PDBsum entry: 1shf

Phosphotransferase

PDB-id

1shf


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PDB id:

1shf

Name:

Phosphotransferase

Title:

Crystal structure of the sh3 domain in human fyn; comparison of the three-dimensional structures of sh3 domains in tyrosine kinases and spectrin

Structure:

Fyn tyrosine kinase sh3 domain. Chain: a, b. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606

Biological unit:

Tetramer (from PQS)

UniProt:

Chains A, B: P06241 (FYN_HUMAN)

Seq:

Struc:

Seq:

Struc:

Seq:

537 a.a.

Struc:

59 a.a.

Key:		PfamA domain
		Secondary structure			CATH domain

Enzyme class:

E.C.2.7.10.2 [IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate

Resolution:

1.90Å

R-factor:

0.180

Authors:

M.Noble,A.Musacchio,M.Saraste,R.Wierenga

Key ref:

M.E.Noble et al. (1993). Crystal structure of the SH3 domain in human Fyn; comparison of the three-dimensional structures of SH3 domains in tyrosine kinases and spectrin.. Embo J, 12, 2617-2624. [PubMed id: 7687536]

Date:

19-May-93

Release date:

31-Oct-93

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Key reference

Full text Embo J 12:2617-2624 (1993)

PubMed id: 7687536

Crystal structure of the SH3 domain in human Fyn; comparison of the three-dimensional structures of SH3 domains in tyrosine kinases and spectrin.

M.E.Noble, A.Musacchio, M.Saraste, S.A.Courtneidge, R.K.Wierenga.

ABSTRACT

The Src-homology 3 (SH3) region is a protein domain consisting of approximately 60 residues. It occurs in a large number of eukaryotic proteins involved in signal transduction, cell polarization and membrane--cytoskeleton interactions. The function is unknown, but it is probably involved in specific protein--protein interactions. Here we report the crystal structure of the SH3 domain of Fyn (a Src family tyrosine kinase) at 1.9 A resolution. The crystals have two SH3 molecules per asymmetric unit. These two Fyn SH3 domains are not related by a local twofold axis. The crystal structures of spectrin and Fyn SH3 domains as well as the solution structure of the Src SH3 domain show that these all have the same basic fold. A protein domain which has the same topology as SH3 is present in the prokaryotic regulatory enzyme BirA. The comparison between the crystal structures of Fyn and spectrin SH3 domains shows that a conserved surface patch, consisting mainly of aromatic residues, is flanked by two hairpin-like loops (residues 94-104 and 114-118 in Fyn). These loops are different in tyrosine kinase and spectrin SH3 domains. They could modulate the binding properties of the aromatic surface.

Literature references that cite this PDB file's key reference

PubMed id Reference

19491935 A.I.Bartlett, and S.E.Radford (2009).
An expanding arsenal of experimental methods yields an explosion of insights into protein folding mechanisms.

Nat Struct Mol Biol, 16, 582-588.

18767152 G.R.Bowman, and V.S.Pande (2009).
Simulated tempering yields insight into the low-resolution Rosetta scoring functions.

Proteins, 74, 777-788.

18305200 P.J.Farber, and A.Mittermaier (2008).
Side chain burial and hydrophobic core packing in protein folding transition states.

Protein Sci, 17, 644-651.

18366663 R.Merkl, and M.Zwick (2008).
H2r: identification of evolutionary important residues by means of an entropy based analysis of multiple sequence alignments.

BMC Bioinformatics, 9, 151.

17898173 P.Neudecker, A.Zarrine-Afsar, A.R.Davidson, and L.E.Kay (2007).
Phi-value analysis of a three-state protein folding pathway by NMR relaxation dispersion spectroscopy.

Proc Natl Acad Sci U S A, 104, 15717-15722.

17189480 Q.Wang, M.A.Deloia, Y.Kang, C.Litchke, N.Zhang, M.A.Titus, and K.J.Walters (2007).
The SH3 domain of a M7 interacts with its C-terminal proline-rich region.

Protein Sci, 16, 189-196.

PDB code: 2i0n

16373478 A.Zarrine-Afsar, A.Mittermaier, L.E.Kay, and A.R.Davidson (2006).
Protein stabilization by specific binding of guanidinium to a functional arginine-binding surface on an SH3 domain.

Protein Sci, 15, 162-170.

