1.70 Å X-ray structure of human apo kallikrein 1: Structural changes upon peptide inhibitor/substrate binding

Proteins: Structure, Function and Genetics

Volumn 58, Issue 4, 2005, Pages 802-814

  Laxmikanthan, Gurunathan ^a   Blaber, Sachiko I ^a   Bernett, Matthew J ^a   Scarisbrick, Isobel A ^b   Juliano, Maria Aparecida ^c   Blaber, Michael ^a  

^a FLORIDA STATE UNIVERSITY   (United States)

^b MAYO CLINIC   (United States)

^c FEDERAL UNIVERSITY OF SÃO PAULO   (Brazil)

Author keywords

Induced fit; Kallikrein; Serine protease; Solvent structure; Substrate specificity

Indexed keywords

ARGININE; BIOLOGICAL MARKER; HISTIDINE; KALLIKREIN; KALLIKREIN 1; LOW MOLECULAR WEIGHT KININOGEN; LYSINE; METHIONINE; PROTEIN INHIBITOR; RECOMBINANT ENZYME; SERINE; SERINE PROTEINASE; SOLVENT; UNCLASSIFIED DRUG; APROTININ; LIGAND; PEPTIDE; PRIMER DNA; RECOMBINANT PROTEIN; TISSUE KALLIKREIN;

ALZHEIMER DISEASE; AMINO ACID SEQUENCE; ARTICLE; BLOOD PRESSURE REGULATION; BREAST CANCER; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME SPECIFICITY; ENZYME SUBSTRATE COMPLEX; HYDROLYSIS; INFLAMMATION; PARKINSON DISEASE; PRIORITY JOURNAL; PROSTATE CANCER; PROTEIN FAMILY; SWINE; ANIMAL; BINDING SITE; BLOOD PRESSURE; CATTLE; CHEMICAL STRUCTURE; CHEMISTRY; DRUG ANTAGONISM; HUMAN; MASS SPECTROMETRY; METHODOLOGY; MOLECULAR CLONING; POLYACRYLAMIDE GEL ELECTROPHORESIS; PROTEIN BINDING; PROTEIN CONFORMATION; X RAY CRYSTALLOGRAPHY;

ANIMALS; APROTININ; BINDING SITES; BIOLOGICAL MARKERS; BLOOD PRESSURE; CATTLE; CLONING, MOLECULAR; CRYSTALLOGRAPHY, X-RAY; DNA PRIMERS; ELECTROPHORESIS, POLYACRYLAMIDE GEL; HISTIDINE; HUMANS; HYDROLYSIS; INFLAMMATION; LIGANDS; MODELS, MOLECULAR; PEPTIDES; PROTEIN BINDING; PROTEIN CONFORMATION; RECOMBINANT PROTEINS; SERINE; SERINE ENDOPEPTIDASES; SOLVENTS; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION; SUBSTRATE SPECIFICITY; SWINE; TISSUE KALLIKREINS;

EID: 13944276781     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20368     Document Type: Article

References (62)

