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(-) Description

Title :  THE NMR MINIMIZED AVERAGE STRUCTURE OF THE ITK SH2 DOMAIN BOUND TO A PHOSPHOPEPTIDE
 
Authors :  M. Sundd, E. V. Pletneva, D. B. Fulton, A. H. Andreotti
Date :  27 Oct 05  (Deposition) - 07 Feb 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B
Keywords :  Cis/Trans Isomerization, Interleukin-2 Tyrosine Kinase, Itk, T-Cell Specific Kinase, Tsk, Src Homology 2, Sh2, Proline, Phosphotyrosine Binding, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. V. Pletneva, M. Sundd, D. B. Fulton, A. H. Andreotti
Molecular Details Of Itk Activation By Prolyl Isomerization And Phospholigand Binding: The Nmr Structure Of The Itk Sh2 Domain Bound To A Phosphopeptide.
J. Mol. Biol. V. 357 550 2006
PubMed-ID: 16436281  |  Reference-DOI: 10.1016/J.JMB.2005.12.073
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TYROSINE-PROTEIN KINASE ITK/TSK
    Chains: A
    EC Number: 2.7.1.112
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PGEX(2T)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: SH2 DOMAIN
    Gene: ITK, EMT, TLK, TSK
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: T-CELL-SPECIFIC KINASE, IL-2-INDUCIBLE T-CELL KINASE, KINASE EMT, KINASE TLK, ITK
 
Molecule 2 - LYMPHOCYTE CYTOSOLIC PROTEIN 2 PHOSPHOPEPTIDE FRAGMENT
    Chains: B
    Engineered: YES
    Fragment: PHOSPHOPEPTIDE FRAGMENT SEQUENCE DATABASE RESIDUES 143-148
    Other Details: THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN MUS MUSCULUS (MOUSE).
    Synonym: SH2 DOMAIN-CONTAINING LEUCOCYTE PROTEIN OF 76 KDA, SLP-76 TYROSINE PHOSPHOPROTEIN, SLP76
    Synthetic: YES

 Structural Features

(-) Chains, Units

  
NMR Structure : 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

NMR Structure (3, 4)
No.NameCountTypeFull Name
1ACE2Mod. Amino AcidACETYL GROUP
2NH21Mod. Amino AcidAMINO GROUP
3PTR1Mod. Amino AcidO-PHOSPHOTYROSINE

(-) Sites  (3, 3)

NMR Structure (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:5BINDING SITE FOR RESIDUE ACE A 3
2AC2SOFTWAREASP B:120 , PTR B:121 , PRO B:123BINDING SITE FOR RESIDUE ACE B 118
3AC3SOFTWAREPRO B:124BINDING SITE FOR RESIDUE NH2 B 125

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

NMR Structure
No.Residues
1Ser A:72 -Pro A:73

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ETZ)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH2PS50001 Src homology 2 (SH2) domain profile.ITK_MOUSE245-343  1A:11-109

(-) Exons   (0, 0)

(no "Exon" information available for 2ETZ)

(-) 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:109
 aligned with ITK_MOUSE | Q03526 from UniProtKB/Swiss-Prot  Length:625

    Alignment length:109
                                   246       256       266       276       286       296       306       316       326       336         
            ITK_MOUSE   237 PNNLETYEWYNKSISRDKAEKLLLDTGKEGAFMVRDSRTPGTYTVSVFTKAIISENPCIKHYHIKETNDSPKRYYVAEKYVFDSIPLLIQYHQYNGGGLVTRLRYPVCS 345
               SCOP domains -d2etza1 A:4-111 Itk/tsk protein tyrosine kinase                                                              SCOP domains
               CATH domains -2etzA00 A:4-111 SHC Adaptor Protein                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhhhhhhhhh...eeeee.......eeeeee...........eeeeeee.......ee.....ee.hhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------SH2  PDB: A:11-109 UniProt: 245-343                                                                -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 2etz A   3 xNNLETYEWYNKSISRDKAEKLLLDTGKEGAFMVRDSRTPGTYTVSVFTKAIISENPCIKHYHIKETNDSPKRYYVAEKYVFDSIPLLIQYHQYNGGGLVTRLRYPVCG 111
                            |       12        22        32        42        52        62        72        82        92       102         
                            |                                                                                                            
                            3-ACE                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:8
 aligned with LCP2_MOUSE | Q60787 from UniProtKB/Swiss-Prot  Length:533

