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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HUMAN CLK3 IN COMPLEX WITH V25
 
Authors :  J. R. C. Muniz, O. Fedorov, O. King, P. Filippakopoulos, A. N. Bullock, C. Phillips, T. Heightman, E. Ugochukwu, F. Von Delft, C. H. Arrowsmith, F. Bracher, K. Huber, A. M. Edwards, J. Weigelt, C. Bountra, S. Knapp
Date :  30 Sep 09  (Deposition) - 20 Oct 09  (Release) - 07 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  A
Keywords :  Transferase, Kinase, Tyrosine-Protein Kinase, Serine/Threonine-Protein Kinase, Nucleotide-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  O. Fedorov, K. Huber, A. Eisenreich, P. Filippakopoulos, O. King, A. N. Bullock, D. Szklarczyk, L. J. Jensen, D. Fabbro, J. Trappe, U. Rauch, F. Bracher, S. Knapp
Specific Clk Inhibitors From A Novel Chemotype For Regulation Of Alternative Splicing.
Chem. Biol V. 18 67 2011
PubMed-ID: 21276940  |  Reference-DOI: 10.1016/J.CHEMBIOL.2010.11.009

(-) Compounds

Molecule 1 - DUAL SPECIFICITY PROTEIN KINASE CLK3
    ChainsA
    EC Number2.7.12.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)-R3
    Expression System Taxid469008
    FragmentRESIDUES 127-484
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCDC-LIKE KINASE 3, CDC-LIKE KINASE 3 ISOFORM HCLK3
    TissueMUSCLE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2SO45Ligand/IonSULFATE ION
3V251Ligand/IonETHYL 3-[(E)-2-AMINO-1-CYANOETHENYL]-6,7-DICHLORO-1-METHYL-1H-INDOLE-2-CARBOXYLATE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:162 , GLY A:163 , GLU A:164 , PHE A:167 , VAL A:170 , ALA A:184 , LYS A:186 , VAL A:220 , PHE A:236 , GLU A:237 , GLU A:287 , ASN A:288 , LEU A:290 , ASP A:320 , HOH A:2043 , HOH A:2045BINDING SITE FOR RESIDUE V25 A1483
2AC2SOFTWAREARG A:195 , ARG A:199 , LYS A:405 , HOH A:2158BINDING SITE FOR RESIDUE SO4 A1484
3AC3SOFTWAREARG A:272 , HIS A:275 , THR A:462 , LEU A:463 , ALA A:464 , HOH A:2159 , HOH A:2160 , HOH A:2161BINDING SITE FOR RESIDUE SO4 A1485
4AC4SOFTWAREHIS A:330 , THR A:332 , THR A:333 , HOH A:2162BINDING SITE FOR RESIDUE SO4 A1486
5AC5SOFTWAREHIS A:396 , HIS A:399BINDING SITE FOR RESIDUE SO4 A1487
6AC6SOFTWAREVAL A:191 , GLY A:192 , ARG A:338 , ASN A:379 , HOH A:2163 , HOH A:2164BINDING SITE FOR RESIDUE SO4 A1488
7AC7SOFTWAREHIS A:330 , HIS A:331BINDING SITE FOR RESIDUE CL A1489
8AC8SOFTWAREARG A:338BINDING SITE FOR RESIDUE CL A1490

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WU7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2WU7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 3)

Asymmetric/Biological Unit (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_040413R486CCLK3_HUMANPolymorphism  ---AR338C
2UniProtVAR_045579Q607RCLK3_HUMANPolymorphism  ---AQ459R
3UniProtVAR_045580R628WCLK3_HUMANPolymorphism  ---AR480W

  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.CLK3_HUMAN310-334  1A:162-186
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.CLK3_HUMAN427-439  1A:279-291

(-) Exons   (6, 6)

Asymmetric/Biological Unit (6, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2aENST000003950662aENSE00002172364chr15:74907335-74908239905CLK3_HUMAN-00--
1.3ENST000003950663ENSE00002172098chr15:74911538-74911689152CLK3_HUMAN1-51510--
1.4ENST000003950664ENSE00001257949chr15:74912350-74912566217CLK3_HUMAN51-123730--
1.5bENST000003950665bENSE00001257892chr15:74914461-7491455797CLK3_HUMAN124-156330--
1.6ENST000003950666ENSE00001758841chr15:74914835-7491490167CLK3_HUMAN156-178230--
1.7aENST000003950667aENSE00001795938chr15:74917243-74917359117CLK3_HUMAN178-217400--
1.8ENST000003950668ENSE00001702735chr15:74918143-74918309167CLK3_HUMAN217-273570--
1.9ENST000003950669ENSE00001775239chr15:74919693-7491978795CLK3_HUMAN273-304321A:135-15622
1.10ENST0000039506610ENSE00001725915chr15:74919880-74920009130CLK3_HUMAN305-348441A:157-20044
1.11ENST0000039506611ENSE00001710495chr15:74920311-7492039383CLK3_HUMAN348-375281A:200-22728
1.12ENST0000039506612ENSE00001643549chr15:74920945-7492102480CLK3_HUMAN376-402271A:228-25427
1.13ENST0000039506613ENSE00001592747chr15:74921283-7492137391CLK3_HUMAN402-432311A:254-28431
1.14bENST0000039506614bENSE00002179194chr15:74922048-74922467420CLK3_HUMAN433-490581A:285-34258

