Three-Dimensional Structures and Mechanisms of Snake Venom Serine Proteinases, Metalloproteinases, and Phospholipase A2s

  • M. A. Coronado
  • F. R. de Moraes
  • A. Ullah
  • R. Masood
  • V. S. Santana
  • R. Mariutti
  • H. Brognaro
  • D. Georgieva
  • M. T. Murakami
  • C. Betzel
  • R. K. Arni
Living reference work entry


High-resolution crystal structures provide accurate information of the positions of the atoms which can be used to understand substrate specificity, secondary binding sites, and catalytic mechanisms. Detailed structural information and mechanisms of serine proteinases, metalloproteinases, and phospholipases A2s are presented.


Disulfide Bridge Snake Venom Catalytic Triad Carbonyl Oxygen Atom Solvent Water Molecule 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


  1. Akao PK, Tonoli CC, Navarro MS, Cintra AC, Neto JR, Arni RK, Murakami MT. Structural studies of BmooMPalpha-I, a non-hemorrhagic metalloproteinase from Bothrops moojeni venom. Toxicon. 2010;55(2–3):361–8.PubMedCrossRefGoogle Scholar
  2. Arni RK, Ward RJ. Phospholipase A2 – a structural review. Toxicon. 1996;34(8):827–41.PubMedCrossRefGoogle Scholar
  3. Bajaj M, Blundell T. Evolution and the tertiary structure of proteins. Annu Rev Biophys Bioeng. 1984;13:453–92.PubMedCrossRefGoogle Scholar
  4. Baker NA, Sept D, Joseph S, Holst MJ, McCamoon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci U S A. 2001;28;98(18):10037–41.Google Scholar
  5. Birktoft JJ, Blow DM. Structure of crystalline -chymotrypsin. V. The atomic structure of tosyl- -chymotrypsin at 2 A resolution. J Mol Biol. 1972;68(2):187–240.PubMedCrossRefGoogle Scholar
  6. Birktoft JJ, Kraut J, Freer ST. A detailed structural comparison between the charge relay system in chymotrypsinogen and in alpha-chymotrypsin. Biochemistry. 1976;15(20):4481–5.PubMedCrossRefGoogle Scholar
  7. Bode W, Huber R. Crystal structure analysis and refinement of two variants of trigonal trypsinogen: trigonal trypsin and PEG (polyethylene glycol) trypsinogen and their comparison with orthorhombic trypsin and trigonal trypsinogen. FEBS Lett. 1978;90(2):265–9.PubMedCrossRefGoogle Scholar
  8. Bode W, Schwager P, Huber R. The transition of bovine trypsinogen to a trypsin-like state upon strong ligand binding. The refined crystal structures of the bovine trypsinogen-pancreatic trypsin inhibitor complex and of its ternary complex with Ile-Val at 1.9 A resolution. J Mol Biol. 1978;118(1):99–112.PubMedCrossRefGoogle Scholar
  9. Bode W, Grams F, Reinemer P, Gomis-Rüth FX, Baumann U, McKay DB, Stöcker W. The metzincin-superfamily of zinc-peptidases. AdvExp Med Biol. 1996;389:1–11.CrossRefGoogle Scholar
  10. Calvete JJ. The continuing saga of snake venom disintegrins. Toxicon. 2013;62:40–9.PubMedCrossRefGoogle Scholar
  11. Calvete JJ, Moreno-Murciano MP, Theakston RD, Kisiel DG, Marcinkiewicz C. Snake venom disintegrins: novel dimeric disintegrins and structural diversification by disulphide bond engineering. Biochem J. 2003;372(Pt 3):725–34.PubMedCrossRefPubMedCentralGoogle Scholar
  12. Calvete JJ, Juárez P, Sanz L. Snake venomics. Strategy and applications. J Mass Spectrom. 2007;42(11):1405–14.PubMedCrossRefGoogle Scholar
  13. Chothia C, Lesk AM. The relation between the divergence of sequence and structure in proteins. EMBO J. 1986;5(4):823–6.PubMedPubMedCentralGoogle Scholar
  14. Coronado MA, Georgieva D, Buck F, Gabdoulkhakov AH, Ullah A, Spencer PJ, Arni RK, Betzel C. Purification, crystallization and preliminary X-ray diffraction analysis of crotamine, a myotoxic polypeptide from the Brazilian snake Crotalus durissus terrificus. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012;68(Pt 9):1052–4.PubMedCrossRefPubMedCentralGoogle Scholar
