Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

The NMR structure of the inhibited catalytic domain of human stromelysin–1

Abstract

The three–dimensional structure of the catalytic domain of stromelysin–1 complexed with an N–carboxyl alkyl inhibitor has been determined by NMR methods. The global fold consists of three helices, a five stranded β–sheet and a methionine located in a turn near the catalytic histidines, classifying stromelysin–1 as a metzincin. Stromelysin–1 is unique in having two independent zinc binding sites: a catalytic site and a structural site. The inhibitor binds in an extended conformation. The S1′ subsite is a deep hydrophobic pocket, whereas S2′ appears shallow and S3′ open.

This is a preview of subscription content, access via your institution

Access options

Buy article

Get time limited or full article access on ReadCube.

$32.00

All prices are NET prices.

References

  1. Woessner, Jr., J.F. Matrix metalloproteinases and their inhibitors in connective tissue remodeling. FASEB J. 5, 2145–2154 (1991).

    Article  CAS  Google Scholar 

  2. Saus, J., Quinones, S., Otani, Y., Nagase, H., Harris Jr., E.D. & Kurkinen, M. The Complete Primary Structure of Human Matrix Metalloproteinase-3. J. biol. Chem. 263, 6742–6745 (1988).

    CAS  PubMed  Google Scholar 

  3. MacNaul, K.L., Chartrain, N., Lark, M., Tocci, M.J. & Hutchinson, N.I., Expression of Stromelysin, Collagenase, and Tissue Inhibitor of Metalloproteinases-1 in Rheumatoid Human Synovial Fibroblasts. J. biol. Chem. 265, 17238–17245 (1990).

    CAS  PubMed  Google Scholar 

  4. Marcy, A.I. et al. Human Fibroblast Stromelysin Catalytic Domain: Expression, Purification, and Characterization of a C-Terminally Truncated Form. Biochemistry 30, 6476–6483 (1991).

    Article  CAS  Google Scholar 

  5. Salowe, S.P. et al. Characterization of Zinc-Binding Sites in Human Stromelysin-1: Stoichiometry of the Catalytic Domain and Identification of a Cysteine Ligand in the Proenzyme. Biochemistry 31, 4535–4540 (1992).

    Article  CAS  Google Scholar 

  6. Holz, R.C., Salowe, S.P., Smith, C.K., Cuca, G.C. & Que, Jr., L. EXAFS Evidence for a “Cysteine Switch” in the Activation of Prostromelysin. J. Am. chem. Soc. 114, 9611–9614 (1992).

    Article  CAS  Google Scholar 

  7. Gooley, P.R. et al. Secondary Structure and Zinc Ligation of Human Recombinant Short-Form Stromelysin by Multidimensional Heteronuclear NMR. Biochemistry 32, 13098–13108 (1993).

    Article  CAS  Google Scholar 

  8. Bode, W., Gomis-Rüth, F.X., Huber, R., Zwilling, R. & Stöcker, W. Structure of astacin and implications for activation of astacin and zinc-ligation of collagenases. Nature 358, 164–167 (1992).

    Article  CAS  Google Scholar 

  9. Bode, W., Gomis-Rüth, F.X. & Stöcker, W., Astacins, serralysins, snake venom and matrix metalloproteinases exhibit identical zinc-binding environments (HExxHxxGxxH and Met-turn) and topologies and should be grouped into a common family, the ‘metzincins’. FEBS Lett. 331, 134–140 (1993).

    Article  CAS  Google Scholar 

  10. Chapman, K.T. et al. Inhibition of Matrix Metalloproteinases by N-Carboxyalkyl Peptides. J. med. Chem. 36, 4293–4301 (1993).

    Article  CAS  Google Scholar 

  11. Nilges, M., Clore, G.M. & Gronenborn, A.M. Determination of three-dimensional structures of proteins from interproton distance data by hybrid distance geometry-dynamical simulated annealing calculations. FEBS Lett. 229, 317–324 (1988).

