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. 2000 Nov;9(11):2170–2180. doi: 10.1110/ps.9.11.2170

The identification of conserved interactions within the SH3 domain by alignment of sequences and structures.

S M Larson 1, A R Davidson 1
PMCID: PMC2144485  PMID: 11152127

Abstract

The SH3 domain, comprised of approximately 60 residues, is found within a wide variety of proteins, and is a mediator of protein-protein interactions. Due to the large number of SH3 domain sequences and structures in the databases, this domain provides one of the best available systems for the examination of sequence and structural conservation within a protein family. In this study, a large and diverse alignment of SH3 domain sequences was constructed, and the pattern of conservation within this alignment was compared to conserved structural features, as deduced from analysis of eighteen different SH3 domain structures. Seventeen SH3 domain structures solved in the presence of bound peptide were also examined to identify positions that are consistently most important in mediating the peptide-binding function of this domain. Although residues at the two most conserved positions in the alignment are directly involved in peptide binding, residues at most other conserved positions play structural roles, such as stabilizing turns or comprising the hydrophobic core. Surprisingly, several highly conserved side-chain to main-chain hydrogen bonds were observed in the functionally crucial RT-Src loop between residues with little direct involvement in peptide binding. These hydrogen bonds may be important for maintaining this region in the precise conformation necessary for specific peptide recognition. In addition, a previously unrecognized yet highly conserved beta-bulge was identified in the second beta-strand of the domain, which appears to provide a necessary kink in this strand, allowing it to hydrogen bond to both sheets comprising the fold.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Akutsu T., Tashimo H. Protein structure comparison using representation by line segment sequences. Pac Symp Biocomput. 1996:25–40. [PubMed] [Google Scholar]
  2. Alexandropoulos K., Cheng G., Baltimore D. Proline-rich sequences that bind to Src homology 3 domains with individual specificities. Proc Natl Acad Sci U S A. 1995 Apr 11;92(8):3110–3114. doi: 10.1073/pnas.92.8.3110. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Altschul S. F., Madden T. L., Schäffer A. A., Zhang J., Zhang Z., Miller W., Lipman D. J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997 Sep 1;25(17):3389–3402. doi: 10.1093/nar/25.17.3389. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Arold S., Franken P., Strub M. P., Hoh F., Benichou S., Benarous R., Dumas C. The crystal structure of HIV-1 Nef protein bound to the Fyn kinase SH3 domain suggests a role for this complex in altered T cell receptor signaling. Structure. 1997 Oct 15;5(10):1361–1372. doi: 10.1016/s0969-2126(97)00286-4. [DOI] [PubMed] [Google Scholar]
  5. Bashford D., Chothia C., Lesk A. M. Determinants of a protein fold. Unique features of the globin amino acid sequences. J Mol Biol. 1987 Jul 5;196(1):199–216. doi: 10.1016/0022-2836(87)90521-3. [DOI] [PubMed] [Google Scholar]
  6. Benner S. A., Jenny T. F., Cohen M. A., Gonnet G. H. Predicting the conformation of proteins from sequences. Progress and future progress. Adv Enzyme Regul. 1994;34:269–353. doi: 10.1016/0065-2571(94)90021-3. [DOI] [PubMed] [Google Scholar]
  7. Borchert T. V., Mathieu M., Zeelen J. P., Courtneidge S. A., Wierenga R. K. The crystal structure of human CskSH3: structural diversity near the RT-Src and n-Src loop. FEBS Lett. 1994 Mar 14;341(1):79–85. doi: 10.1016/0014-5793(94)80244-0. [DOI] [PubMed] [Google Scholar]
