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(-) Description

Title :  X-RAY STRUCTURE OF THE N-TERMINAL DOMAIN OF HUMAN DOUBLECORTIN
 
Authors :  M. H. Kim, D. R. Cooper, U. Derewenda, Z. S. Derewenda
Date :  27 Apr 05  (Deposition) - 19 Jul 06  (Release) - 01 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Dcx Domain, Ubiquitin-Like Fold, Microtubule Associated, Signaling Protein, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Cierpicki, M. H. Kim, D. R. Cooper, U. Derewenda, J. H. Bushweller, Z. S. Derewenda
The Dc-Module Of Doublecortin: Dynamics, Domain Boundaries, And Functional Implications.
Proteins V. 64 874 2006
PubMed-ID: 16835924  |  Reference-DOI: 10.1002/PROT.21068

(-) Compounds

Molecule 1 - NEURONAL MIGRATION PROTEIN DOUBLECORTIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGSTUNI1
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentN-TERMINAL DOMAIN RESIDUES 45-150
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDOUBLECORTIN, LISSENCEPHALIN-X, LIS-X, DOUBLIN

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2BQQ)

(-) Sites  (0, 0)

(no "Site" information available for 2BQQ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (16, 16)

Asymmetric Unit (16, 16)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_007822R59HDCX_HUMANDisease (SBHX)122457137AR59H
02UniProtVAR_007821R59LDCX_HUMANDisease (SBHX)122457137AR59L
03UniProtVAR_026024N60DDCX_HUMANDisease (LISX1)  ---AN60D
04UniProtVAR_007823D62NDCX_HUMANDisease (SBHX)104894779AD62N
05UniProtVAR_026025G67EDCX_HUMANDisease (SBHX)  ---AG67E
06UniProtVAR_026026A71SDCX_HUMANDisease (LISX1)104894786AA71S
07UniProtVAR_010202R78HDCX_HUMANPolymorphism104894784AR78H
08UniProtVAR_007824R78LDCX_HUMANDisease (SBHX)104894784AR78L
09UniProtVAR_007825D86HDCX_HUMANDisease (SBHX)  ---AD86H
10UniProtVAR_010536R89GDCX_HUMANDisease (SBHX)104894785AR89G
11UniProtVAR_026027L97RDCX_HUMANDisease (SBHX)587783537AL97R
12UniProtVAR_007826G100ADCX_HUMANDisease (SBHX)  ---AG100A
13UniProtVAR_007827R102SDCX_HUMANDisease (LISX1)  ---AR102S
14UniProtVAR_026028I104TDCX_HUMANDisease (SBHX)  ---AI104T
15UniProtVAR_007829Y125DDCX_HUMANDisease (SBHX)  ---AY125D
16UniProtVAR_007828Y125HDCX_HUMANDisease (SBHX)104894781AY125H

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (16, 32)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_007822R59HDCX_HUMANDisease (SBHX)122457137AR59H
02UniProtVAR_007821R59LDCX_HUMANDisease (SBHX)122457137AR59L
03UniProtVAR_026024N60DDCX_HUMANDisease (LISX1)  ---AN60D
04UniProtVAR_007823D62NDCX_HUMANDisease (SBHX)104894779AD62N
05UniProtVAR_026025G67EDCX_HUMANDisease (SBHX)  ---AG67E
06UniProtVAR_026026A71SDCX_HUMANDisease (LISX1)104894786AA71S
07UniProtVAR_010202R78HDCX_HUMANPolymorphism104894784AR78H
08UniProtVAR_007824R78LDCX_HUMANDisease (SBHX)104894784AR78L
09UniProtVAR_007825D86HDCX_HUMANDisease (SBHX)  ---AD86H
10UniProtVAR_010536R89GDCX_HUMANDisease (SBHX)104894785AR89G
11UniProtVAR_026027L97RDCX_HUMANDisease (SBHX)587783537AL97R
12UniProtVAR_007826G100ADCX_HUMANDisease (SBHX)  ---AG100A
13UniProtVAR_007827R102SDCX_HUMANDisease (LISX1)  ---AR102S
14UniProtVAR_026028I104TDCX_HUMANDisease (SBHX)  ---AI104T
15UniProtVAR_007829Y125DDCX_HUMANDisease (SBHX)  ---AY125D
16UniProtVAR_007828Y125HDCX_HUMANDisease (SBHX)104894781AY125H

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DCPS50309 Doublecortin domain profile.DCX_HUMAN53-139
180-263
  1A:53-139
-
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DCPS50309 Doublecortin domain profile.DCX_HUMAN53-139
180-263
  2A:53-139
-

(-) Exons   (0, 0)

(no "Exon" information available for 2BQQ)

(-) Sequences/Alignments

Asymmetric 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:96
 aligned with DCX_HUMAN | O43602 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:96
                                    61        71        81        91       101       111       121       131       141      
            DCX_HUMAN    52 AKKVRFYRNGDRYFKGIVYAVSSDRFRSFDALLADLTRSLSDNINLPQGVRYIYTIDGSRKIGSMDELEEGESYVCSSDNFFKKVEYTKNVNPNWS 147
               SCOP domains d2bqqa_ A: automated matches                                                                     SCOP domains
               CATH domains 2bqqA00 A:52-147  [code=3.10.20.230, no name defined]                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee........eeeee......hhhhhhhhhhhhhh..........eeee........hhhhh....eeeee................... Sec.struct. author
             SAPs(SNPs) (1) -------HD-N----E---S------H-------H--G-------R--A-S-T--------------------D---------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------L------------------L----------------------------------------------H---------------------- SAPs(SNPs) (2)
                    PROSITE -DC  PDB: A:53-139 UniProt: 53-139                                                      -------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 2bqq A  52 AKKVRFYRNGDRYFKGIVYAVSSDRFRSFDALLADLTRSLSDNINLPQGVRYIYTIDGSRKIGSMDELEEGESYVCSSDNFFDDVEYTKNVNPNWS 147
                                    61        71        81        91       101       111       121       131       141      

   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 Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BQQ)

(-) Gene Ontology  (31, 31)

Asymmetric Unit(hide GO term definitions)
Chain A   (DCX_HUMAN | O43602)
molecular function
    GO:0009931    calcium-dependent protein serine/threonine kinase activity    Catalysis of the reactions: ATP + a protein serine = ADP + protein serine phosphate; and ATP + a protein threonine = ADP + protein threonine phosphate. These reactions are dependent on the presence of calcium ions.
    GO:0005516    calmodulin binding    Interacting selectively and non-covalently with calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states.
    GO:0004683    calmodulin-dependent protein kinase activity    Catalysis of the reactions: ATP + a protein serine = ADP + protein serine phosphate; and ATP + a protein threonine = ADP + protein threonine phosphate. These reactions require the presence of calcium-bound calmodulin.
    GO:0008017    microtubule binding    Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers.
    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: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.
biological process
    GO:0048675    axon extension    Long distance growth of a single axon process involved in cellular development.
    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:0021766    hippocampus development    The progression of the hippocampus over time from its initial formation until its mature state.
    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:0021819    layer formation in cerebral cortex    The detachment of cells from radial glial fibers at the appropriate time when they cease to migrate and form distinct layer in the cerebral cortex.
    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:0018105    peptidyl-serine phosphorylation    The phosphorylation of peptidyl-serine to form peptidyl-O-phospho-L-serine.
    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:0021860    pyramidal neuron development    The progression of a pyramidal neuron from its initial formation to its mature state.
    GO:0051602    response to electrical stimulus    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 an electrical stimulus.
cellular component
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0030425    dendrite    A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
    GO:0005874    microtubule    Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle.
    GO:0005875    microtubule associated complex    Any multimeric complex connected to a microtubule.
    GO:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    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
        DCX_HUMAN | O436021mjd 2xrp 4atu 5ikc 5in7 5io9 5ioi 5ip4

(-) Related Entries Specified in the PDB File

1mjd STRUCTURE OF N-TERMINAL DOMAIN OF HUMAN DOUBLECORTIN