    Article  CAS  Google Scholar 

  12. Brunger, A. X-PLOR Manual, Version 3.1 (Yale University Press, New Haven and London, 1992).

    Google Scholar 

  13. Van Doren, S.R. et al. Assignments for the Main-Chain Nuclear Magnetic Resonances and Delineation of the Secondary Structure of the Catalytic Domain of Human Stromelysin-1 As Obtained from Triple-Resonance 3D NMR Experiments. Biochemistry 32, 13109–13122 (1993).

    Article  CAS  Google Scholar 

  14. Richardson, J.S. β-Sheet topology and the relatedness of proteins. Nature 268, 495–500 (1977).

    Article  CAS  Google Scholar 

  15. Reynolds, W.F., Peat, I.R., Freedman, M.H. & Lyerla, Jr., J.H. Determination of theTautomeric Form of the Imidazole Ring of L-Histidine in Basic Solution by Carbon-13 Magnetic Resonance Spectroscopy. J. Am. chem. Soc. 95, 328–331 (1973).

    Article  CAS  Google Scholar 

  16. Vallee, B.L. & Auld, D.S., and Structure of Zinc Enzymes and Other Proteins. Biochemistry 29, 5647–5659 (1990).

    Article  CAS  Google Scholar 

  17. Schechter, I. & Berger, A. On the Size of the Active Site in Proteases. Biochem. Biophys. Res. Commun. 27, 157–162 (1967).

    Article  CAS  Google Scholar 

  18. Mathews, B.W., Jansonius, J.N., Colman, P.M., Schoenborn, B.P. & Dupourque, D., Three-dimensional Structure of Thermolysin. Nature new Biol. 238, 37–41 (1972).

    Article  Google Scholar 

  19. Pauptit, R.A. et al. Crystal Structure of Neutral Protease from Bacillus cereus Refined at 3.0 Å Resolution and Comparison with the Homologous But More Thermostable Enzyme Thermolysin. J. molec. Biol. 199, 525–537 (1988).

    Article  CAS  Google Scholar 

  20. Thayer, M.M. Flaherty, K.M. & MacKay, D.B. Three-Dimensional Structure of the Elastase of Pseudomonas aeruginosa at 1.5-Å Resolution. J. biol. Chem. 266, 2864–2871 (1991).

    CAS  PubMed  Google Scholar 

  21. Gomis-Rüth, F.X., Stöcker, W., Huber, R., Zwilling, R. & Bode, W. Refined 1.8 Å X-ray Crystal Structure of Astacin, a Zinc-endopeptidase from the Crayfish Asfacus astacus L. Structure Determination, Refinement, Molecular Structure and Comparison with Thermolysin. J. molec. Biol. 229, 945–968 (1993).

    Article  Google Scholar 

  22. Gomis-Rüth, F.X., Kress, L.F. & Bode, W. First structure of a snake venom metalloproteinase: a prototype for matrix metalloproteinases/collagenases. EMBO J. 12, 4151–4157 (1993).

    Article  Google Scholar 

  23. Murphy, G.J.P., Murphy, G. & Reynolds, J.J. The origin of matrix metalloproteinases and their familial relationships. FEBS Lett. 289, 4–7 (1991).

    Article  CAS  Google Scholar 

  24. Dumermuth, E. et al. The Astacin Family of Metalloendopeptidases. J. biol. Chem. 266, 21381–21385 (1991).

    CAS  PubMed  Google Scholar 

  25. Duong, F., Lazdunski, A., Cami, B. & Murgier, M. Sequence of a cluster of genes controlling synthesis and secretion of alkaline protease in Pseudomonas aeruginosa: relationships to other secretory pathways. Gene 121, 47–54 (1992).

    Article  CAS  Google Scholar 

  26. Weaver, L.H., Kester, W.R. & Mathews, B.W. A Crystallographic Study of the Complex of Phosphoramidon with Thermolysin. A model for the Presumed Catalytic Transition State and for the Binding of Extended Substrates. J. molec. Biol. 114, 119–132 (1977).

