |706        
                                                       446-MSE                                           496-MSE                                                                         576-MSE                            611-MSE                                         659-MSE                                     703-MSE       

   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 2QR7)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit

(-) Pfam Domains  (1, 1)

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

(-) 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

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

UniProtKB/Swiss-Prot
        KS6A3_MOUSE | P186542qr8 3g51 3ubd 4el9 4gue 4m8t 4mao

(-) Related Entries Specified in the PDB File

2qr8 2.0A X-RAY STRUCTURE OF C-TERMINAL KINASE DOMAIN OF P90 RIBOSOMAL S6 KINASE RSK2