(-) 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:348
 aligned with CLK3_HUMAN | P49761 from UniProtKB/Swiss-Prot  Length:638

    Alignment length:348
                                   292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622        
           CLK3_HUMAN   283 SVEDDKEGHLVCRIGDWLQERYEIVGNLGEGTFGKVVECLDHARGKSQVALKIIRNVGKYREAARLEINVLKKIKEKDKENKFLCVLMSDWFNFHGHMCIAFELLGKNTFEFLKENNFQPYPLPHVRHMAYQLCHALRFLHENQLTHTDLKPENILFVNSEFETLYNEHKSCEEKSVKNTSIRVADFGSATFDHEHHTTIVATRHYRPPEVILELGWAQPCDVWSIGCILFEYYRGFTLFQTHENREHLVMMEKILGPIPSHMIHRTRKQKYFYKGGLVWDENSSDGRYVKENCKPLKSYMLQDSLEHVQLFDLMRRMLEFDPAQRITLAEALLHPFFAGLTPEERSF 630
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2wu7A01 A:135-215,A:220-238 Phosphorylase Kinase; domain 1                       2wu72wu7A01            2wu7A02 A:216-219,A:239-482 Transferase(Phosphotransferase) domain 1                                                                                                                                                                                 CATH domains
               Pfam domains ---------------------Pkinase-2wu7A01 A:156-472                                                                                                                                                                                                                                                                                                    ---------- Pfam domains
         Sec.struct. author ................ee...eee...........eeeeee.....eeeeeee.....hhhhhhhhhhhhhhhhhhhh.........eeeeee....eeeeee....hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee....eeeeee....eeeeee....eee......ee..........hhhhhhhhhhh.....hhhhhhhh.hhhhhhhh........hhhhhhhhhhhhh...hhhhhhhh.hhhhh..............hhhhhhh.hhhhhh...hhhhhhhhhhhhhhh........hhhhhhhhhhhh..hhhhhhh Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C------------------------------------------------------------------------------------------------------------------------R--------------------W-- SAPs(SNPs)
                    PROSITE ---------------------------PROTEIN_KINASE_ATP       --------------------------------------------------------------------------------------------PROTEIN_KINAS----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.9 [INCOMPLETE] Exon 1.10  PDB: A:157-200 UniProt: 305-348  ---------------------------Exon 1.12  PDB: A:228-254  ------------------------------Exon 1.14b  PDB: A:285-342 UniProt: 433-490               -------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------Exon 1.11  PDB: A:200-227   --------------------------Exon 1.13  PDB: A:254-284      ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 2wu7 A 135 SVEDDKEGHLVCRIGDWLQERYEIVGNLGEGTFGKVVECLDHARGKSQVALKIIRNVGKYREAARLEINVLKKIKEKDKENKFLCVLMSDWFNFHGHMCIAFELLGKNTFEFLKENNFQPYPLPHVRHMAYQLCHALRFLHENQLTHTDLKPENILFVNSEFETLYNEHKSCEEKSVKNTSIRVADFGSATFDHEHHTTIVATRHYRPPEVILELGWAQPCDVWSIGCILFEYYRGFTLFQTHENREHLVMMEKILGPIPSHMIHRTRKQKYFYKGGLVWDENSSDGRYVKENCKPLKSYMLQDSLEHVQLFDLMRRMLEFDPAQRITLAEALLHPFFAGLTPEERSF 482
                                   144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474        

   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 2WU7)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CLK3_HUMAN | P49761)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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: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: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:0004712    protein serine/threonine/tyrosine kinase activity    Catalysis of the reactions: ATP + a protein serine = ADP + protein serine phosphate; ATP + a protein threonine = ADP + protein threonine phosphate; and ATP + a protein tyrosine = ADP + protein tyrosine phosphate.
    GO:0004713    protein tyrosine kinase activity    Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine 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:0018108    peptidyl-tyrosine phosphorylation    The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine.
    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: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:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0043484    regulation of RNA splicing    Any process that modulates the frequency, rate or extent of RNA splicing, the process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.
cellular component
    GO:0001669    acrosomal vesicle    A structure in the head of a spermatozoon that contains acid hydrolases, and is concerned with the breakdown of the outer membrane of the ovum during fertilization. It lies just beneath the plasma membrane and is derived from the lysosome.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0045111    intermediate filament cytoskeleton    Cytoskeletal structure made from intermediate filaments, typically organized in the cytosol as an extended system that stretches from the nuclear envelope to the plasma membrane. Some intermediate filaments run parallel to the cell surface, while others traverse the cytosol; together they form an internal framework that helps support the shape and resilience of the cell.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0016607    nuclear speck    A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CLK3_HUMAN | P497612eu9 2exe 2wu6 3raw

(-) Related Entries Specified in the PDB File

2eu9 CRYSTAL STRUCTURE OF CLK3
2exe CRYSTAL STRUCTURE OF THE PHOSPHORYLATED CLK3
2wu6 CRYSTAL STRUCTURE OF THE HUMAN CLK3 IN COMPLEX WITH DKI