1arb › Citations

The primary structure and structural characteristics of Achromobacter lyticus protease I, a lysine-specific serine protease.

Tsunasawa S, Masaki T, Hirose M, Soejima M, Sakiyama F
J Biol Chem 264 3832-9 (1989)
Cited: 72 times
EuropePMC logo PMID: 2492988

Abstract

The complete amino acid sequence of Achromobacter lyticus protease I (EC 3.4.21.50), which specifically hydrolyzes lysyl peptide bonds, has been established. This has been achieved by sequence analysis of the reduced and S-carboxymethylated protease and of peptides obtained by enzymatic digestion with Achromobacter protease I itself and Staphylococcus aureus V8 protease and by chemical cleavage with cyanogen bromide. The protease consists of 268 residues with three disulfide bonds, which have been assigned to Cys6-Cys216, Cys12-Cys80, and Cys36-Cys58. Comparison of the amino acid sequence of Achromobacter protease and other serine proteases of bacterial and mammalian origins has revealed that Achromobacter protease I is a mammalian-type serine protease of which the catalytic triad comprises His57, Asp113, and Ser194. It has also been shown that the protease has 9- and 26-residue extensions of the peptide chain at the N and C termini, respectively, and overall sequence homology is as low as 20% with bovine trypsin. The presence of a disulfide bridge between the N-terminal extension Cys6 and Cys216 close to the putative active site in the C-terminal region is thought to be responsible for the generation of maximal proteolytic function in the pH range 8.5-10.7 and enhanced stability to denaturation.

Articles - 1arb mentioned but not cited (35)

