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PDBsum entry 1lum

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Transferase PDB id
1lum
Jmol
Contents
Protein chain
110 a.a. *
* Residue conservation analysis
PDB id:
1lum
Name: Transferase
Title: Nmr structure of the itk sh2 domain, pro287trans, 20 low energy structures
Structure: Tyrosine-protein kinase itk/tsk. Chain: a. Fragment: src homology 2 (sh2) domain (residues 238-344). Synonym: interleukin-2 tyrosine kinase, t-cell-specific kinase, il-2-inducible t-cell kinase, kinase emt, kinase tlk. Engineered: yes
Source: Mus musculus. House mouse. Organism_taxid: 10090. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
NMR struc: 20 models
Authors: R.J.Mallis,K.N.Brazin,D.B.Fulton,A.H.Andreotti
Key ref:
R.J.Mallis et al. (2002). Structural characterization of a proline-driven conformational switch within the Itk SH2 domain. Nat Struct Biol, 9, 900-905. PubMed id: 12402030 DOI: 10.1038/nsb864
Date:
22-May-02     Release date:   27-Nov-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q03526  (ITK_MOUSE) -  Tyrosine-protein kinase ITK/TSK
Seq:
Struc:
 
Seq:
Struc:
625 a.a.
109 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.2.7.10.2  - Non-specific protein-tyrosine kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate
ATP
+ [protein]-L-tyrosine
= ADP
+ [protein]-L-tyrosine phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1038/nsb864 Nat Struct Biol 9:900-905 (2002)
PubMed id: 12402030  
 
 
Structural characterization of a proline-driven conformational switch within the Itk SH2 domain.
R.J.Mallis, K.N.Brazin, D.B.Fulton, A.H.Andreotti.
 