16778768 K.Tatebayashi, K.Yamamoto, K.Tanaka, T.Tomida, T.Maruoka, E.Kasukawa, and H.Saito (2006).
Adaptor functions of Cdc42, Ste50, and Sho1 in the yeast osmoregulatory HOG MAPK pathway.

EMBO J, 25, 3033-3044.

15778956 D.Segal, and M.Eisenstein (2005).
The effect of resolution-dependent global shape modifications on rigid-body protein-protein docking.

Proteins, 59, 580-591.

15698139 M.Habeck, M.Nilges, and W.Rieping (2005).
Replica-exchange Monte Carlo scheme for bayesian data analysis.

Phys Rev Lett, 94, 018105.

16002620 W.Rieping, M.Habeck, and M.Nilges (2005).
Inferential structure determination.

Science, 309, 303-306.

PDB code: 1zbj

15148398 A.A.Di Nardo, D.M.Korzhnev, P.J.Stogios, A.Zarrine-Afsar, L.E.Kay, and A.R.Davidson (2004).
Dramatic acceleration of protein folding by stabilization of a nonnative backbone conformation.

Proc Natl Acad Sci U S A, 101, 7954-7959.

15162493 A.Berchanski, B.Shapira, and M.Eisenstein (2004).
Hydrophobic complementarity in protein-protein docking.

Proteins, 56, 130-142.

15044737 A.Mittermaier, and L.E.Kay (2004).
The response of internal dynamics to hydrophobic core mutations in the SH3 domain from the Fyn tyrosine kinase.

Protein Sci, 13, 1088-1099.

15282609 D.M.Korzhnev, X.Salvatella, M.Vendruscolo, A.A.Di Nardo, A.R.Davidson, C.M.Dobson, and L.E.Kay (2004).
Low-populated folding intermediates of Fyn SH3 characterized by relaxation dispersion NMR.

Nature, 430, 586-590.

15469926 J.E.Ollerenshaw, H.Kaya, H.S.Chan, and L.E.Kay (2004).
Sparsely populated folding intermediates of the Fyn SH3 domain: matching native-centric essential dynamics and experiment.

Proc Natl Acad Sci U S A, 101, 14748-14753.

14976559 N.Lu, D.J.Guarnieri, and M.A.Simon (2004).
Localization of Tec29 to ring canals is mediated by Src64 and PtdIns(3,4,5)P3-dependent mechanisms.

EMBO J, 23, 1089-1100.

12545174 B.Chan, A.Lanyi, H.K.Song, J.Griesbach, M.Simarro-Grande, F.Poy, D.Howie, J.Sumegi, C.Terhorst, and M.J.Eck (2003).
SAP couples Fyn to SLAM immune receptors.

Nat Cell Biol, 5, 155-160.

PDB code: 1m27

11711548 H.Delbrück, G.Ziegelin, E.Lanka, and U.Heinemann (2002).
An Src homology 3-like domain is responsible for dimerization of the repressor protein KorB encoded by the promiscuous IncP plasmid RP4.

J Biol Chem, 277, 4191-4198.

PDB codes: 1igq 1igu

11714929 A.Chapman-Smith, T.D.Mulhern, F.Whelan, J.E.Cronan, and J.C.Wallace (2001).
The C-terminal domain of biotin protein ligase from E. coli is required for catalytic activity.

Protein Sci, 10, 2608-2617.

11714930 L.H.Weaver, K.Kwon, D.Beckett, and B.W.Matthews (2001).
Competing protein:protein interactions are proposed to control the biological switch of the E coli biotin repressor.

Protein Sci, 10, 2618-2622.

PDB codes: 1k67 1k69

11406576 M.Nishida, K.Nagata, Y.Hachimori, M.Horiuchi, K.Ogura, V.Mandiyan, J.Schlessinger, and F.Inagaki (2001).
Novel recognition mode between Vav and Grb2 SH3 domains.

EMBO J, 20, 2995-3007.

PDB codes: 1gcp 1gcq

10856234 H.Kang, C.Freund, J.S.Duke-Cohan, A.Musacchio, G.Wagner, and C.E.Rudd (2000).
SH3 domain recognition of a proline-independent tyrosine-based RKxxYxxY motif in immune cell adaptor SKAP55.

EMBO J, 19, 2889-2899.

10975574 K.Kwon, and D.Beckett (2000).
Function of a conserved sequence motif in biotin holoenzyme synthetases.

Protein Sci, 9, 1530-1539.