  15. Coronado MA, Gabdulkhakov A, Georgieva D, Sankaran B, Murakami MT, Arni RK, Betzel C. Structure of the polypeptide crotamine from the Brazilian rattlesnake Crotalus durissus terrificus. Acta Crystallogr D Biol Crystallogr. 2013;69(Pt 10):1958–64.PubMedCrossRefPubMedCentralGoogle Scholar
  16. Dolinsky TJ, Czodrowski P, Li H, Nielsen JE, Jensen JH, Klebe G, Baker NA. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res. 2007;(35):W522–W525.Google Scholar
  17. Dufton MJ, Hider RC. Classification of phospholipases A2 according to sequence. Evolutionary and pharmacological implications. Eur J Biochem. 1983;137(3):545–51.PubMedCrossRefGoogle Scholar
  18. Epstein DM, Abeles RH. Role of serine 214 and tyrosine 171, components of the S2 subsite of alpha-lytic protease, in catalysis. Biochemistry. 1992;31(45):11216–23.PubMedCrossRefGoogle Scholar
  19. Fadel V, Bettendorff P, Herrmann T, De Azevedo Jr WF, Oliveira EB, Yamane T, Wüthrich K. Automated NMR structure determination and disulfide bond identification of the myotoxin crotamine from Crotalus durissus terrificus. Toxicon. 2005;46(7):759–67.PubMedCrossRefGoogle Scholar
  20. Fernandes de Oliveira LM, Ullah A, Masood R, Zelanis A, Spencer PJ, Serrano SM, Arni RK. Rapid purification of serine proteinases from Bothrops alternatus and Bothrops moojeni venoms. Toxicon. 2013;76:282–90.PubMedCrossRefGoogle Scholar
  21. Finkelstein AV, Ptitsyn OB. Why do globular proteins fit the limited set of folding patterns? Prog Biophys Mol Biol. 1987;50:171–90.PubMedCrossRefGoogle Scholar
  22. Fujii Y, Okuda D, Fujimoto Z, Horii K, Morita T, Mizuno H. Crystal structure of trimestatin, a disintegrin containing a cell adhesion recognition motif RGD. J Mol Biol. 2003;332(5):1115–22.PubMedCrossRefGoogle Scholar
  23. Gempeler-Messina PM, Volz K, Bühler B, Müller C. Protein C activators from snake venoms and their diagnostic use. Haemostasis. 2001;31(3–6):266–72.PubMedGoogle Scholar
  24. Georgieva DN, Rypniewski W, Gabdoulkhakov A, Genov N, Betzel C. Asp49 phospholipase A(2)-elaidoylamide complex: a new mode of inhibition. Biochem Biophys Res Commun. 2004;319(4):1314–21.PubMedCrossRefGoogle Scholar
  25. Georgieva D, Arni RK, Betzel C. Proteome analysis of snake venom toxins: pharmacological insights. Expert Rev Proteomics. 2008;5(6):787–97.PubMedCrossRefGoogle Scholar
  26. Georgieva D, Coronado M, Oberthür D, Buck F, Duhalov D, Arni RK, Betzel C. Crystal structure of a dimeric Ser49- PLA2-like myotoxic component of the Vipera ammodytes meridionalis venomics reveals determinants of myotoxicity and membrane damaging activity. Mol Biosyst. 2012;8(5):1405–11.PubMedCrossRefGoogle Scholar
  27. Gomis-Ruth FX, Kress LF, Kellermann J, Mayr I, Lee X, Huber R, and Bode, W. Refined 2 Å X-ray crystal structure of the snake venom zinc-endopeptidase adamalysin II. Primary and tertiary structure determination, refinement, molecular structure and comparison with astacin, collagenase and thermolysin. J Mol Biol. 1994;(239):513–544.Google Scholar
  28. Hasson MS, Schlichting I, Moulai J, Taylor K, Barrett W, Kenyon GL, Babbitt PC, Gerlt JA, Petsko GA, Ringe D. Evolution of an enzyme active site: the structure of a new crystal form of muconate lactonizing enzyme compared with mandelate racemase and enolase. Proc Natl Acad Sci USA. 1998;95(18):10396–401.PubMedCrossRefPubMedCentralGoogle Scholar
  29. Hedstrom L. Serine protease mechanism and specificity. Chem Rev. 2002a;102(12):4501–24.PubMedCrossRefGoogle Scholar
