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(-) Description

Title :  STRUCTURE OF N-TERMINAL DOUBLECORTIN DOMAIN FROM DCLK: SELENOMETHIONINE LABELED PROTEIN
 
Authors :  M. H. Kim, T. Cierpickil, U. Derewenda, D. Krowarsch, Y. Feng, Y. Devedjiev, Z. Dauter, C. A. Walsh, J. Otlewski, J. H. Bushweller, Z. Derewenda
Date :  13 Aug 02  (Deposition) - 29 Apr 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Doublecortin, Doublecortin-Like Kinase, X-Ray Structure, Microtubule Bundling, Cortex Development, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. H. Kim, T. Cierpickil, U. Derewenda, D. Krowarsch, Y. Feng, Y. Devedjiev, Z. Dauter, C. A. Walsh, J. Otlewski, J. H. Bushweller, Z. Derewenda
The Dcx-Domain Tandems Of Doublecortin And Doublecortin-Like Kinase
Nat. Struct. Biol. V. 10 324 2003
PubMed-ID: 12692530  |  Reference-DOI: 10.1038/NSB918
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DOUBLECORTIN-LIKE KINASE (N-TERMINAL DOMAIN)
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGSTUNIL
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Fragment(N-TERMINAL DOMAIN), RESIDUES 49-154
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDOUBLECORTIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1MSE1Mod. Amino AcidSELENOMETHIONINE
2SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:101 , PRO A:102 , SER A:133 , ILE A:134 , GLU A:135 , HOH A:1008 , HOH A:1018 , HOH A:1036 , HOH A:1073 , HOH A:1092BINDING SITE FOR RESIDUE SO4 A 1001
2AC2SOFTWARETYR A:109 , LYS A:116 , PRO A:136 , PHE A:137 , HOH A:1057 , HOH A:1101 , HOH A:1107 , HOH A:1120 , HOH A:1128BINDING SITE FOR RESIDUE SO4 A 1002

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_045675R93QDCLK1_HUMANUnclassified  ---AR93Q

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DCPS50309 Doublecortin domain profile.DCLK1_HUMAN57-143
186-269
  1A:57-143
-

(-) Exons   (2, 2)

Asymmetric/Biological Unit (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003606311ENSE00001363906chr13:36705443-36705251193DCLK1_HUMAN-00--
1.2ENST000003606312ENSE00001406064chr13:36700293-36699899395DCLK1_HUMAN1-1261261A:49-12678
1.3ENST000003606313ENSE00000938675chr13:36686352-36686006347DCLK1_HUMAN126-2411161A:126-15429
1.4ENST000003606314ENSE00001003745chr13:36521594-36521495100DCLK1_HUMAN242-275340--
1.5ENST000003606315ENSE00001093760chr13:36445477-36445361117DCLK1_HUMAN275-314400--
1.7ENST000003606317ENSE00000938821chr13:36428730-3642863695DCLK1_HUMAN314-345320--
1.9ENST000003606319ENSE00000817083chr13:36413313-3641322985DCLK1_HUMAN346-374290--
1.10ENST0000036063110ENSE00000817080chr13:36410278-36410170109DCLK1_HUMAN374-410370--
1.11ENST0000036063111ENSE00000680576chr13:36402444-3640238758DCLK1_HUMAN410-429200--
1.12ENST0000036063112ENSE00000817078chr13:36401891-36401772120DCLK1_HUMAN430-469400--
1.13ENST0000036063113ENSE00000680573chr13:36397012-36396866147DCLK1_HUMAN470-518490--
1.14ENST0000036063114ENSE00000680572chr13:36385105-36384972134DCLK1_HUMAN519-563450--
1.15ENST0000036063115ENSE00001183960chr13:36383232-3638315578DCLK1_HUMAN563-589270--
1.16bENST0000036063116bENSE00000817073chr13:36382457-3638236197DCLK1_HUMAN589-621330--
1.17aENST0000036063117aENSE00000817072chr13:36379916-3637983681DCLK1_HUMAN622-648270--
1.18ENST0000036063118ENSE00000817070chr13:36367616-36367503114DCLK1_HUMAN649-686380--
1.20aENST0000036063120aENSE00001710872chr13:36348836-363454783359DCLK1_HUMAN687-740540--