1. Kraut H, Frey EK, Werle E. Der nachweis eines kreislaufhormon in der Pankreasdruse. Hoppe-Seyler's Zeitschrifft fur physiologische Chemie 1930;189:97-106.
2. Qin H, Kemp J, Yip M, Lam-Po-Tang PRL, Morris BJ. Localization of human glandular kallikrein-1 gene to chromosome 19q13.3-13.4 by in-situ hybridization. Hum Hered 1991;41:222-226.
3. Riegman PH, Vlietstra RJ, Suurmeijer L, Cleutjens CB, Trapman J. Characterization of the human kallikrein locus. Genomics 1992;14:6-11.
4. Yousef GM, Diamandis EP. The new human tissue kallikrein gene family: structure, function, and association to disease. Endocr Rev 2001;22:184-204.
5. Olsson AY, Lundwall A. Organization and evolution of the glandular kallikrein locus in Mus musculus. Biochem Biophys Res Commun 2002;299:305-311.
6. Oesterling JE. Prostate-specific antigen: a critical assessment of the most useful tumor marker for adenocarcinoma of the prostate. J Urol 1991;145:907-923.
7. Catalona WJ, Smith DS, Ratliff TL, Dodds KM, Coplen DE, Yuan JJ, Petros JA, Andriole GL. Measurement of prostate-specific antigen in serum as a screening test for prostate cancer. New Engl J Med 1991;324:1156-1161.
8. Diamandis EP, Okui A, Mitsui S, Luo LY, Soosaipillai A, Grass L, Nakamura T, Howarth DJ, Yamaguchi N. Human kallikrein 11: a new biomarker of prostate and ovarian carcinoma. Cancer Res 2002;62:295-300.
9. Yousef GM, Magklara A, Chang A, Jung K, Katsaros D, Diamandis EP. Cloning of a new member of the human kallikrein gene family, KLK14, which is down-regulated in different malignancies. Cancer Res 2001;61:3425-3431.
10. Diamandis EP, Yousef GM, Petraki C, Soosaipillai AR. Human kallikrein 6 as a biomarker of alzheimer's disease. Clin Biochem 2000;33:663-667.
11. Diamandis EP, Yousef GM, Soosaipillai AR, Bunting P. Human kallikrein 6 (zyme/protease M/neurosin): a new serum biomarker of ovarian carcinoma. Clin Biochem 2000;33:579-583.
12. Luo LY, Bunting P, Scorilas A, Diamandis EP. Human kallikrein 10: a novel tumor marker for ovarian carcinoma? Clin Chim Acta 2001;306:111-118.
13. Yamanaka H, He X, Matsumoto K, Shiosaka S, Yoshida S. Protease M/neurosin mRNA is expressed in mature oligodendrocytes. Brain Res Mol Brain Res 1999;71:217-224.
14. Scarisbrick IA, Asakura K, Blaber S, Blaber M, Isackson PJ, Bieto T, Rodriguez M, Windebank AJ. Preferential expression of myelencephalon-specific protease by oligodendrocytes of the adult rat spinal cord white matter. Glia 2000;30:219-230.
15. Scarisbrick IA, Isackson PJ, Ciric B, Windebank AJ, Rodriguez M. MSP, a trypsin-like serine protease, is abundantly expressed in the human nervous system. J Comp Neurol 2001;431:347-61.
16. Scarisbrick IA, Towner MD, Isackson PJ. Nervous system-specific expression of a novel serine protease: regulation in the adult rat spinal cord by excitotoxic injury. J Neurosci 1997;17:8156-8168.
17. Blaber SI, Scarisbrick IA, Bernett MJ, Dhanarajan P, Seavy MA, Jin Y, Schwartz MA, Rodriguez M, Blaber M. Enzymatic properties of rat myelencephalon specific protease. Biochemistry 2002;41: 1165-1173.
18. Ogawa K, Yamada T, Tsujioka Y, Taguchi J, Takahashi M, Tsuboi Y, Fujino Y, Nakajima M, Yamamoto T, Akatsu H and others. Localization of a novel type trypsin-like serine protease, neurosin, in brain tissues of Alzheimer's disease and Parkinson's disease. Psychiatry Clin Neurosci 2000;54:419-426.
19. Kishi T, Kato M, Shimizu T, Kato K, Matsumoto K, Yoshida S, Shiosaka S, Hakoshima T. Crystallization and preliminary X-ray analysis of neuropsin, a serine protease expressed in the limbic system of mouse brain. J Struct Biol 1997;118:248-251.
20. Kishi T, Kato M, Shimizu T, Kato K, Matsumoto K, Yoshida S, Shiosaka S, Hakoshima T. Crystal structure of neuropsin, a hippocampal protease involved in kindling epileptogenesis. J Biol Chem 1999;274:4220-4224.