  1. A graph-theory algorithm for rapid protein side-chain prediction. Canutescu AA, Shelenkov AA, Dunbrack RL. Protein Sci. 12 2001-2014 (2003)
  2. Evaluating conformational free energies: the colony energy and its application to the problem of loop prediction. Xiang Z, Soto CS, Honig B. Proc. Natl. Acad. Sci. U.S.A. 99 7432-7437 (2002)
  3. Recognition of functional sites in protein structures. Shulman-Peleg A, Nussinov R, Wolfson HJ. J Mol Biol 339 607-633 (2004)
  4. Side-chain modeling with an optimized scoring function. Liang S, Grishin NV. Protein Sci. 11 322-331 (2002)
  5. Toward better refinement of comparative models: predicting loops in inexact environments. Sellers BD, Zhu K, Zhao S, Friesner RA, Jacobson MP. Proteins 72 959-971 (2008)
  6. Improved side-chain prediction accuracy using an ab initio potential energy function and a very large rotamer library. Peterson RW, Dutton PL, Wand AJ. Protein Sci 13 735-751 (2004)
  7. Multiple structural alignment by secondary structures: algorithm and applications. Dror O, Benyamini H, Nussinov R, Wolfson HJ. Protein Sci 12 2492-2507 (2003)
  8. What role do surfaces play in GB models? A new-generation of surface-generalized born model based on a novel gaussian surface for biomolecules. Yu Z, Jacobson MP, Friesner RA. J Comput Chem 27 72-89 (2006)
  9. Prediction of Protein Loop Conformations using the AGBNP Implicit Solvent Model and Torsion Angle Sampling. Felts AK, Gallicchio E, Chekmarev D, Paris KA, Friesner RA, Levy RM. J Chem Theory Comput 4 855-868 (2008)
  10. Incorporating dipolar solvents with variable density in Poisson-Boltzmann electrostatics. Azuara C, Orland H, Bon M, Koehl P, Delarue M. Biophys. J. 95 5587-5605 (2008)
  11. MUSTANG-MR structural sieving server: applications in protein structural analysis and crystallography. Konagurthu AS, Reboul CF, Schmidberger JW, Irving JA, Lesk AM, Stuckey PJ, Whisstock JC, Buckle AM. PLoS One 5 e10048 (2010)
  12. Exploring protein dynamics space: the dynasome as the missing link between protein structure and function. Hensen U, Meyer T, Haas J, Rex R, Vriend G, Grubmüller H. PLoS ONE 7 e33931 (2012)
  13. A stochastic algorithm for global optimization and for best populations: a test case of side chains in proteins. Glick M, Rayan A, Goldblum A. Proc. Natl. Acad. Sci. U.S.A. 99 703-708 (2002)
  14. H-bonding in protein hydration revisited. Petukhov M, Rychkov G, Firsov L, Serrano L. Protein Sci 13 2120-2129 (2004)
  15. Beyond the Poisson-Boltzmann model: modeling biomolecule-water and water-water interactions. Koehl P, Orland H, Delarue M. Phys. Rev. Lett. 102 087801 (2009)
  16. Beyond rotamers: a generative, probabilistic model of side chains in proteins. Harder T, Boomsma W, Paluszewski M, Frellsen J, Johansson KE, Hamelryck T. BMC Bioinformatics 11 306 (2010)
  17. Comparative computational analysis of prion proteins reveals two fragments with unusual structural properties and a pattern of increase in hydrophobicity associated with disease-promoting mutations. Kuznetsov IB, Rackovsky S. Protein Sci 13 3230-3244 (2004)
  18. Crystal structure of the serine protease domain of Sesbania mosaic virus polyprotein and mutational analysis of residues forming the S1-binding pocket. Gayathri P, Satheshkumar PS, Prasad K, Nair S, Savithri HS, Murthy MR. Virology 346 440-451 (2006)
  19. Atomic-accuracy prediction of protein loop structures through an RNA-inspired Ansatz. Das R. PLoS One 8 e74830 (2013)
  20. Design of an optimal Chebyshev-expanded discrimination function for globular proteins. Fain B, Xia Y, Levitt M. Protein Sci 11 2010-2021 (2002)
  21. Modeling of loops in proteins: a multi-method approach. Jamroz M, Kolinski A. BMC Struct. Biol. 10 5 (2010)
  22. GEM: a Gaussian Evolutionary Method for predicting protein side-chain conformations. Yang JM, Tsai CH, Hwang MJ, Tsai HK, Hwang JK, Kao CY. Protein Sci 11 1897-1907 (2002)
  23. A second lysine-specific serine protease from Lysobacter sp. strain IB-9374. Chohnan S, Shiraki K, Yokota K, Ohshima M, Kuroiwa N, Ahmed K, Masaki T, Sakiyama F. J. Bacteriol. 186 5093-5100 (2004)
  24. Deciphering the Arginine-binding preferences at the substrate-binding groove of Ser/Thr kinases by computational surface mapping. Ben-Shimon A, Niv MY. PLoS Comput. Biol. 7 e1002288 (2011)
  25. Identification of the catalytic triad of family S46 exopeptidases, closely related to clan PA endopeptidases. Suzuki Y, Sakamoto Y, Tanaka N, Okada H, Morikawa Y, Ogasawara W. Sci Rep 4 4292 (2014)
  26. Sampling multiple scoring functions can improve protein loop structure prediction accuracy. Li Y, Rata I, Jakobsson E. J Chem Inf Model 51 1656-1666 (2011)
  27. Analysis of binding properties and specificity through identification of the interface forming residues (IFR) for serine proteases in silico docked to different inhibitors. Ribeiro C, Togawa RC, Neshich IA, Mazoni I, Mancini AL, Minardi RC, da Silveira CH, Jardine JG, Santoro MM, Neshich G. BMC Struct. Biol. 10 36 (2010)
  28. Configurational Entropy of Folded Proteins and Its Importance for Intrinsically Disordered Proteins. Liu M, Das AK, Lincoff J, Sasmal S, Cheng SY, Vernon RM, Forman-Kay JD, Head-Gordon T. Int J Mol Sci 22 3420 (2021)
  29. Expanded explorations into the optimization of an energy function for protein design. Huang YM, Bystroff C. IEEE/ACM Trans Comput Biol Bioinform 10 1176-1187 (2013)
  30. New Deep Learning Methods for Protein Loop Modeling. Nguyen SP, Li Z, Xu D, Shang Y. IEEE/ACM Trans Comput Biol Bioinform 16 596-606 (2019)
  31. Homology modeling and virtual screening for antagonists of protease from yellow head virus. Unajak S, Sawatdichaikul O, Songtawee N, Rattanabunyong S, Tassnakajon A, Areechon N, Hirono I, Kondo H, Khunrae P, Rattanarojpong T, Choowongkomon K. J Mol Model 20 2116 (2014)
  32. An effective sequence-alignment-free superpositioning of pairwise or multiple structures with missing data. Lu J, Xu G, Zhang S, Lu B. Algorithms Mol Biol 11 18 (2016)
  33. Crystallization and preliminary crystallographic analysis of Achromobacter protease I mutants. Ito L, Shiraki K, Uchida T, Okumura M, Yamaguchi H. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 66 1531-1532 (2010)
  34. Structural comparison strengthens the higher-order classification of proteases related to chymotrypsin. Mönttinen HAM, Ravantti JJ, Poranen MM. PLoS ONE 14 e0216659 (2019)
  35. The Energetic Origins of Pi-Pi Contacts in Proteins. Carter-Fenk K, Liu M, Pujal L, Loipersberger M, Tsanai M, Vernon RM, Forman-Kay JD, Head-Gordon M, Heidar-Zadeh F, Head-Gordon T. J Am Chem Soc (2023)


Reviews citing this publication (3)