    Alignment length:8
           LCP2_MOUSE   142 AADYEPPP 149
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ........ Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                 2etz B 118 xADyEPPx 125
                            |  |   |
                          118-ACE  |
                             121-PTR
                                 125-NH2
   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
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (36, 43)

NMR Structure(hide GO term definitions)
Chain A   (ITK_MOUSE | Q03526)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0004713    protein tyrosine kinase activity    Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate.
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    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:0038095    Fc-epsilon receptor signaling pathway    A series of molecular signals initiated by the binding of the Fc portion of immunoglobulin E (IgE) to an Fc-epsilon receptor on the surface of a signal-receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription. The Fc portion of an immunoglobulin is its C-terminal constant region.
    GO:0001865    NK T cell differentiation    The process in which a precursor cell type acquires the specialized features of a NK T cell.
    GO:0050852    T cell receptor signaling pathway    A series of molecular signals initiated by the cross-linking of an antigen receptor on a T cell.
    GO:0007202    activation of phospholipase C activity    The initiation of the activity of the inactive enzyme phospolipase C as the result of a series of molecular signals generated as a consequence of a G-protein coupled receptor binding to its physiological ligand.
    GO:0002250    adaptive immune response    An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory).
    GO:0001816    cytokine production    The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0032609    interferon-gamma production    The appearance of interferon-gamma due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Interferon-gamma is also known as type II interferon.
    GO:0032633    interleukin-4 production    The appearance of interleukin-4 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
    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:0038083    peptidyl-tyrosine autophosphorylation    The phosphorylation by a protein of one or more of its own tyrosine amino acid residues, or a tyrosine residue on an identical protein.
    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:0042127    regulation of cell proliferation    Any process that modulates the frequency, rate or extent of cell proliferation.
    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:0005911    cell-cell junction    A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0031234    extrinsic component of cytoplasmic side of plasma membrane    The component of a plasma membrane consisting of gene products and protein complexes that are loosely bound to its cytoplasmic surface, but not integrated into the hydrophobic region.

Chain B   (LCP2_MOUSE | Q60787)
molecular function
    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).
biological process
    GO:0050852    T cell receptor signaling pathway    A series of molecular signals initiated by the cross-linking of an antigen receptor on a T cell.
    GO:0050663    cytokine secretion    The regulated release of cytokines from a cell. Cytokines are any of a group of proteins that function to control the survival, growth and differentiation of tissues and cells, and which have autocrine and paracrine activity.
    GO:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    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:0045576    mast cell activation    The change in morphology and behavior of a mast cell resulting from exposure to a cytokine, chemokine, soluble factor, or to (at least in mammals) an antigen which the mast cell has specifically bound via IgE bound to Fc-epsilonRI receptors.
    GO:0045860    positive regulation of protein kinase activity    Any process that activates or increases the frequency, rate or extent of protein kinase activity.
    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:0036398    TCR signalosome    A multi-protein complex containing at least the T-cell receptor complex and the LAT (linker for activation of T cells) scaffold protein. Also contains a variety of signaling proteins including co-receptors, kinases, phosphatases and adaptors such as CD8. Connects events on the plasma membrane to distal signaling cascades to ultimately modulate T cell biology.
    GO:0005911    cell-cell junction    A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0044853    plasma membrane raft    A membrane raft that is part of the plasma membrane.

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  2etz
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  ITK_MOUSE | Q03526
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  LCP2_MOUSE | Q60787
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  2.7.1.112
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 Related Entries

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

UniProtKB/Swiss-Prot
        ITK_MOUSE | Q03526: 1awj 1lui 1luk 1lum 1lun 2eu0 2k79 2k7a 2rn8 2rna 3s9k
        LCP2_MOUSE | Q60787: 1oeb 2eu0

(-) Related Entries Specified in the PDB File

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1luk NMR STRUCTURE OF THE ITK SH2 DOMAIN, PRO287CIS, ENERGY MINIMIZED AVERAGE STRUCTURE
1lum NMR STRUCTURE OF THE ITK SH2 DOMAIN, PRO287TRANS, 20 LOW ENERGY STRUCTURES
1lun NMR STRUCTURE OF THE ITK SH2 DOMAIN, PRO287TRANS, ENERGY MINIMIZED AVERAGE STRUCTURE
2eu0 THE NMR ENSEMBLE STRUCTURE OF THE ITK SH2 DOMAIN BOUND TO A PHOSPHOPEPTIDE