  30. Hedstrom L. An overview of serine proteases. Curr Protoc Protein Sci. 2002b; Chapter 21. ps2110s26.Google Scholar
  31. Hedstrom L, Lin TY, Fast W. Hydrophobic interactions control zymogen activation in the trypsin family of serine proteases. Biochemistry. 1996;35(14):4515–23.PubMedCrossRefGoogle Scholar
  32. Harley BS, Shotton DM. The Enzymes. Academic Press, New York. 1971;1 Ed.Google Scholar
  33. Hooper NM. Families of zinc metalloproteases. FEBS Lett. 1994;354(1):1–6.PubMedCrossRefGoogle Scholar
  34. Huber R, Bode W. Structural basis of the activation and action of trypsin. Acc Chem Res. 1978;11:114–22.CrossRefGoogle Scholar
  35. Jain MK, Gelb MH, Rogers J, Berg OG. Kinetic basis for interfacial catalysis by phospholipase A2. Methods Enzymol. 1995;249:567–614.PubMedCrossRefGoogle Scholar
  36. Kamiguti AS, Hay CR, Theakston RD, Zuzel M. Insights into the mechanism of haemorrhage caused by snake venom metalloproteinases. Toxicon. 1996;34(6):627–42.PubMedCrossRefGoogle Scholar
  37. Kang TS, Georgieva D, Genov N, Murakami MT, Sinha M, Kumar RP, Kaur P, Kumar S, Dey S, Sharma S, Vrielink A, Betzel C, Takeda S, Arni RK, Singh TP, Kini RM. Enzymatic toxins from snake venom: structural characterization and mechanism of catalysis. FEBS J. 2011;278(23):4544–76.PubMedCrossRefGoogle Scholar
  38. Kasuya A, Thornton JM. Three-dimensional structure analysis of PROSITE patterns. J Mol Biol. 1999;286(5):1673–91.PubMedCrossRefGoogle Scholar
  39. Kini RM. Serine proteases affecting blood coagulation and fibrinolysis from snake venoms. Pathophysiol Haemost Thromb. 2005;34(4–5):200–4.PubMedCrossRefGoogle Scholar
  40. Kraut J. Serine proteases: Structure and mechanism of catalysis. Annu Rev Biochem. 1977;46:331–58.PubMedCrossRefGoogle Scholar
  41. Kudo I, Murakami M, Hara S, Inoue K. Mammalian non-pancreatic phospholipases A2. Biochim Biophys Acta. 1993; 1170:217–231.Google Scholar
  42. Lesk AM, Chothia C. How different amino acid sequences determine similar protein structures: the structure and evolutionary dynamics of the globins. J Mol Biol. 1980;136(3):225–70.PubMedCrossRefGoogle Scholar
  43. Lingott T, Schleberger C, Gutiérrez JM. MerfortI. High-resolution crystal structure of the snake venom metalloproteinase BaP1 complexed with a peptidomimetic: insight into inhibitor binding. Biochemistry. 2009;48(26):6166–74.PubMedCrossRefGoogle Scholar
  44. McGrath ME, Vásquez JR, Craik CS, Yang AS, Honig B, Fletterick RJ. Perturbing the polar environment of Asp102 in trypsin: consequences of replacing conserved Ser214. Biochemistry. 1992;31(12):3059–64.PubMedCrossRefGoogle Scholar
  45. Moura-da-Silva AM, Ramos OH, Baldo C, Niland S, Hansen U, Ventura JS, Furlan S, Butera D, Della-Casa MS, Tanjoni I, Clissa PB, Fernandes I, Chudzinski-Tavassi AM, Eble JA. Collagen binding is a key factor for the hemorrhagic activity of snake venom metalloproteinases. Biochimie. 2008;90(3):484–92.PubMedCrossRefGoogle Scholar
  46. Murakami MT, Arni RK. Thrombomodulin-independent activation of protein C and specificity of hemostatically active snake venom serine proteinases: crystal structures of native and inhibited Agkistrodon contortrix contortrix protein C activator. J Biol Chem. 2005;280(47):39309–15.PubMedCrossRefGoogle Scholar
  47. Neurath H. Evolution of proteolytic enzymes. Science. 1984;224(4647):350–7.PubMedCrossRefGoogle Scholar
  48. Nicastro G, Franzoni L, de Chiara C, Mancin AC, Giglio JR, Spisni A. Solution structure of crotamine, a Na + channel affecting toxin from Crotalus durissus terrificus venom. Eur J Biochem. 2003;270(9):1969–79.PubMedCrossRefGoogle Scholar