  ABSTRACT  
 
Interleukin-2 tyrosine kinase (Itk) is a T cell-specific kinase required for a proper immune response following T cell receptor engagement. In addition to the kinase domain, Itk is composed of several noncatalytic regulatory domains, including a Src homology 2 (SH2) domain that contains a conformationally heterogeneous Pro residue. Cis-trans isomerization of a single prolyl imide bond within the SH2 domain mediates conformer-specific ligand recognition that may have functional implications in T cell signaling. To better understand the mechanism by which a proline switch regulates ligand binding, we have used NMR spectroscopy to determine two structures of Itk SH2 corresponding to the cis and trans imide bond-containing conformers. The structures indicate that the heterogeneous Pro residue acts as a hinge that modulates ligand recognition by controlling the relative orientation of protein-binding surfaces.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. NMR structures of the cis and trans Itk SH2 conformers. a, Stereo view of 20 low energy structures of the cis (coral) and trans (turquoise) conformations of the Itk SH2 domain. Backbone heavy atoms within the secondary structural elements over the entire sequence were used for superpositions. b, Ribbon diagrams of the energy minimized average structures of the cis (left) and trans (right) conformers. Secondary structural elements and ligand-binding pockets are labeled in (a,b) according to standard nomenclature for SH2 domains8. Pro 287 is labeled in each structure. c, Sequence of the Itk SH2 domain and sequence alignment of the CD loop regions in the SH2 domains of several tyrosine kinases. The residues that give rise to nondegenerate chemical shifts2 are bold and underlined, and Pro 287 is labeled. d, Solvent-accessible surface plot of the cis conformer. The residues that give rise to dual resonances because of Pro cis-trans isomerization are highlighted in white. The trans conformer shows a similar contiguous surface for the heterogeneous residues (data not shown). e, Overlay of the energy minimized average structures of the cis (coral) and trans (turquoise) conformers. Expanded views of the CD loop (left), the central -sheet (right) and the BG loop regions (middle) are shown. All structures are rendered using MolMol31.
Figure 3.
Figure 3. Hydrophobic packing involving residues in the CD loop of the cis SH2 structure provides stabilization energy. a, Overlay of 20 lowest energy structures including the CD loop, the central -sheet and A of the cis (left) and trans (right) conformers. Side chains of Leu 254 and Pro 287 are yellow. His 291 and Glu 250 are also labeled. b, Overlay of 20 lowest energy structures (rotated clockwise with respect to (a)) showing the CD loop of the cis (left) and trans (right) conformers. Side chains of Ile 282, Ala 281 and Cys 288 are labeled and shown in yellow. Additional side chains are included without labels for clarity. c, Three-dimensional 13C-edited NOESY experiment showing through-space proximity between the -methyl protons of Ile 282 and one of the -methylene protons of Cys 288. The NOE is observed only for the cis conformer (left panel). The total number of NOEs unique to the cis and trans structures is shown in Table 1. d, Three-dimensional 15N-edited TOCSY experiment illustrating the nondegenerate resonance frequencies for the Cys 288 -methylenes in the cis conformer (left). The same protons resonate at a single frequency in the trans conformer (right). e, Expansion of the 1H-15N HSQC spectra showing the amide signal of Gly 260 (6260) in the cis and trans forms. Left, unmodified, reduced Itk SH2 domain. Middle, spectrum acquired following reaction of the Itk SH2 domain with glutathione disulfide (GSSG) (20 mM GSSG, pH 7.4, 40 min, 25 C). Right, spectrum acquired following reaction with methyl methane thiosulfonate (MMTS) (5 mM MMTS, pH 7.4, 20 min). The percentage of SH2 domain in the cis conformation in each of these experiments as measured by peak volumes of Gly 260 (cis) and Gly 260 (trans) was 48, 5 and 32% for the reduced, GSSG-treated and MMTS-treated proteins, respectively. The backbone amide resonance of Cys 288 was monitored over the course of both reactions and the reactions were allowed to proceed until no further chemical shift changes occurred. The completeness of the S-glutathiolation reaction was also assessed by separation of the domain with nondenaturing isoelectric focusing (IEF) gel electrophoresis over a pH range of 3.5 -10 as described^33.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2002, 9, 900-905) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21164511 L.K.Nicholson, and S.De (2011).
Structural biology: The twist in Crk signaling revealed.
  Nat Chem Biol, 7, 5-6.  
21131971 P.Sarkar, T.Saleh, S.R.Tzeng, R.B.Birge, and C.G.Kalodimos (2011).
Structural basis for regulation of the Crk signaling protein by a proline switch.
  Nat Chem Biol, 7, 51-57.
PDB codes: 2l3p 2l3q 2l3s
21227701 T.Kaneko, S.S.Sidhu, and S.S.Li (2011).
Evolving specificity from variability for protein interaction domains.
  Trends Biochem Sci, 36, 183-190.  
20237289 L.Min, W.Wu, R.E.Joseph, D.B.Fulton, L.Berg, and A.H.Andreotti (2010).
Disrupting the intermolecular self-association of Itk enhances T cell signaling.
  J Immunol, 184, 4228-4235.  
19361414 A.Severin, R.E.Joseph, S.Boyken, D.B.Fulton, and A.H.Andreotti (2009).
Proline isomerization preorganizes the Itk SH2 domain for binding to the Itk SH3 domain.
  J Mol Biol, 387, 726-743.  
19128175 D.Hamelberg, and J.A.McCammon (2009).
Mechanistic insight into the role of transition-state stabilization in cyclophilin A.