9889187 J.Myllyharju, and K.I.Kivirikko (1999).
Identification of a novel proline-rich peptide-binding domain in prolyl 4-hydroxylase.

EMBO J, 18, 306-312.

9722599 A.J.Chien, T.Gao, E.Perez-Reyes, and M.M.Hosey (1998).
Membrane targeting of L-type calcium channels. Role of palmitoylation in the subcellular localization of the beta2a subunit.

J Biol Chem, 273, 23590-23597.

9670010 A.Wechsler, and V.I.Teichberg (1998).
Brain spectrin binding to the NMDA receptor is regulated by phosphorylation, calcium and calmodulin.

EMBO J, 17, 3931-3939.

9736607 D.J.Owen, P.Wigge, Y.Vallis, J.D.Moore, P.R.Evans, and H.T.McMahon (1998).
Crystal structure of the amphiphysin-2 SH3 domain and its role in the prevention of dynamin ring formation.

EMBO J, 17, 5273-5285.

PDB code: 1bb9

9819209 K.L.Maxwell, and A.R.Davidson (1998).
Mutagenesis of a buried polar interaction in an SH3 domain: sequence conservation provides the best prediction of stability effects.

Biochemistry, 37, 16172-16182.

9485402 K.W.Plaxco, J.I.Guijarro, C.J.Morton, M.Pitkeathly, I.D.Campbell, and C.M.Dobson (1998).
The folding kinetics and thermodynamics of the Fyn-SH3 domain.

Biochemistry, 37, 2529-2537.

9778343 S.Arold, R.O'Brien, P.Franken, M.P.Strub, F.Hoh, C.Dumas, and J.E.Ladbury (1998).
RT loop flexibility enhances the specificity of Src family SH3 domains for HIV-1 Nef.

Biochemistry, 37, 14683-14691.

PDB code: 1bu1

9593201 S.Knapp, P.T.Mattson, P.Christova, K.D.Berndt, A.Karshikoff, M.Vihinen, C.I.Smith, and R.Ladenstein (1998).
Thermal unfolding of small proteins with SH3 domain folding pattern.

Proteins, 31, 309-319.

9566119 D.C.Dalgarno, M.C.Botfield, and R.J.Rickles (1997).
SH3 domains and drug design: ligands, structure, and biological function.

Biopolymers, 43, 383-400.

9408950 H.V.Patel, S.R.Tzeng, C.Y.Liao, S.H.Chen, and J.W.Cheng (1997).
SH3 domain of Bruton's tyrosine kinase can bind to proline-rich peptides of TH domain of the kinase and p120cbl.

Proteins, 29, 545-552.

9144769 J.E.Gready, S.Ranganathan, P.R.Schofield, Y.Matsuo, and K.Nishikawa (1997).
Predicted structure of the extracellular region of ligand-gated ion-channel receptors shows SH2-like and SH3-like domains forming the ligand-binding site.

Protein Sci, 6, 983-998.

9303002 K.V.Kishan, G.Scita, W.T.Wong, P.P.Di Fiore, and M.E.Newcomer (1997).
The SH3 domain of Eps8 exists as a novel intertwined dimer.

Nat Struct Biol, 4, 739-743.

PDB code: 1aoj

9326643 M.I.Wahl, A.C.Fluckiger, R.M.Kato, H.Park, O.N.Witte, and D.J.Rawlings (1997).
Phosphorylation of two regulatory tyrosine residues in the activation of Bruton's tyrosine kinase via alternative receptors.

Proc Natl Acad Sci U S A, 94, 11526-11533.

9190214 T.Lila, and D.G.Drubin (1997).
Evidence for physical and functional interactions among two Saccharomyces cerevisiae SH3 domain proteins, an adenylyl cyclase-associated protein and the actin cytoskeleton.

Mol Biol Cell, 8, 367-385.

8856081 A.Weijland, G.Neubauer, S.A.Courtneidge, M.Mann, R.K.Wierenga, and G.Superti-Furga (1996).
The purification and characterization of the catalytic domain of Src expressed in Schizosaccharomyces pombe. Comparison of unphosphorylated and tyrosine phosphorylated species.

Eur J Biochem, 240, 756-764.