21. Silva J-A, Jr., Araujo RC, Baltatu O, Oliveira SM, Tschope C, Fink E, Hoffmann S, Plehm R, Chai KX, Chao J and others. Reduced cardiac hypertrophy and altered blood pressure control in transgenic rats with the human tissue kallikrein gene. FASEB J 2000;14:1858-1860.
22. Fiedler F, Leysath G. Substrate specificity of porcine pancreatic kallikrein. Adv Exp Med Biol 1979;120A:261-271.
23. Clements JA. The molecular biology of the kallikreins and their roles in inflammation. In: Farmer SG, editor. The Kinin system. Volume 5. San Diego: Academic Press; 1997. p 71-97.
24. Margolius HS. Kallikreins, kinins and cardiovascular diseases: a short review. Biol Res 1998;31:135-141.
25. Margolius HS. Tissue kallikreins structure, regulation, and participation in mammalian physiology and disease. Clin Rev Allergy Immunol 1998;16:337-349.
26. Crackower MA, Sarao R, Oudit GY, Yagil C, Kozieradzki I, Scanga SE, Oliveira-dos-Santos AJ, da Costa J, Zhang L, Pei Y and others. Angiotensin-converting enzyme 2 is an essential regulator of heart function. Nature 2002;417:822-828.
27. Erdos EG. Conversion of angiotensin I to angiotensin II. Am J Med 1976;60:749-759.
28. Bode W, Chen Z, Bartels K, Kutzbach C, Schmidt-Kastner G, Bartunik H. Refined 2 Å X-ray crystal structure of porcine pancreatic kallikrein A, a specific trypsin-like serine proteinase. Crystallization, structure determination, crystallographic refinement, structure and its comparison with bovine trypsin. J Mol Biol 1983;164:237-282.
29. Chen Z, Bode W. Refined 2.5 Å X-ray crystal structure of the complex formed by porcine kallikrein A and the bovine pancreatic trypsin inhibitor. Crystallization, Patterson search, structure determination, refinement, structure and comparison with its components and with the bovine trypsin-pancreatic trypsin inhibitor complex. J Mol Biol 1983;164:283-311.
30. Mittl PR, Di Marco S, Fendrich G, Pohlig G, Hein J, Sommerhoff C, Fritz H, Priestel JP, Grutter MG. A new structural class of serine protease inhibitors revealed by the structure of the hirustasin-kallikrein complex. Structure 1997;5:253-264.
31. Carvalho AL, Sanz L, Barettino D, Romero A, Calvete JJ, Romao MJ. Crystal structure of a prostate kallikrein isolated from stallion seminal plasma: a homologue of human PSA. J Mol Biol 2002;322:325-337.
32. Bax B, Blundell TL, Murray-Rust J, McDonald NQ. Structure of mouse 7S NGF: a complex of nerve growth factor with four binding proteins. Structure 1997;5:1275-1285.
33. Timm DE. The crystal structure of the mouse glandular kallikrein-13 (prorenin converting enzyme). Protein Sci 1997;6:1418-1425.
34. Fujinaga M, James MN. Rat submaxillary gland serine protease, tonin. Structure solution and refinement at 1.8 Å resolution. J Mol Biol 1987;195:373-396.
35. Bernett MJ, Blaber SI, Scarisbrick IA, Dhanarajan P, Thompson SM, Blaber M. Crystal structure and biochemical characterization of human kallikrein 6 reveals a trypsin-like kallikrein is expressed in the central nervous system. J Biol Chem 2002;277: 24562-24570.
36. Gomis-Ruth FX, Bayes A, Sotiropoulou G, Pampalakis G, Tsetsenis T, Villegas V, Aviles FX, Coll M. The structure of human prokallikrein 6 reveals a novel activation mechanism for the kallikrein family. J Biol Chem 2002;277:27273-27281.
37. Gill SC, von Hippel PH. Calculation of protein extinction coefficients from amino acid sequence data. Anal Biochem 1989;182: 319-326.
38. Jancarik J, Kim S-H. Sparse matrix sampling: a screening method for crystallization of proteins. J Appl Crystallogr 1991;24:409-411.
39. Otwinowski Z. Oscillation data reduction program. In: Sawyer L, Isaacs N, Bailey S, editors; 1993, Jan 29-30. SERC Daresbury Laboratory, England, p 56-62.