(-) 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:106
 aligned with DCLK1_HUMAN | O15075 from UniProtKB/Swiss-Prot  Length:740

    Alignment length:106
                                    58        68        78        88        98       108       118       128       138       148      
          DCLK1_HUMAN    49 TLSSEKKAKKVRFYRNGDRYFKGIVYAISPDRFRSFEALLADLTRTLSDNVNLPQGVRTIYTIDGLKKISSLDQLVEGESYVCGSIEPFKKLEYTKNVNPNWSVNV 154
               SCOP domains d1mfwa_ A: Doublecortin-like kinase Dclk                                                                   SCOP domains
               CATH domains 1mfwA00 A:49-154  [code=3.10.20.230, no name defined]                                                      CATH domains
               Pfam domains -------------------------DCX-1mfwA01 A:74-138                                             ---------------- Pfam domains
         Sec.struct. author ...hhhhheeeeeee........eeeee......hhhhhhhhhhhhhh..........eeee........hhhhh....eeeee..............hhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------Q------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------DC  PDB: A:57-143 UniProt: 57-143                                                      ----------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:49-126 UniProt: 1-126 [INCOMPLETE]                           ---------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------Exon 1.3  PDB: A:126-154      Transcript 1 (2)
                 1mfw A  49 TLSSEKKAKKVRFYRNGDRYFKGIVYAISPDRFRSFEALLADLTRTLSDNVNLPQGVRTIYTIDGLKKISSmDQLVEGESYVCGSIEPFKKLEYTKNVNPNWSVNV 154
                                    58        68        78        88        98       108       118 |     128       138       148      
                                                                                                 120-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  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (24, 24)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DCLK1_HUMAN | O15075)
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: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:0005057    signal transducer activity, downstream of receptor    Conveys a signal from an upstream receptor or intracellular signal transducer, converting the signal into a form where it can ultimately trigger a change in the state or activity of a cell.
    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:0048675    axon extension    Long distance growth of a single axon process involved in cellular development.
    GO:0007409    axonogenesis    De novo generation of a long process of a neuron, that carries efferent (outgoing) action potentials from the cell body towards target cells. Refers to the morphogenesis or creation of shape or form of the developing axon.
    GO:0007420    brain development    The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.).
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0007417    central nervous system development    The process whose specific outcome is the progression of the central nervous system over time, from its formation to the mature structure. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain and spinal cord. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord.
    GO:0021952    central nervous system projection neuron axonogenesis    Generation of a long process of a CNS neuron, that carries efferent (outgoing) action potentials from the cell body towards target cells in a different central nervous system region.
    GO:0048813    dendrite morphogenesis    The process in which the anatomical structures of a dendrite are generated and organized. A dendrite is a freely branching protoplasmic process of a nerve cell.
    GO:0016197    endosomal transport    The directed movement of substances into, out of, or mediated by an endosome, a membrane-bounded organelle that carries materials newly ingested by endocytosis. It passes many of the materials to lysosomes for degradation.
    GO:0030900    forebrain development    The process whose specific outcome is the progression of the forebrain over time, from its formation to the mature structure. The forebrain is the anterior of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes especially the cerebral hemispheres, the thalamus, and the hypothalamus and especially in higher vertebrates is the main control center for sensory and associative information processing, visceral functions, and voluntary motor functions).
    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:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:0001764    neuron migration    The characteristic movement of an immature neuron from germinal zones to specific positions where they will reside as they mature.
    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:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0009615    response to virus    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a virus.
cellular component
    GO:0005887    integral component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DCLK1_HUMAN | O150751mg4 1uf0 5jzj 5jzn

(-) Related Entries Specified in the PDB File

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