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(-) Description

Title :  THE SOLUTION STRUCTURE OF SAM DOMAIN FROM THE RECEPTOR TYROSINE KINASE EPHB2, NMR, 10 STRUCTURES
 
Authors :  M. Smalla, P. Schmieder, M. Kelly, A. Ter Laak, G. Krause, L. Ball, M. Wahl, P. Bork, H. Oschkinat
Date :  08 Jan 99  (Deposition) - 06 Oct 99  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (10x)
Keywords :  Nmr, Receptor Oligomerization, Eph Receptors, Tyrosine Phosphorylation, Signal Transduction, Tyrosine-Protein Kinase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Smalla, P. Schmieder, M. Kelly, A. Ter Laak, G. Krause, L. Ball, M. Wahl, P. Bork, H. Oschkinat
Solution Structure Of The Receptor Tyrosine Kinase Ephb2 Sam Domain And Identification Of Two Distinct Homotypic Interaction Sites.
Protein Sci. V. 8 1954 1999
PubMed-ID: 10548040
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - EPHRIN TYPE-B RECEPTOR 2
    ChainsA
    EC Number2.7.1.112
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Cellular LocationCYTOPLASM
    Expression System Cell LineBL21
    Expression System PlasmidPET 28D
    Expression System Taxid562
    Expression System TissueEMBRYO
    FragmentSAM DOMAIN
    Organism CommonCHICKEN
    Organism ScientificGALLUS GALLUS
    Organism Taxid9031
    Other DetailsPOTENTIAL TYROSINE PHOSPHORYLATION AT Y 25

 Structural Features

(-) Chains, Units

  
NMR Structure (10x)

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1SGG)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_DOMAINPS50105 SAM domain profile.EPHB2_CHICK931-995  1A:8-72

(-) Exons   (0, 0)

(no "Exon" information available for 1SGG)

(-) 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:67
 aligned with EPHB2_CHICK | P28693 from UniProtKB/Swiss-Prot  Length:1004

    Alignment length:67
                                   939       949       959       969       979       989       
          EPHB2_CHICK   930 YTSFNTVDEWLDAIKMSQYKESFASAGFTTFDIVSQMTVEDILRVGVTLAGHQKKILNSIQVMRAQM 996
               SCOP domains d1sgga_ A: EphB2 receptor                                           SCOP domains
               CATH domains 1sggA00 A:7-73 Transcription Factor, Ets-1                          CATH domains
               Pfam domains SAM_1-1sggA01 A:7-70                                            --- Pfam domains
         Sec.struct. author .....hhhhhhhhh..hhhhhhhhh......hhhhh..hhhhhhh......hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -SAM_DOMAIN  PDB: A:8-72 UniProt: 931-995                         - PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                 1sgg A   7 YTSFNTVDEWLDAIKMSQYKESFASAGFTTFDIVSQMTVEDILRVGVTLAGHQKKILNSIQVMRAQM  73
                                    16        26        36        46        56        66       

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  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

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: SAM (26)

(-) Gene Ontology  (31, 31)

NMR Structure(hide GO term definitions)
Chain A   (EPHB2_CHICK | P28693)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0005003    ephrin receptor activity    Combining with an ephrin to initiate a change in cell activity.
    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: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.
    GO:0004714    transmembrane receptor protein tyrosine kinase activity    Combining with a signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity by catalysis of the reaction: ATP + a protein-L-tyrosine = ADP + a protein-L-tyrosine phosphate.
    GO:0005005    transmembrane-ephrin receptor activity    Combining with a transmembrane ephrin to initiate a change in cell activity.
biological process
    GO:0001525    angiogenesis    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
    GO:0007411    axon guidance    The chemotaxis process that directs the migration of an axon growth cone to a specific target site in response to a combination of attractive and repulsive cues.
    GO:0007413    axonal fasciculation    The collection of axons into a bundle of rods, known as a fascicle.
    GO:0060996    dendritic spine development    The process whose specific outcome is the progression of the dendritic spine over time, from its formation to the mature structure. A dendritic spine is a protrusion from a dendrite and a specialized subcellular compartment involved in synaptic transmission.
    GO:0060997    dendritic spine morphogenesis    The process in which the anatomical structures of a dendritic spine are generated and organized. A dendritic spine is a protrusion from a dendrite and a specialized subcellular compartment involved in synaptic transmission.
    GO:0048013    ephrin receptor signaling pathway    The series of molecular signals generated as a consequence of an ephrin receptor binding to an ephrin.
    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: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:0051965    positive regulation of synapse assembly    Any process that activates, maintains or increases the frequency, rate or extent of synapse assembly, the aggregation, arrangement and bonding together of a set of components to form a synapse.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0021963    spinothalamic tract morphogenesis    Generation of a long process of a CNS neuron, that carries efferent (outgoing) action potentials from the cell body in the spinal cord towards target cells in the thalamus. This axonal process is a member of those that make up the spinothalamic tract, one of the major routes of nociceptive signaling.
    GO:0007169    transmembrane receptor protein tyrosine kinase signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses tyrosine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
    GO:0030424    axon    The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    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:0016021    integral component of membrane    The component of a 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.
    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.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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