  8. Bowie J. U., Lüthy R., Eisenberg D. A method to identify protein sequences that fold into a known three-dimensional structure. Science. 1991 Jul 12;253(5016):164–170. doi: 10.1126/science.1853201. [DOI] [PubMed] [Google Scholar]
  9. Chan A. W., Hutchinson E. G., Harris D., Thornton J. M. Identification, classification, and analysis of beta-bulges in proteins. Protein Sci. 1993 Oct;2(10):1574–1590. doi: 10.1002/pro.5560021004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Chen Y. J., Lin S. C., Tzeng S. R., Patel H. V., Lyu P. C., Cheng J. W. Stability and folding of the SH3 domain of Bruton's tyrosine kinase. Proteins. 1996 Dec;26(4):465–471. doi: 10.1002/(SICI)1097-0134(199612)26:4<465::AID-PROT7>3.0.CO;2-A. [DOI] [PubMed] [Google Scholar]
  11. Chothia C., Gelfand I., Kister A. Structural determinants in the sequences of immunoglobulin variable domain. J Mol Biol. 1998 May 1;278(2):457–479. doi: 10.1006/jmbi.1998.1653. [DOI] [PubMed] [Google Scholar]
  12. Dalgarno D. C., Botfield M. C., Rickles R. J. SH3 domains and drug design: ligands, structure, and biological function. Biopolymers. 1997;43(5):383–400. doi: 10.1002/(SICI)1097-0282(1997)43:5<383::AID-BIP4>3.0.CO;2-R. [DOI] [PubMed] [Google Scholar]
  13. Dill K. A. Dominant forces in protein folding. Biochemistry. 1990 Aug 7;29(31):7133–7155. doi: 10.1021/bi00483a001. [DOI] [PubMed] [Google Scholar]
  14. Feng S., Chen J. K., Yu H., Simon J. A., Schreiber S. L. Two binding orientations for peptides to the Src SH3 domain: development of a general model for SH3-ligand interactions. Science. 1994 Nov 18;266(5188):1241–1247. doi: 10.1126/science.7526465. [DOI] [PubMed] [Google Scholar]
  15. Filimonov V. V., Azuaga A. I., Viguera A. R., Serrano L., Mateo P. L. A thermodynamic analysis of a family of small globular proteins: SH3 domains. Biophys Chem. 1999 Mar 29;77(2-3):195–208. doi: 10.1016/s0301-4622(99)00025-3. [DOI] [PubMed] [Google Scholar]
  16. Grantcharova V. P., Baker D. Folding dynamics of the src SH3 domain. Biochemistry. 1997 Dec 16;36(50):15685–15692. doi: 10.1021/bi971786p. [DOI] [PubMed] [Google Scholar]
  17. Grantcharova V. P., Riddle D. S., Santiago J. V., Baker D. Important role of hydrogen bonds in the structurally polarized transition state for folding of the src SH3 domain. Nat Struct Biol. 1998 Aug;5(8):714–720. doi: 10.1038/1412. [DOI] [PubMed] [Google Scholar]
  18. Henikoff S., Henikoff J. G. Position-based sequence weights. J Mol Biol. 1994 Nov 4;243(4):574–578. doi: 10.1016/0022-2836(94)90032-9. [DOI] [PubMed] [Google Scholar]
  19. Holm L., Sander C. Removing near-neighbour redundancy from large protein sequence collections. Bioinformatics. 1998 Jun;14(5):423–429. doi: 10.1093/bioinformatics/14.5.423. [DOI] [PubMed] [Google Scholar]
  20. Hooft R. W., Vriend G., Sander C., Abola E. E. Errors in protein structures. Nature. 1996 May 23;381(6580):272–272. doi: 10.1038/381272a0. [DOI] [PubMed] [Google Scholar]
  21. Hutchinson E. G., Thornton J. M. A revised set of potentials for beta-turn formation in proteins. Protein Sci. 1994 Dec;3(12):2207–2216. doi: 10.1002/pro.5560031206. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Kabsch W., Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 1983 Dec;22(12):2577–2637. doi: 10.1002/bip.360221211. [DOI] [PubMed] [Google Scholar]
  23. Kishan K. V., Scita G., Wong W. T., Di Fiore P. P., Newcomer M. E. The SH3 domain of Eps8 exists as a novel intertwined dimer. Nat Struct Biol. 1997 Sep;4(9):739–743. doi: 10.1038/nsb0997-739. [DOI] [PubMed] [Google Scholar]