40. Otwinowski Z, Minor W. Processing of x-ray diffraction data collected in oscillation mode. Meth Enzymol 1997;276:307-326.
41. Brunger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang JS, Kuszewski J, Nilges M, Pannu NS and others. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr 1998;54:905-921.
42. Brunger AT. Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 1992;355:472-475.
43. Jones TA, Zou JY, Cowan SW, Kjeldgaard M. Improved methods for the building of protein models in electron density maps and the location of errors in these models. Acta Crystallographica 1991;A47: 110-119.
44. Guex N, Peitsch MC. SWISS-MODEL and the Swiss-Pdb Viewer: An environment for comparative protein modeling. Electrophoresis 1997;18:2714-2723.
45. Shimamoto K, Chao J, Margolius HS. The radioimmunoassay of human urinary; kallikrein and comparisons with kallikrein activity measurements. J Endocrinol Metabol 1980;51:840-859.
46. Sampaio CA, Sampaio MU, Prado ES. Active-site titration of horse urinary kallikrein. Hoppe-Seyler's Zeitschrifft fur physiologische Chemie 1984;365:297-302.
47. Hirata IY, Cezari MHS, Nakaie C, Boschcov P, Ito AS, Juliano M, Juliano L. Internally quenched fluorogenic protease substrates: Solid-phase synthesis and fluorescence spectroscopy of peptides containing ortho-aminobenzoyl/ dinitrophenyl groups as donor-acceptor pairs. Lett Pept Sci 1994;1:299-308.
48. Wilkinson GN. Statistical estimations in enzyme kinetics. Biochem J 1961;80:324-332.
49. Matthews BW. Solvent content of protein crystals. J Mol Biol 1968;33:491-497.
50. Katz BA, Beishan L, Barnes M, Springman EB. Crystal structure of recombinant human tissue kallikrein at 2.0 Å resolution. Protein Sci 1998;7:875-885.
51. Villoutreix BO, Getzoff ED, Griffin JH. A structural model for the prostate disease marker, human prostate-specific antigen. Protein Sci 1994;3:2033-2044.
52. Matthews BW, Sigler PB, Henderson R, Blow DM. Three-dimensional structure of tosyl-α-chymotrypsin. Nature 1967;214: 652-656.
53. Birktoft JJ, Blow DM. Structure of crystalline chymotrypsin. V. The atomic structure of tosyl- chymotrypsin at 2 Å resolution. J Mol Biol 1972;68:187-240.
54. Freer ST, Kraut J, Robertus JD, Wright HT, Xuong NG. Chymotrypsinogen: 2.50-Å crystal structure, comparison with α-chymotrypsin, and implications for zymogen activation. Biochemistry 1970;9:1997-2Q09.
55. Kossiakoff AA, Chambers JL, Kay LM, Stroud KM. Structure of bovine trypsinogen at 1.9 Å resolution. Biochemistry 1977;16:654-664.
56. Bode W, Schwager P. The refined crystal structure of bovine β-trypsin at 1.8 Å resolution. J Mol Biol 1975;98:693-717.
57. Bartunik HD, Summers LJ, Bartsch HH. Crystal structure of bovine b-trypsin at 1.5 Å resolution in a crystal form with low molecular packing density. J Mol Biol 1989;210:813-828.
58. Deshpande MS, Burton J. Mapping the binding site of tissue kallikrein: preparation and testing of all possible substrate analog inhibitors homologous with the sequence of kininogen between Ser386 and Gln392. J Med Chem 1992;35:3094-3102.
59. Chagas JR, Portaro FC, Hirata IY, Almeida PC, Juliano MA, Juliano L, Prado ES. Determinants of the unusual cleavage specificity of lysyl-bradykinin-releasing kallikreins. Biochem J 1995;306:63-69.
60. Heiland R, Otlewski J, Sundheim O, Dadlez M, Smalas AO. The crystal structures of the complexes between bovine β-trypsin and ten P1 variants of BPTI. 1999;284:923-942.
61. Meyer E, Cole G, Radhakrishnan R, Epp O. Structure of native porcine pancreatic elastase at 1.65 Å resolution. Acta Crystallogr B 1988;44:26-38.
62. Hamelberg D, McCammon JA. Standard free energy of releasing a localized water molecule from the binding pockets of proteins: double-decoupling method. J Am Chem Soc 2004;126:7683-7689.