    Article  CAS  Google Scholar 

  27. Mathews, B.W. Structural Basis of the Action of Thermolysin and Related Zinc Peptidases. Acc. chem. Res. 21, 333–340 (1988).

    Article  Google Scholar 

  28. Ikura, M., Kay, L.E., Tschudin, R. & Bax, A. Three-Dimensional NOESY-HMQC Spectroscopy of a 13C-labelled Protein. J. magn. Reson. 86, 204–209 (1990).

    CAS  Google Scholar 

  29. Zuiderweg, E.R.P. & Fesik, S . Heteronuclear Three-Dimensional NMR Spectroscopy of the Inflammatory Protein C5a. Biochemistry 28, 2387–2391 (1989).

    Article  CAS  Google Scholar 

  30. Clore, G.M., Kay, L.E., Bax, A. & Gronenborn, A.M. Four-Dimensional 13C/13C-Edited Nuclear Overhauser Enhancement Spectroscopy of a Protein in Solution: Application to Interleukin 1β. Biochemistry 30, 12–18 (1991).

    Article  CAS  Google Scholar 

  31. Suri, A.K. & Levy, R.M. Estimation of Interatomic Distances in Proteins from NOE Spectra at Longer Mixing Times Using an Empirical Two-Spin Equation. J. magn. Reson. 101, 320–324 (1993).

    Article  CAS  Google Scholar 

  32. Kay, L.E. & Bax, A., Methods for the Measurement of NH-CαH Coupling Constants in 15N-Labeled Proteins. J. magn. Reson. 86, 110–126 (1990).

    CAS  Google Scholar 

  33. Powers, R., Gronenborn, A.M., Clore, G.M. & Bax, A., Triple-Resonance NMR of 13C/15N-Enriched Proteins Using Constant-Time Evolution. J. magn. Reson. 94, 209–213 (1991).

    CAS  Google Scholar 

  34. Vuister, G.W., Delaglio, F. & Bax, A., An Empirical Correlation between 1JCαHα and Protein Backbone Conformation. J. Am. chem. Soc. 114, 9674–9675 (1992).

    Article  CAS  Google Scholar 

  35. Spera, S. & Bax, A., Correlation between Protein backbone Conformation and Cα and Cβ 13C Nuclear Magnetic resonance Chemical Shifts. J. Am. chem. Soc. 113, 5490–5492 (1991).

    Article  CAS  Google Scholar 

  36. Neri, D., Szperski, T., Otting, G., Senn, H. & Wuthrich, K. Stereospecific Nuclear Magnetic Resonance Assignments of the Methyl Groups of Valine and Leucine in the DNA-Binding Domain of the 434 Represser by Biosynthetically Directed Fractional 13C Labeling. Biochemistry 28, 7510–7516 (1989).

    Article  CAS  Google Scholar 

  37. Otting, G. & Wüthrich, K. Heteronuclear filters in two-dimensional [1H,1H]-NMR Spectroscopy: combined use with isotope labelling for studies of macromolecular conformation and intermolecular interactions. Q. Rev. Biophys. 23, 39–96 (1990).

    Article  CAS  Google Scholar 

  38. Petros, A.M., Kawai, M., Luly, J.R. & Fesik, S.W. Conformation of two non-immunosuppressive FK506 analogs when bound to FKBP by isotope-filtered NMR. FEBS Lett. 308, 309–314 (1992).

    Article  CAS  Google Scholar 

  39. Horrocks, Jr., W.D., Ishley, J.N. & Whittle, R.R. Models for Cobalt(II)-Substituted Zinc Metalloenzymes. 1. Comparison of the Crystal Structures of Complexes of the Type {M(RCOO)2(Im)2] (Im = Imidazole; M = Co, Zn; R = CH3, C2H5). Inorg. Chem. 21, 3265–3269 (1982).