  24. Larson S. M., Di Nardo A. A., Davidson A. R. Analysis of covariation in an SH3 domain sequence alignment: applications in tertiary contact prediction and the design of compensating hydrophobic core substitutions. J Mol Biol. 2000 Oct 27;303(3):433–446. doi: 10.1006/jmbi.2000.4146. [DOI] [PubMed] [Google Scholar]
  25. Lee C. H., Saksela K., Mirza U. A., Chait B. T., Kuriyan J. Crystal structure of the conserved core of HIV-1 Nef complexed with a Src family SH3 domain. Cell. 1996 Jun 14;85(6):931–942. doi: 10.1016/s0092-8674(00)81276-3. [DOI] [PubMed] [Google Scholar]
  26. Lesk A. M., Fordham W. D. Conservation and variability in the structures of serine proteinases of the chymotrypsin family. J Mol Biol. 1996 May 10;258(3):501–537. doi: 10.1006/jmbi.1996.0264. [DOI] [PubMed] [Google Scholar]
  27. Lim W. A. Reading between the lines: SH3 recognition of an intact protein. Structure. 1996 Jun 15;4(6):657–659. doi: 10.1016/s0969-2126(96)00071-8. [DOI] [PubMed] [Google Scholar]
  28. Lim W. A., Richards F. M. Critical residues in an SH3 domain from Sem-5 suggest a mechanism for proline-rich peptide recognition. Nat Struct Biol. 1994 Apr;1(4):221–225. doi: 10.1038/nsb0494-221. [DOI] [PubMed] [Google Scholar]
  29. Lim W. A., Richards F. M., Fox R. O. Structural determinants of peptide-binding orientation and of sequence specificity in SH3 domains. Nature. 1994 Nov 24;372(6504):375–379. doi: 10.1038/372375a0. [DOI] [PubMed] [Google Scholar]
  30. Martinez J. C., Pisabarro M. T., Serrano L. Obligatory steps in protein folding and the conformational diversity of the transition state. Nat Struct Biol. 1998 Aug;5(8):721–729. doi: 10.1038/1418. [DOI] [PubMed] [Google Scholar]
  31. Maxwell K. L., Davidson A. R. Mutagenesis of a buried polar interaction in an SH3 domain: sequence conservation provides the best prediction of stability effects. Biochemistry. 1998 Nov 17;37(46):16172–16182. doi: 10.1021/bi981788p. [DOI] [PubMed] [Google Scholar]
  32. Mayer B. J., Hamaguchi M., Hanafusa H. A novel viral oncogene with structural similarity to phospholipase C. Nature. 1988 Mar 17;332(6161):272–275. doi: 10.1038/332272a0. [DOI] [PubMed] [Google Scholar]
  33. Michnick S. W., Shakhnovich E. A strategy for detecting the conservation of folding-nucleus residues in protein superfamilies. Fold Des. 1998;3(4):239–251. doi: 10.1016/S1359-0278(98)00035-2. [DOI] [PubMed] [Google Scholar]
  34. Minor D. L., Jr, Kim P. S. Measurement of the beta-sheet-forming propensities of amino acids. Nature. 1994 Feb 17;367(6464):660–663. doi: 10.1038/367660a0. [DOI] [PubMed] [Google Scholar]
  35. Mirny L. A., Abkevich V. I., Shakhnovich E. I. How evolution makes proteins fold quickly. Proc Natl Acad Sci U S A. 1998 Apr 28;95(9):4976–4981. doi: 10.1073/pnas.95.9.4976. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Pawson T. Protein modules and signalling networks. Nature. 1995 Feb 16;373(6515):573–580. doi: 10.1038/373573a0. [DOI] [PubMed] [Google Scholar]
  37. Pisabarro M. T., Serrano L. Rational design of specific high-affinity peptide ligands for the Abl-SH3 domain. Biochemistry. 1996 Aug 20;35(33):10634–10640. doi: 10.1021/bi960203t. [DOI] [PubMed] [Google Scholar]
  38. Plaxco K. W., Guijarro J. I., Morton C. J., Pitkeathly M., Campbell I. D., Dobson C. M. The folding kinetics and thermodynamics of the Fyn-SH3 domain. Biochemistry. 1998 Feb 24;37(8):2529–2537. doi: 10.1021/bi972075u. [DOI] [PubMed] [Google Scholar]
  39. Plaxco K. W., Larson S., Ruczinski I., Riddle D. S., Thayer E. C., Buchwitz B., Davidson A. R., Baker D. Evolutionary conservation in protein folding kinetics. J Mol Biol. 2000 Apr 28;298(2):303–312. doi: 10.1006/jmbi.1999.3663. [DOI] [PubMed] [Google Scholar]
