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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN CLK1 IN COMPLEX WITH 10Z-HYMENIALDISINE
 
Authors :  J. Debreczeni, S. Das, S. Knapp, A. Bullock, K. Guo, A. Amos, O. Fedorov, A. Edwards, M. Sundstrom, F. Von Delft, F. H. Niesen, L. Ball, F. Sobot C. Arrowsmith, Structural Genomics Consortium (Sgc)
Date :  17 Mar 05  (Deposition) - 12 Apr 05  (Release) - 29 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Protein Tyrosine Kinase, Dual Specificity, Splicing, Human, 10Z- Hymendialdisine, Structural Genomics, Structural Genomics Consortium, Sgc, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. N. Bullock, S. Das, J. E. Debreczeni, P. Rellos, O. Fedorov, F. H. Niesen, K. Guo, E. Papagrigoriou, A. L. Amos, S. Cho, B. E. Turk, G. Ghosh, S. Knapp
Kinase Domain Insertions Define Distinct Roles Of Clk Kinases In Sr Protein Phosphorylation.
Structure V. 17 352 2009
PubMed-ID: 19278650  |  Reference-DOI: 10.1016/J.STR.2008.12.023

(-) Compounds

Molecule 1 - DUAL SPECIFICITY PROTEIN KINASE CLK1
    ChainsA
    EC Number2.7.12.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidHCLK1-PLIC
    Expression System StrainBL21-DE3
    Expression System Taxid469008
    Expression System Vector TypePLIC-SGC
    FragmentRESIDUES 148-484
    GeneCLK1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCDC LIKE KINASE 1

 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
1DBQ1Ligand/IonDEBROMOHYMENIALDISINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:172 , ALA A:189 , LYS A:191 , PHE A:241 , GLU A:242 , LEU A:243 , LEU A:244 , ASN A:293 , LEU A:295 , ASP A:325 , HOH A:499 , HOH A:518 , HOH A:537BINDING SITE FOR RESIDUE DBQ A 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Z57)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Z57)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_040412M440TCLK1_HUMANPolymorphism35393352AM440T
2UniProtVAR_051620E459GCLK1_HUMANPolymorphism12709AE459G

  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.CLK1_HUMAN167-191  1A:167-191
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.CLK1_HUMAN284-296  1A:284-296

(-) Exons   (10, 10)

Asymmetric/Biological Unit (10, 10)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003213561aENSE00001464368chr2:201729422-201729287136CLK1_HUMAN-00--
1.3aENST000003213563aENSE00002169022chr2:201726585-201726425161CLK1_HUMAN1-54540--
1.3cENST000003213563cENSE00002196398chr2:201726189-201725961229CLK1_HUMAN54-130770--
1.3iENST000003213563iENSE00001664086chr2:201724938-20172484891CLK1_HUMAN131-161311A:-2-16116
1.3kENST000003213563kENSE00001608435chr2:201724469-20172440367CLK1_HUMAN161-183231A:161-18323
1.4bENST000003213564bENSE00001663450chr2:201722812-201722696117CLK1_HUMAN183-222401A:183-22240
1.5aENST000003213565aENSE00001792660chr2:201722607-201722441167CLK1_HUMAN222-278571A:222-27857
1.5cENST000003213565cENSE00001606598chr2:201721708-20172161495CLK1_HUMAN278-309321A:278-30629
1.6ENST000003213566ENSE00001599503chr2:201721534-201721405130CLK1_HUMAN310-353441A:311-35343
1.7ENST000003213567ENSE00001686268chr2:201719809-20171972783CLK1_HUMAN353-380281A:353-38028
1.8bENST000003213568bENSE00001653001chr2:201719418-20171933980CLK1_HUMAN381-407271A:381-40727
1.9dENST000003213569dENSE00001782254chr2:201718716-20171862691CLK1_HUMAN407-437311A:407-43731
1.10kENST0000032135610kENSE00001823451chr2:201718172-201717732441CLK1_HUMAN438-484471A:438-48245

(-) 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:333
 aligned with CLK1_HUMAN | P49759 from UniProtKB/Swiss-Prot  Length:484