  1. Structural and energetic determinants of the S1-site specificity in serine proteases. Czapinska H, Otlewski J. Eur. J. Biochem. 260 571-595 (1999)
  2. CARD-FISH for environmental microorganisms: technical advancement and future applications. Kubota K. Microbes Environ. 28 3-12 (2013)
  3. All fifteen possible arrangements of three disulfide bridges in proteins are known. Warne NW, Laskowski M. Biochem. Biophys. Res. Commun. 172 1364-1370 (1990)

Articles citing this publication (34)

  1. Isolation of a novel cytokine from human fibroblasts that specifically inhibits osteoclastogenesis. Tsuda E, Goto M, Mochizuki S, Yano K, Kobayashi F, Morinaga T, Higashio K. Biochem. Biophys. Res. Commun. 234 137-142 (1997)
  2. Evolutionary families of peptidases. Rawlings ND, Barrett AJ. Biochem. J. 290 ( Pt 1) 205-218 (1993)
  3. Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature. Tsodikov OV, Record MT, Sergeev YV. J Comput Chem 23 600-609 (2002)
  4. An improved protocol for quantification of freshwater Actinobacteria by fluorescence in situ hybridization. Sekar R, Pernthaler A, Pernthaler J, Warnecke F, Posch T, Amann R. Appl. Environ. Microbiol. 69 2928-2935 (2003)
  5. Hydrophilicity of cavities in proteins. Zhang L, Hermans J. Proteins 24 433-438 (1996)
  6. Analytical shape computation of macromolecules: I. Molecular area and volume through alpha shape. Liang J, Edelsbrunner H, Fu P, Sudhakar PV, Subramaniam S. Proteins 33 1-17 (1998)
  7. Packing at the protein-water interface. Gerstein M, Chothia C. Proc. Natl. Acad. Sci. U.S.A. 93 10167-10172 (1996)
  8. Cloning and sequence analysis of the rat augmenter of liver regeneration (ALR) gene: expression of biologically active recombinant ALR and demonstration of tissue distribution. Hagiya M, Francavilla A, Polimeno L, Ihara I, Sakai H, Seki T, Shimonishi M, Porter KA, Starzl TE. Proc. Natl. Acad. Sci. U.S.A. 91 8142-8146 (1994)
  9. Antibodies against 70-kD heat shock cognate protein inhibit mediated nuclear import of karyophilic proteins. Imamoto N, Matsuoka Y, Kurihara T, Kohno K, Miyagi M, Sakiyama F, Okada Y, Tsunasawa S, Yoneda Y. J. Cell Biol. 119 1047-1061 (1992)
  10. Internal sequence analysis of proteins separated on polyacrylamide gels at the submicrogram level: improved methods, applications and gene cloning strategies. Tempst P, Link AJ, Riviere LR, Fleming M, Elicone C. Electrophoresis 11 537-553 (1990)
  11. Structure of West Nile virus NS3 protease: ligand stabilization of the catalytic conformation. Robin G, Chappell K, Stoermer MJ, Hu SH, Young PR, Fairlie DP, Martin JL. J. Mol. Biol. 385 1568-1577 (2009)
  12. Site-directed mutagenesis of La protease. A catalytically active serine residue. Amerik AYu, Antonov VK, Gorbalenya AE, Kotova SA, Rotanova TV, Shimbarevich EV. FEBS Lett. 287 211-214 (1991)
  13. Biosynthesis of archaeosine, a novel derivative of 7-deazaguanosine specific to archaeal tRNA, proceeds via a pathway involving base replacement on the tRNA polynucleotide chain. Watanabe M, Matsuo M, Tanaka S, Akimoto H, Asahi S, Nishimura S, Katze JR, Hashizume T, Crain PF, McCloskey JA, Okada N. J. Biol. Chem. 272 20146-20151 (1997)
  14. The chemical and dynamical influence of the anti-viral drug amantadine on the M2 proton channel transmembrane domain. Hu J, Fu R, Cross TA. Biophys. J. 93 276-283 (2007)
  15. Structural basis for the lower affinity of the insulin-like growth factors for the insulin receptor. Gauguin L, Klaproth B, Sajid W, Andersen AS, McNeil KA, Forbes BE, De Meyts P. J Biol Chem 283 2604-2613 (2008)
  16. Cloning and expression of a cDNA encoding mouse indoleamine 2,3-dioxygenase. Habara-Ohkubo A, Takikawa O, Yoshida R. Gene 105 221-227 (1991)