  40. Ptitsyn O. B. Protein folding and protein evolution: common folding nucleus in different subfamilies of c-type cytochromes? J Mol Biol. 1998 May 8;278(3):655–666. doi: 10.1006/jmbi.1997.1620. [DOI] [PubMed] [Google Scholar]
  41. Rickles R. J., Botfield M. C., Zhou X. M., Henry P. A., Brugge J. S., Zoller M. J. Phage display selection of ligand residues important for Src homology 3 domain binding specificity. Proc Natl Acad Sci U S A. 1995 Nov 21;92(24):10909–10913. doi: 10.1073/pnas.92.24.10909. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Rost B., Sander C. Combining evolutionary information and neural networks to predict protein secondary structure. Proteins. 1994 May;19(1):55–72. doi: 10.1002/prot.340190108. [DOI] [PubMed] [Google Scholar]
  43. Shenkin P. S., Erman B., Mastrandrea L. D. Information-theoretical entropy as a measure of sequence variability. Proteins. 1991;11(4):297–313. doi: 10.1002/prot.340110408. [DOI] [PubMed] [Google Scholar]
  44. Sicheri F., Moarefi I., Kuriyan J. Crystal structure of the Src family tyrosine kinase Hck. Nature. 1997 Feb 13;385(6617):602–609. doi: 10.1038/385602a0. [DOI] [PubMed] [Google Scholar]
  45. Smith C. K., Withka J. M., Regan L. A thermodynamic scale for the beta-sheet forming tendencies of the amino acids. Biochemistry. 1994 May 10;33(18):5510–5517. doi: 10.1021/bi00184a020. [DOI] [PubMed] [Google Scholar]
  46. Sparks A. B., Rider J. E., Hoffman N. G., Fowlkes D. M., Quillam L. A., Kay B. K. Distinct ligand preferences of Src homology 3 domains from Src, Yes, Abl, Cortactin, p53bp2, PLCgamma, Crk, and Grb2. Proc Natl Acad Sci U S A. 1996 Feb 20;93(4):1540–1544. doi: 10.1073/pnas.93.4.1540. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Steipe B., Schiller B., Plückthun A., Steinbacher S. Sequence statistics reliably predict stabilizing mutations in a protein domain. J Mol Biol. 1994 Jul 15;240(3):188–192. doi: 10.1006/jmbi.1994.1434. [DOI] [PubMed] [Google Scholar]
  48. Thompson J. D., Higgins D. G., Gibson T. J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994 Nov 11;22(22):4673–4680. doi: 10.1093/nar/22.22.4673. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. Viguera A. R., Arrondo J. L., Musacchio A., Saraste M., Serrano L. Characterization of the interaction of natural proline-rich peptides with five different SH3 domains. Biochemistry. 1994 Sep 13;33(36):10925–10933. doi: 10.1021/bi00202a011. [DOI] [PubMed] [Google Scholar]
  50. Vogt G., Etzold T., Argos P. An assessment of amino acid exchange matrices in aligning protein sequences: the twilight zone revisited. J Mol Biol. 1995 Jun 16;249(4):816–831. doi: 10.1006/jmbi.1995.0340. [DOI] [PubMed] [Google Scholar]
  51. Weng Z., Rickles R. J., Feng S., Richard S., Shaw A. S., Schreiber S. L., Brugge J. S. Structure-function analysis of SH3 domains: SH3 binding specificity altered by single amino acid substitutions. Mol Cell Biol. 1995 Oct;15(10):5627–5634. doi: 10.1128/mcb.15.10.5627. [DOI] [PMC free article] [PubMed] [Google Scholar]
  52. Xu W., Harrison S. C., Eck M. J. Three-dimensional structure of the tyrosine kinase c-Src. Nature. 1997 Feb 13;385(6617):595–602. doi: 10.1038/385595a0. [DOI] [PubMed] [Google Scholar]
  53. Yi Q., Bystroff C., Rajagopal P., Klevit R. E., Baker D. Prediction and structural characterization of an independently folding substructure in the src SH3 domain. J Mol Biol. 1998;283(1):293–300. doi: 10.1006/jmbi.1998.2072. [DOI] [PubMed] [Google Scholar]

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