8961927 D.A.Renzoni, D.J.Pugh, G.Siligardi, P.Das, C.J.Morton, C.Rossi, M.D.Waterfield, I.D.Campbell, and J.E.Ladbury (1996).
Structural and thermodynamic characterization of the interaction of the SH3 domain from Fyn with the proline-rich binding site on the p85 subunit of PI3-kinase.

Biochemistry, 35, 15646-15653.

PDB codes: 1a0n 1azg

8668162 D.E.Afar, H.Park, B.W.Howell, D.J.Rawlings, J.Cooper, and O.N.Witte (1996).
Regulation of Btk by Src family tyrosine kinases.

Mol Cell Biol, 16, 3465-3471.

8789085 D.M.van Aalten, A.Amadei, R.Bywater, J.B.Findlay, H.J.Berendsen, C.Sander, and P.F.Stouten (1996).
A comparison of structural and dynamic properties of different simulation methods applied to SH3.

Biophys J, 70, 684-692.

8718852 M.T.Pisabarro, and L.Serrano (1996).
Rational design of specific high-affinity peptide ligands for the Abl-SH3 domain.

Biochemistry, 35, 10634-10640.

8824280 P.M.Finan, C.J.Soames, L.Wilson, D.L.Nelson, D.M.Stewart, O.Truong, J.J.Hsuan, and S.Kellie (1996).
Identification of regions of the Wiskott-Aldrich syndrome protein responsible for association with selected Src homology 3 domains.

J Biol Chem, 271, 26291-26295.

8810341 S.C.Bunnell, P.A.Henry, R.Kolluri, T.Kirchhausen, R.J.Rickles, and L.J.Berg (1996).
Identification of Itk/Tsk Src homology 3 domain ligands.

J Biol Chem, 271, 25646-25656.

7588629 C.H.Lee, B.Leung, M.A.Lemmon, J.Zheng, D.Cowburn, J.Kuriyan, and K.Saksela (1995).
A single amino acid in the SH3 domain of Hck determines its high affinity and specificity in binding to HIV-1 Nef protein.

EMBO J, 14, 5006-5015.

8536694 D.S.Dorow, L.Devereux, G.F.Tu, G.Price, J.K.Nicholl, G.R.Sutherland, and R.J.Simpson (1995).
Complete nucleotide sequence, expression, and chromosomal localisation of human mixed-lineage kinase 2.

Eur J Biochem, 234, 492-500.

7536925 K.Alexandropoulos, G.Cheng, and D.Baltimore (1995).
Proline-rich sequences that bind to Src homology 3 domains with individual specificities.

Proc Natl Acad Sci U S A, 92, 3110-3114.

7782338 M.Sudol, P.Bork, A.Einbond, K.Kastury, T.Druck, M.Negrini, K.Huebner, and D.Lehman (1995).
Characterization of the mammalian YAP (Yes-associated protein) gene and its role in defining a novel protein module, the WW domain.

J Biol Chem, 270, 14733-14741.

8618911 S.Feng, C.Kasahara, R.J.Rickles, and S.L.Schreiber (1995).
Specific interactions outside the proline-rich core of two classes of Src homology 3 ligands.

Proc Natl Acad Sci U S A, 92, 12408-12415.

PDB codes: 1qwe 1qwf

7534229 T.Erpel, G.Superti-Furga, and S.A.Courtneidge (1995).
Mutational analysis of the Src SH3 domain: the same residues of the ligand binding surface are important for intra- and intermolecular interactions.

EMBO J, 14, 963-975.

7657668 W.Yang, S.N.Malek, and S.Desiderio (1995).
An SH3-binding site conserved in Bruton's tyrosine kinase and related tyrosine kinases mediates specific protein interactions in vitro and in vivo.

J Biol Chem, 270, 20832-20840.

7565714 Z.Weng, R.J.Rickles, S.Feng, S.Richard, A.S.Shaw, S.L.Schreiber, and J.S.Brugge (1995).
Structure-function analysis of SH3 domains: SH3 binding specificity altered by single amino acid substitutions.

Mol Cell Biol, 15, 5627-5634.

7664083 A.Musacchio, M.Saraste, and M.Wilmanns (1994).
High-resolution crystal structures of tyrosine kinase SH3 domains complexed with proline-rich peptides.

Nat Struct Biol, 1, 546-551.

PDB codes: 1abo 1abq 1fyn

7664069 D.Cowburn (1994).
Helical encounter.

Nat Struct Biol, 1, 489-491.

