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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ITK SH2 DOMAIN.
 
Authors :  R. E. Joseph, N. D. Ginder, J. A. Hoy, J. C. Nix, B. D. Fulton, R. B. Honzatk A. H. Andreotti
Date :  01 Jun 11  (Deposition) - 08 Feb 12  (Release) - 15 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Proline Isomerization, Cis Proline, Domain Swapped Dimer, Sh2 Domain, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. E. Joseph, N. D. Ginder, J. A. Hoy, J. C. Nix, D. B. Fulton, R. B. Honzatko, A. H. Andreotti
Structure Of The Interleukin-2 Tyrosine Kinase Src Homology 2 Domain; Comparison Between X-Ray And Nmr-Derived Structures.
Acta Crystallogr. , Sect. F V. 68 145 2012
PubMed-ID: 22297986  |  Reference-DOI: 10.1107/S1744309111049761
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TYROSINE-PROTEIN KINASE ITK/TSK
    ChainsA
    EC Number2.7.10.2
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX-2T
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentSH2 DOMAIN (UNP RESIDUES 236-344)
    GeneEMT, IL-2 INDUCIBLE T CELL KINASE, ITK, TLK, TSK
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymIL-2-INDUCIBLE T-CELL KINASE, KINASE EMT, KINASE TLK, T- CELL-SPECIFIC KINASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1CIT2Ligand/IonCITRIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:9 , GLU A:10 , ARG A:18 , ARG A:37 , ARG A:40BINDING SITE FOR RESIDUE CIT A 335

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3S9K)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asn A:58 -Pro A:59
2Ser A:72 -Pro A:73

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3S9K)

(-) PROSITE Motifs  (3, 3)

Asymmetric Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH2PS50001 Src homology 2 (SH2) domain profile.ITK_MOUSE245-343  1A:11-109
2PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.ITK_MOUSE374-396  1A:111-112
3PROTEIN_KINASE_TYRPS00109 Tyrosine protein kinases specific active-site signature.ITK_MOUSE483-495  1A:115-118
Biological Unit 1 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH2PS50001 Src homology 2 (SH2) domain profile.ITK_MOUSE245-343  1A:11-109
2PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.ITK_MOUSE374-396  1A:111-112
3PROTEIN_KINASE_TYRPS00109 Tyrosine protein kinases specific active-site signature.ITK_MOUSE483-495  1A:115-118
Biological Unit 2 (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH2PS50001 Src homology 2 (SH2) domain profile.ITK_MOUSE245-343  2A:11-109
2PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.ITK_MOUSE374-396  2A:111-112
3PROTEIN_KINASE_TYRPS00109 Tyrosine protein kinases specific active-site signature.ITK_MOUSE483-495  2A:115-118

(-) Exons   (0, 0)

(no "Exon" information available for 3S9K)

(-) 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:114
 aligned with ITK_MOUSE | Q03526 from UniProtKB/Swiss-Prot  Length:625

    Alignment length:249
                                   248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478         
            ITK_MOUSE   239 NLETYEWYNKSISRDKAEKLLLDTGKEGAFMVRDSRTPGTYTVSVFTKAIISENPCIKHYHIKETNDSPKRYYVAEKYVFDSIPLLIQYHQYNGGGLVTRLRYPVCSWRQKAPVTAGLRYGKWVIQPSELTFVQEIGSGQFGLVHLGYWLNKDKVAIKTIQEGAMSEEDFIEEAEVMMKLSHPKLVQLYGVCLEQAPICLVFEFMEHGCLSDYLRSQRGLFAAETLLGMCLDVCEGMAYLEKACVIHRD 487
               SCOP domains d3s9ka_ A: automated matches                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.......hhhhhhhhhhhhh....eeeee......eeeeeee........eeeeeeeee.......eeee......hhhhhhhhhhhh.............------------------------------..-----------------------..----------------------------------------------------------------------------------.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------SH2  PDB: A:11-109 UniProt: 245-343                                                                ------------------------------PROTEIN_KINASE_ATP     --------------------------------------------------------------------------------------PROTE PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s9k A   5 NLETYEWYNKSISRDKAEKLLLDTGKEGAFMVRDSRTPGTYTVSVFTKAIISENPCIKHYHIKETNDSPKRYYVAEKYVFDSIPLLIQYHQYNGGGLVTRLRYPVC------------------------------GS-----------------------PG----------------------------------------------------------------------------------IHRD 118
                                    14        24        34        44        54        64        74        84        94       104     |   -         -         -      || -         -         - ||      -         -         -         -         -         -         -         -     |   
                                                                                                                                   110                            111|                     113|                                                                                115   
                                                                                                                                                                   112                      114                                                                                      

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (0, 0)

(no "CATH Domain" information available for 3S9K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3S9K)

(-) Gene Ontology  (30, 30)

Asymmetric Unit(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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ITK_MOUSE | Q035261awj 1lui 1luk 1lum 1lun 2etz 2eu0 2k79 2k7a 2rn8 2rna

(-) Related Entries Specified in the PDB File

1luk NMR STRUCTURE OF THE ITK SH2 DOMAIN, PRO287CIS, ENERGY MINIMIZED AVERAGE STRUCTURE
1lun NMR STRUCTURE OF THE ITK SH2 DOMAIN, PRO287TRANS, ENERGY MINIMIZED AVERAGE STRUCTURE
2etz THE NMR MINIMIZED AVERAGE STRUCTURE OF THE ITK SH2 DOMAIN BOUND TO A PHOSPHOPEPTIDE
2k79 SOLUTION STRUCTURE OF THE BINARY COMPLEX BETWEEN THE SH3 AND SH2 DOMAIN OF INTERLEUKIN-2 TYROSINE KINASE