    Article  CAS  Google Scholar 

  40. Bear, C.A., Duggan, K.A. & Freeman, H.C., Tetraimidazolezinc(II) Pechlorate. Acta. Crystallog. 31, 2713–2715 (1975).

    Article  Google Scholar 

  41. Garrett, T.P.J., Guss, J.M. & Freeman, H.C. Hexakis(imidazole)manganese(II) Dichloride Tetrahydrate, [Mn(C3H4N2)6]Cl2.4H2O, and Hexakis(imidazole)zinc(II) DichlorideTetrahydrate,[Zn(C3H4N2)6]Cl2.4H2O. Acta. Crystallog. 39, 1027–1031 (1983).

    Google Scholar 

  42. Ashby, C.I.H., Cheng, C.P., Duesler, E.N. & Brown, T.L., Structure and 14N Nuclear Quadrupole Resonance Spectrum of Catena-m-imidazolato-bis(imidazole)zinc Nitrate. Donor Characteristics of Coordinated Imidazolate. J. Am. chem. Soc. 100, 6063–6067 (1978).

    Article  CAS  Google Scholar 

  43. Brooks, B.R., Bruccoleri, R.E., States, D.J., Swaminathan, S. & Karplus, M. CHARMM: a program for macromolecular energy,minimization, and dynamics calculations. J. comput. Chem. 4, 187–217 (1983).

    Article  CAS  Google Scholar 

  44. Holmes, M.A. & Mathews, B.W. Structure of Thermolysin Refined at 1.6 Å Resolution. J. molec. Biol. 160, 623–639 (1982).

    Article  CAS  Google Scholar 

  45. Berstein, F.C. et al. The Protein Data Bank: A Computer-based Archival File for Macromolecular Structures. J. molec. Biol. 112,, 535–542 (1977).

    Article  Google Scholar 

  46. Hasty, K.A. et al. Human Neutrophil Collagenase. A Distinct gene Product with Homology To Other Metalloproteinases. J. biol. Chem. 265, 11421–11424 (1990).

    CAS  PubMed  Google Scholar 

  47. Colman, P.M., Jansonius, J.N. & Mathews, B.W., Structure of Thermolysin: An Electron Density Map at 2.3 Å Resolution. J. molec. Biol. 70, 701–724 (1972).

    Article  CAS  Google Scholar 

  48. Niedzwiecki, L., Teahan, J., Harrison, R.K. & Stein, R.L., Specificity of the Human Matrix Metalloproteinase Stromelysin and the Development of Continuous Flurometric Assays. Biochemistry 31, 12618–12623 (1992).

    Article  CAS  Google Scholar 

  49. Netzel-Arnett, S., Fields, G., Birkedal-Hansen, H. & Van Wart, H.E., Specificities of Human Fibroblast and Neutrophil Collagenases. J. biol. Chem. 266, 6747–6755 (1991).

    CAS  PubMed  Google Scholar 

  50. Netzel-Arnett, S., Sang, Q.-X., Moore, W.G.I., Navre, M., Birkedal-Hansen, H. & Van Wart, H.E. Specificities of Human 72- and 92-kDa Gelatinases (Type IV Collagenases) and PUMP (Matrilysin). Biochemistry 32, 6427–6432 (1993).

    Article  CAS  Google Scholar 

  51. Krauhs, E., Dörsam, H., Little, M., Zwilling, R. & Ponstingl, H. A Protease from Astacus fluviatilis as an Aid in Protein Sequencing. Analyt. Biochem. 119, 153–157 (1982).

    Article  CAS  Google Scholar 

  52. Fox, J.W., Campbell, R., Beggerly, L., Bjarnason, J.B. Substrate specificities and inhibition of two hemorrhagic zinc proteases Ht-c and Ht-d from Crotalus atrox venom. Eur. J. Biochem. 156, 65–72 (1986).

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Gooley, P., O'Connell, J., Marcy, A. et al. The NMR structure of the inhibited catalytic domain of human stromelysin–1. Nat Struct Mol Biol 1, 111–118 (1994). https://doi.org/10.1038/nsb0294-111

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nsb0294-111

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing