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(-) Description

Title :  N-TERMINAL HALF OF MIDKINE
 
Authors :  W. Iwasaki, K. Nagata, H. Hatanaka, K. Ogura, T. Inui, T. Kimura, T. Muramatsu, K. Yoshida, M. Tasumi, F. Inagaki
Date :  16 Mar 99  (Deposition) - 23 Mar 99  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A
Keywords :  Heparin-Binding Growth Factor (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  W. Iwasaki, K. Nagata, H. Hatanaka, T. Inui, T. Kimura, T. Muramatsu, K. Yoshida, M. Tasumi, F. Inagaki
Solution Structure Of Midkine, A New Heparin-Binding Growth Factor.
Embo J. V. 16 6936 1997
PubMed-ID: 9384573  |  Reference-DOI: 10.1093/EMBOJ/16.23.6936
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (MIDKINE)
    ChainsA
    EngineeredYES
    FragmentN-TERMINAL HALF
    Other DetailsTHE PROTEIN WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PROTEIN IS NATURALLY FOUND IN HOMO SAPIENS (HUMAN).
    SyntheticYES

 Structural Features

(-) Chains, Units

  
NMR Structure 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1MKN)

(-) Sites  (0, 0)

(no "Site" information available for 1MKN)

(-) SS Bonds  (3, 3)

NMR Structure
No.Residues
1A:15 -A:39
2A:23 -A:48
3A:30 -A:52

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1MKN)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PTN_MK_1PS00619 PTN/MK heparin-binding protein family signature 1.MK_HUMAN35-59  1A:13-37
2PTN_MK_2PS00620 PTN/MK heparin-binding protein family signature 2.MK_HUMAN70-94  1A:48-59

(-) Exons   (2, 2)

NMR Structure (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2bENST000003955662bENSE00001890528chr11:46403226-4640330883MK_HUMAN-00--
1.2iENST000003955662iENSE00002141825chr11:46403607-4640368377MK_HUMAN1-26261A:1-44
1.3cENST000003955663cENSE00000712415chr11:46403844-46404011168MK_HUMAN26-82571A:4-5956
1.4bENST000003955664bENSE00001181863chr11:46404137-46404298162MK_HUMAN82-136550--
1.5dENST000003955665dENSE00001875238chr11:46405019-46405356338MK_HUMAN136-14380--

(-) Sequences/Alignments

NMR Structure
   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:59
 aligned with MK_HUMAN | P21741 from UniProtKB/Swiss-Prot  Length:143

    Alignment length:59
                                    32        42        52        62        72         
              MK_HUMAN   23 KKKDKVKKGGPGSECAEWAWGPCTPSSKDCGVGFREGTCGAQTQRIRCRVPCNWKKEFG 81
               SCOP domains d1mkna_ A:                                                  SCOP domains
               CATH domains 1mknA00 A:1-59                                              CATH domains
               Pfam domains -PTN_MK_N-1mknA01 A:2-58                                  - Pfam domains
         Sec.struct. author ...................eeeeee......eeeeeeee..eeeeeeeee......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------PTN_MK_1  PDB: A:13-37   ----------PTN_MK_2     PROSITE
           Transcript 1 (1) 1.2i------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---Exon 1.3c  PDB: A:4-59 UniProt: 26-82 [INCOMPLETE]       Transcript 1 (2)
                  1mkn A  1 KKKDKVKKGGPGSECAEWAWGPCTPSSKDCGVGFREGTCGAQTQRIRCRVPCNWKKEFG 59
                                    10        20        30        40        50         

   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)

NMR Structure

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

NMR Structure

(-) Gene Ontology  (28, 28)

NMR Structure(hide GO term definitions)
Chain A   (MK_HUMAN | P21741)
molecular function
    GO:0008083    growth factor activity    The function that stimulates a cell to grow or proliferate. Most growth factors have other actions besides the induction of cell growth or proliferation.
    GO:0008201    heparin binding    Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
biological process
    GO:0007219    Notch signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to the receptor Notch on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0030325    adrenal gland development    The process whose specific outcome is the progression of the adrenal gland over time, from its formation to the mature structure. This gland can either be a discrete structure located bilaterally above each kidney, or a cluster of cells in the head kidney that perform the functions of the adrenal gland. In either case, this organ consists of two cells types, aminergic chromaffin cells and steroidogenic cortical cells.
    GO:0001662    behavioral fear response    An acute behavioral change resulting from a perceived external threat.
    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:0016477    cell migration    The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
    GO:0021681    cerebellar granular layer development    The process whose specific outcome is the progression of the cerebellar granule layer over time, from its formation to the mature structure. The granular layer is the innermost layer of the cerebellar cortex. This layer contains densely packed small neurons, mostly granule cells. Some Golgi cells are found at the outer border. Granule neurons send parallel fibers to the upper molecular layer, where they synapse with Purkinje cell dendrites. Mossy fibers from the pontine nuclei in the white matter synapse with granule cell axons, Golgi cell axons and unipolar brush interneuron axons at cerebellar glomeruli in the granule cell layer.
    GO:0021987    cerebral cortex development    The progression of the cerebral cortex over time from its initial formation until its mature state. The cerebral cortex is the outer layered region of the telencephalon.
    GO:0030421    defecation    The expulsion of feces from the rectum.
    GO:0021542    dentate gyrus development    The process whose specific outcome is the progression of the dentate gyrus over time, from its formation to the mature structure. The dentate gyrus is one of two interlocking gyri of the hippocampus. It contains granule cells, which project to the pyramidal cells and interneurons of the CA3 region of the ammon gyrus.
    GO:0021766    hippocampus development    The progression of the hippocampus over time from its initial formation until its mature state.
    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:0043524    negative regulation of neuron apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process in neurons.
    GO:1901215    negative regulation of neuron death    Any process that stops, prevents or reduces the frequency, rate or extent of neuron death.
    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:0051781    positive regulation of cell division    Any process that activates or increases the frequency, rate or extent of cell division.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0050795    regulation of behavior    Any process that modulates the frequency, rate or extent of behavior, the internally coordinated responses (actions or inactions) of whole living organisms (individuals or groups) to internal or external stimuli.
    GO:0042493    response to drug    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 drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0051384    response to glucocorticoid    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 glucocorticoid stimulus. Glucocorticoids are hormonal C21 corticosteroids synthesized from cholesterol with the ability to bind with the cortisol receptor and trigger similar effects. Glucocorticoids act primarily on carbohydrate and protein metabolism, and have anti-inflammatory effects.
    GO:0009725    response to hormone    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 hormone stimulus.
    GO:0009611    response to wounding    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 indicating damage to the organism.
    GO:0007614    short-term memory    The memory process that deals with the storage, retrieval and modification of information received a short time (up to about 30 minutes) ago. This type of memory is typically dependent on direct, transient effects of second messenger activation.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
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:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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 Related Entries

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

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        MK_HUMAN | P217411mkc

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