7521298 D.Cussac, M.Frech, and P.Chardin (1994).
Binding of the Grb2 SH2 domain to phosphotyrosine motifs does not change the affinity of its SH3 domains for Sos proline-rich motifs.

EMBO J, 13, 4011-4021.

7520528 G.Panchamoorthy, T.Fukazawa, L.Stolz, G.Payne, K.Reedquist, S.Shoelson, Z.Songyang, L.Cantley, C.Walsh, and H.Band (1994).
Physical and functional interactions between SH2 and SH3 domains of the Src family protein tyrosine kinase p59fyn.

Mol Cell Biol, 14, 6372-6385.

7634092 H.Baumann, S.Knapp, T.Lundbäck, R.Ladenstein, and T.Härd (1994).
Solution structure and DNA-binding properties of a thermostable protein from the archaeon Sulfolobus solfataricus.

Nat Struct Biol, 1, 808-819.

PDB code: 1sso

7773778 H.Terasawa, D.Kohda, H.Hatanaka, S.Tsuchiya, K.Ogura, K.Nagata, S.Ishii, V.Mandiyan, A.Ullrich, and J.Schlessinger (1994).
Structure of the N-terminal SH3 domain of GRB2 complexed with a peptide from the guanine nucleotide releasing factor Sos.

Nat Struct Biol, 1, 891-897.

7545075 H.Yu, and S.L.Schreiber (1994).
Signalling an interest.

Nat Struct Biol, 1, 417-420.

7984417 J.D.Thompson, D.G.Higgins, and T.J.Gibson (1994).
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.

Nucleic Acids Res, 22, 4673-4680.

7937731 L.Holm, and C.Sander (1994).
Searching protein structure databases has come of age.

Proteins, 19, 165-173.

7892170 M.T.Pisabarro, A.R.Ortiz, L.Serrano, and R.C.Wade (1994).
Homology modeling of the Abl-SH3 domain.

Proteins, 20, 203-215.

PDB code: 1abl

7773779 N.Goudreau, F.Cornille, M.Duchesne, F.Parker, B.Tocqué, C.Garbay, and B.P.Roques (1994).
NMR structure of the N-terminal SH3 domain of GRB2 and its complex with a proline-rich peptide from Sos.

Nat Struct Biol, 1, 898-907.

7634083 P.J.Artymiuk, D.W.Rice, A.R.Poirrette, and P.Willet (1994).
A tale of two synthetases.

Nat Struct Biol, 1, 758-760.

7519238 Q.Zhu, M.Zhang, D.J.Rawlings, M.Vihinen, T.Hagemann, D.C.Saffran, S.P.Kwan, L.Nilsson, C.I.Smith, O.N.Witte, S.H.Chen, and H.D.Ochs (1994).
Deletion within the Src homology domain 3 of Bruton's tyrosine kinase resulting in X-linked agammaglobulinemia (XLA).

J Exp Med, 180, 461-470.

7656049 W.A.Lim, and F.M.Richards (1994).
Critical residues in an SH3 domain from Sem-5 suggest a mechanism for proline-rich peptide recognition.

Nat Struct Biol, 1, 221-225.

7987221 W.A.Lim, R.O.Fox, and F.M.Richards (1994).
Stability and peptide binding affinity of an SH3 domain from the Caenorhabditis elegans signaling protein Sem-5.

Protein Sci, 3, 1261-1266.

8137811 Y.S.Yang, C.Garbay, M.Duchesne, F.Cornille, N.Jullian, N.Fromage, B.Tocque, and B.P.Roques (1994).
Solution structure of GAP SH3 domain by 1H NMR and spatial arrangement of essential Ras signaling-involved sequence.

EMBO J, 13, 1270-1279.

7516469 Z.Weng, S.M.Thomas, R.J.Rickles, J.A.Taylor, A.W.Brauer, C.Seidel-Dugan, W.M.Michael, G.Dreyfuss, and J.S.Brugge (1994).
Identification of Src, Fyn, and Lyn SH3-binding proteins: implications for a function of SH3 domains.

Mol Cell Biol, 14, 4509-4521.

8268793 M.J.Fry, G.Panayotou, G.W.Booker, and M.D.Waterfield (1993).
New insights into protein-tyrosine kinase receptor signaling complexes.

Protein Sci, 2, 1785-1797.

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 code is shown on the right.