    Alignment length:337
                                   155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       
           CLK1_HUMAN   146 EGHLICQSGDVLSARYEIVDTLGEGAFGKVVECIDHKAGGRHVAVKIVKNVDRYCEAARSEIQVLEHLNTTDPNSTFRCVQMLEWFEHHGHICIVFELLGLSTYDFIKENGFLPFRLDHIRKMAYQICKSVNFLHSNKLTHTDLKPENILFVQSDYTEAYNPKIKRDERTLINPDIKVVDFGSATYDDEHHSTLVSTRHYRAPEVILALGWSQPCDVWSIGCILIEYYLGFTVFPTHDSKEHLAMMERILGPLPKHMIQKTRKRKYFHHDRLDWDEHSSAGRYVSRRCKPLKEFMLSQDVEHERLFDLIQKMLEYDPAKRITLREALKHPFFDLLKK 482
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1z57A01 A:-2-220,A:225-243 Phosphorylase Kinase; domain 1                  1z571z57A01            1z57A02 A:221-224,A:244-482 Transferase(Phosphotransferase) dom    ain 1                                                                                                                                                                        CATH domains
               Pfam domains ---------------Pkinase-1z57A01 A:161-477                                                                                                                                                                                                                                                                                                    ----- Pfam domains
         Sec.struct. author hhhhh.....ee...eeeeeeeeee..eeeeeeee......eeeeeee..hhhhhhhhhhhhhhhhhhhhhh.........eeeeeee..eeeeeee....hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee....eeee..----..eeee....eee......ee..........hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh..hhhhhhhh.hhh.ee..ee.....hhhhhhhhhhh.hhhhhh...hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T------------------G----------------------- SAPs(SNPs)
                    PROSITE ---------------------PROTEIN_KINASE_ATP       --------------------------------------------------------------------------------------------PROTEIN_KINAS------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.3i       ---------------------Exon 1.4b  PDB: A:183-222               -------------------------------------------------------Exon 1.5c  PDB: A:278-306       Exon 1.6  PDB: A:311-353 UniProt: 310-353   ---------------------------Exon 1.8b  PDB: A:381-407  ------------------------------Exon 1.10k  PDB: A:438-482 UniProt: 438-484   Transcript 1 (1)
           Transcript 1 (2) ---------------Exon 1.3k              --------------------------------------Exon 1.5a  PDB: A:222-278 UniProt: 222-278               --------------------------------------------------------------------------Exon 1.7  PDB: A:353-380    --------------------------Exon 1.9d  PDB: A:407-437      --------------------------------------------- Transcript 1 (2)
                 1z57 A  -2 SMHLICQSGDVLSARYEIVDTLGEGAFGKVVECIDHKAGGRHVAVKIVKNVDRYCEAARSEIQVLEHLNTTDPNSTFRCVQMLEWFEHHGHICIVFELLGLSTYDFIKENGFLPFRLDHIRKMAYQICKSVNFLHSNKLTHTDLKPENILFVQSDYTEAYN----RDERTLINPDIKVVDFGSATYDDEHHSTLVSTRHYRAPEVILALGWSQPCDVWSIGCILIEYYLGFTVFPTHDSKEHLAMMERILGPLPKHMIQKTRKRKYFHHDRLDWDEHSSAGRYVSRACKPLKEFMLSQDVEHERLFDLIQKMLEYDPAKRITLREALKHPFFDLLKK 482
                             ||    155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305|    | 315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       
                             ||                                                                                                                                                           306  311                                                                                                                                                                           
                            -1|                                                                                                                                                                                                                                                                                                                                              
                            148                                                                                                                                                                                                                                                                                                                                              

   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 1Z57)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (20, 20)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CLK1_HUMAN | P49759)
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:0004715    non-membrane spanning protein tyrosine kinase activity    Catalysis of the reaction: ATP + protein L-tyrosine = ADP + protein L-tyrosine phosphate by a non-membrane spanning protein.
    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:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0018105    peptidyl-serine phosphorylation    The phosphorylation of peptidyl-serine to form peptidyl-O-phospho-L-serine.
    GO:0018107    peptidyl-threonine phosphorylation    The phosphorylation of peptidyl-threonine to form peptidyl-O-phospho-L-threonine.
    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: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
        CLK1_HUMAN | P497592vag 5j1v 5j1w

(-) Related Entries Specified in the PDB File

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