  J Am Chem Soc, 131, 147-152.  
19308324 K.Teilum, J.G.Olsen, and B.B.Kragelund (2009).
Functional aspects of protein flexibility.
  Cell Mol Life Sci, 66, 2231-2247.  
19722642 M.R.Evans, and K.H.Gardner (2009).
Slow transition between two beta-strand registers is dictated by protein unfolding.
  J Am Chem Soc, 131, 11306-11307.  
19689375 N.Sahu, and A.August (2009).
ITK inhibitors in inflammation and immune-mediated disorders.
  Curr Top Med Chem, 9, 690-703.  
19290922 R.E.Joseph, and A.H.Andreotti (2009).
Conformational snapshots of Tec kinases during signaling.
  Immunol Rev, 228, 74-92.  
19920179 R.P.Jakob, G.Zoldák, T.Aumüller, and F.X.Schmid (2009).
Chaperone domains convert prolyl isomerases into generic catalysts of protein folding.
  Proc Natl Acad Sci U S A, 106, 20282-20287.  
19617535 U.Weininger, R.P.Jakob, B.Eckert, K.Schweimer, F.X.Schmid, and J.Balbach (2009).
A remote prolyl isomerization controls domain assembly via a hydrogen bonding network.
  Proc Natl Acad Sci U S A, 106, 12335-12340.  
19515814 Y.F.Li, S.Poole, K.Nishio, K.Jang, F.Rasulova, A.McVeigh, S.J.Savarino, D.Xia, and E.Bullitt (2009).
Structure of CFA/I fimbriae from enterotoxigenic Escherichia coli.
  Proc Natl Acad Sci U S A, 106, 10793-10798.
PDB codes: 3f83 3f84 3f85
19023406 J.M.Carlson, Z.L.Brumme, C.M.Rousseau, C.J.Brumme, P.Matthews, C.Kadie, J.I.Mullins, B.D.Walker, P.R.Harrigan, P.J.Goulder, and D.Heckerman (2008).
Phylogenetic dependency networks: inferring patterns of CTL escape and codon covariation in HIV-1 Gag.
  PLoS Comput Biol, 4, e1000225.  
18599349 N.Isakov (2008).
A new twist to adaptor proteins contributes to regulation of lymphocyte cell signaling.
  Trends Immunol, 29, 388-396.  
18972488 R.Glaves, M.Baer, E.Schreiner, R.Stoll, and D.Marx (2008).
Conformational dynamics of minimal elastin-like polypeptides: the role of proline revealed by molecular dynamics and nuclear magnetic resonance.
  Chemphyschem, 9, 2759-2765.  
17704259 A.K.Mishra, L.Gangwani, R.J.Davis, and D.G.Lambright (2007).
Structural insights into the interaction of the evolutionarily conserved ZPR1 domain tandem with eukaryotic EF1A, receptors, and SMN complexes.
  Proc Natl Acad Sci U S A, 104, 13930-13935.
PDB code: 2qkd
17876319 K.P.Lu, G.Finn, T.H.Lee, and L.K.Nicholson (2007).
Prolyl cis-trans isomerization as a molecular timer.
  Nat Chem Biol, 3, 619-629.  
17897671 R.E.Joseph, D.B.Fulton, and A.H.Andreotti (2007).
Mechanism and functional significance of Itk autophosphorylation.
  J Mol Biol, 373, 1281-1292.  
16408084 A.H.Andreotti (2006).
Opening the pore hinges on proline.
  Nat Chem Biol, 2, 13-14.  
16385008 G.W.Yu, M.D.Allen, A.Andreeva, A.R.Fersht, and M.Bycroft (2006).
Solution structure of the C4 zinc finger domain of HDM2.
  Protein Sci, 15, 384-389.
PDB codes: 2c6a 2c6b
16969585 K.C.Huang, H.T.Cheng, M.T.Pai, S.R.Tzeng, and J.W.Cheng (2006).
Solution structure and phosphopeptide binding of the SH2 domain from the human Bruton's tyrosine kinase.
  J Biomol NMR, 36, 73-78.
PDB code: 2ge9
16455491 M.Vogel, B.Bukau, and M.P.Mayer (2006).
Allosteric regulation of Hsp70 chaperones by a proline switch.
  Mol Cell, 21, 359-367.  
16491092 T.R.Jahn, M.J.Parker, S.W.Homans, and S.E.Radford (2006).
Amyloid formation under physiological conditions proceeds via a native-like folding intermediate.
  Nat Struct Mol Biol, 13, 195-201.  
16641261 Z.Keckesova, L.M.Ylinen, and G.J.Towers (2006).
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  J Virol, 80, 4683-4690.  
15937494 B.Eckert, A.Martin, J.Balbach, and F.X.Schmid (2005).
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  Nat Struct Mol Biol, 12, 619-623.  
15771581 L.J.Berg, L.D.Finkelstein, J.A.Lucas, and P.L.Schwartzberg (2005).
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  Annu Rev Immunol, 23, 549-600.  
15643056 M.Arévalo-Rodríguez, and J.Heitman (2005).
Cyclophilin A is localized to the nucleus and controls meiosis in Saccharomyces cerevisiae.
  Eukaryot Cell, 4, 17-29.  
15998457 P.Wang, and J.Heitman (2005).
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  Genome Biol, 6, 226.  
15609336 S.Lorenzen, B.Peters, A.Goede, R.Preissner, and C.Frömmel (2005).
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15178680 C.M.Santiveri, J.M.Pérez-Cañadillas, M.K.Vadivelu, M.D.Allen, T.J.Rutherford, N.A.Watkins, and M.Bycroft (2004).
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15308100 J.Colgan, M.Asmal, M.Neagu, B.Yu, J.Schneidkraut, Y.Lee, E.Sokolskaja, A.Andreotti, and J.Luban (2004).
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  Immunity, 21, 189-201.  
15322292 P.J.Scharf, J.Witney, R.Daly, and B.A.Lyons (2004).
Solution structure of the human Grb14-SH2 domain and comparison with the structures of the human Grb7-SH2/erbB2 peptide complex and human Grb10-SH2 domain.
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15030488 Y.Suzuki, M.Haruki, K.Takano, M.Morikawa, and S.Kanaya (2004).
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  Eur J Biochem, 271, 1372-1381.  
12794636 A.Velyvis, J.Vaynberg, Y.Yang, O.Vinogradova, Y.Zhang, C.Wu, and J.Qin (2003).
Structural and functional insights into PINCH LIM4 domain-mediated integrin signaling.
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PDB code: 1nyp
12787753 J.H.Wang, and M.J.Eck (2003).
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  Curr Opin Immunol, 15, 286-293.  
12488315 X.Wang, H.Tachikawa, X.Yi, K.M.Manoj, and L.P.Hager (2003).
Two-dimensional NMR study of the heme active site structure of chloroperoxidase.
  J Biol Chem, 278, 7765-7774.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.