  17. Molecular analysis of the gene encoding a novel chitin-binding protease from Alteromonas sp. strain O-7 and its role in the chitinolytic system. Miyamoto K, Nukui E, Itoh H, Sato T, Kobayashi T, Imada C, Watanabe E, Inamori Y, Tsujibo H. J. Bacteriol. 184 1865-1872 (2002)
  18. Synthesis and expression of genes encoding tuna, pigeon, and horse cytochromes c in the yeast Saccharomyces cerevisiae. Hickey DR, Jayaraman K, Goodhue CT, Shah J, Fingar SA, Clements JM, Hosokawa Y, Tsunasawa S, Sherman F. Gene 105 73-81 (1991)
  19. Metastasis-promoting activity of a novel molecule, Ag 243-5, derived from mycoplasma, and the complete nucleotide sequence. Ushio S, Iwaki K, Taniai M, Ohta T, Fukuda S, Sugimura K, Kurimoto M. Microbiol. Immunol. 39 393-400 (1995)
  20. Electrostatic role of aromatic ring stacking in the pH-sensitive modulation of a chymotrypsin-type serine protease, Achromobacter protease I. Shiraki K, Norioka S, Li S, Yokota K, Sakiyama F. Eur. J. Biochem. 269 4152-4158 (2002)
  21. Lysobacter strain with high lysyl endopeptidase production. Chohnan S, Nonaka J, Teramoto K, Taniguchi K, Kameda Y, Tamura H, Kurusu Y, Norioka S, Masaki T, Sakiyama F. FEMS Microbiol. Lett. 213 13-20 (2002)
  22. Preparation of monoclonal antibodies to hirudin and hirudin peptides. A method for studying the hirudin--thrombin interaction. Schlaeppi JM, Vekemans S, Rink H, Chang JY. Eur. J. Biochem. 188 463-470 (1990)
  23. GASS: identifying enzyme active sites with genetic algorithms. Izidoro SC, de Melo-Minardi RC, Pappa GL. Bioinformatics 31 864-870 (2015)
  24. Histidine 210 mutant of a trypsin-type Achromobacter protease I shows broad optimum pH range. Shiraki K, Sakiyama F. J. Biosci. Bioeng. 93 331-333 (2002)
  25. Identifying essential pairwise interactions in elastic network model using the alpha shape theory. Xia F, Tong D, Yang L, Wang D, Hoi SC, Koehl P, Lu L. J Comput Chem 35 1111-1121 (2014)
  26. Accurate mass comparison coupled with two endopeptidases enables identification of protein termini. Kishimoto T, Kondo J, Takai-Igarashi T, Tanaka H. Proteomics 11 485-489 (2011)
  27. Neutron and X-ray crystallographic analysis of Achromobacter protease I at pD 8.0: protonation states and hydration structure in the free-form. Ohnishi Y, Yamada T, Kurihara K, Tanaka I, Sakiyama F, Masaki T, Niimura N. Biochim. Biophys. Acta 1834 1642-1647 (2013)
  28. Preparation of Fab' from murine IgG2a for thiol reactive conjugation. Fowers KD, Callahan J, Byron P, Kopecek JI. J Drug Target 9 281-294 (2001)
  29. Letter The activities of Achromobacter lysyl endopeptidase and Lysobacter lysyl endoproteinase as digestive enzymes for quantitative proteomics. Achour B, Barber J. Rapid Commun. Mass Spectrom. 27 1669-1672 (2013)
  30. Cleavage with phospholipase of the lipid anchor in the cell adhesion molecule, csA, from Dictyostelium discoideum. Yoshida M, Sakuragi N, Kondo K, Tanesaka E. Comp. Biochem. Physiol. B, Biochem. Mol. Biol. 143 138-144 (2006)
  31. Cloning of a Lysobacter enzymogenes gene that encodes an arginyl endopeptidase (endoproteinase Arg-C). Wright DS, Graham LD, Jennings PA. Biochim. Biophys. Acta 1443 369-374 (1998)
  32. Expression, receptor binding, and biophysical characterization of guinea pig insulin desB30: a monomeric insulin variant. Engholm E, Hansen TH, Johansson E, Strauss HM, Vinther TN, Jensen KJ, Hubálek F, Kjeldsen TB. Chembiochem 16 954-958 (2015)
  33. Atomic resolution structure of a lysine-specific endoproteinase from Lysobacter enzymogenes suggests a hydroxyl group bound to the oxyanion hole. Asztalos P, Müller A, Hölke W, Sobek H, Rudolph MG. Acta Crystallogr. D Biol. Crystallogr. 70 1832-1843 (2014)
  34. Pudding Proteomics: Cyclomaltodextrin Glucanotransferase and Microbial Proteases Can Liquefy Extended Shelf Life Dairy Products. Kleinwort KJH, Weigand M, Hoffmann L, Degroote RL, Dietrich R, Märtlbauer E, Hauck SM, Deeg CA. Metabolites 12 254 (2022)


Quick links