  49. Parry MA, Jacob U, Huber R, Wisner A, Bon C, Bode W. The crystal structure of the novel snake venom plasminogen activator TSV-PA: a prototype structure for snake venom serine proteinases. Structure. 1998;6(9):1195–206.PubMedCrossRefGoogle Scholar
  50. Perbandt M, Tsai IH, Fuchs A, Banumathi S, Rajashankar KR, Georgieva D, Kalkura N, Singh TP, Genov N, Betzel C. Structure of the heterodimeric neurotoxic complex viperotoxin F (RV-4/RV-7) from the venom of Vipera russelli formosensis at 1.9 A resolution. Acta Crystallogr D Biol Crystallogr. 2003;59(Pt 10):1679–87.PubMedCrossRefGoogle Scholar
  51. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE. UCSF Chimera – a visualization system for the exploratory research and analysis. J Comput Chem. 2004;25(13):1605–12.Google Scholar
  52. Rádis-Baptista G, Kerkis I. Crotamine, a small basic polypeptide myotoxin from rattlesnake venom with cell-penetrating properties. Curr Pharm Des. 2011;17(38):4351–61.PubMedCrossRefGoogle Scholar
  53. Ramirez F, Jain MK. Phospholipase A2 at the bilayer interface. Proteins. 1991;9(4):229–39.PubMedCrossRefGoogle Scholar
  54. Rawlings ND, Waller M, Barrett AJ, Bateman A. MEROPS: the database of proteolytic enzymes, their substrates and inhibitors. Nucleic Acids Res. 2013.Google Scholar
  55. Renetseder R, Brunie S, Dijkstra BW, Drenth J, Sigler PB. A comparison of the crystal structures of phospholipase A2 from bovine pancreas and Crotalus atrox venom. J Biol Chem. 1985;260(21):11627–34.PubMedGoogle Scholar
  56. Retzios AD, Markland Jr FS. A direct-acting fibrinolytic enzyme from the venom of Agkistrodon contortrix contortrix: effects on various components of the human blood coagulation and fibrinolysis systems. Thromb Res. 1988;52(6):541–52.PubMedCrossRefGoogle Scholar
  57. Rossetto O, Montecucco C. Presynaptic neurotoxins with enzymatic activities. Handb Exp Pharmacol. 2008;184:129–70.PubMedCrossRefGoogle Scholar
  58. Serrano SM. The long road of research on snake venom serine proteinases. Toxicon. 2013;62:19–26.PubMedCrossRefGoogle Scholar
  59. Stöcker W, Grams F, Baumann U, Reinemer P, Gomis-Rüth FX, McKay DB, Bode W. The metzincins–topological and sequential relations between the astacins, adamalysins, serralysins, and matrixins (collagenases) define a superfamily of zinc-peptidases. Protein Sci. 1995;4(5):823–40.PubMedCrossRefPubMedCentralGoogle Scholar
  60. Takeda S, Takeya H, Iwanaga S. Snake venom metalloproteinases: structure, function and relevance to the mammalian ADAM/ADAMTS family proteins. Biochim Biophys Acta. 2012;1824(1):164–76.PubMedCrossRefGoogle Scholar
  61. Teshima K, Kitagawa Y, Samejima Y, Kawauchi S, Fujii S, Ikeda K, Hayashi K, Omori-Satoh T. Role of Ca2+ in the substrate binding and catalytic functions of snake venom phospholipases A2. J Biochem. 1989;106(3):518–27.PubMedGoogle Scholar
  62. Thornton JM, Flores TP, Jones DT, Swindells MB. Protein structure. Prediction of progress at last. Nature. 1991;354:105–6.PubMedCrossRefGoogle Scholar
  63. Ullah A, Souza TA, Zanphorlin LM, Mariutti RB, Santana VS, Murakami MT, Arni RK. Crystal structure of Jararacussin-I: the highly negatively charged catalytic interface contributes to macromolecular selectivity in snake venom thrombin-like enzymes. Protein Sci. 2013;22(1):128–32.PubMedCrossRefPubMedCentralGoogle Scholar
  64. Watanabe L, Shannon JD, Valente RH, Rucavado A, Alape-Girón A, Kamiguti AS, Theakston RD, Fox JW, Gutiérrez JM, Arni RK. Amino acid sequence and crystal structure of BaP1, a metalloproteinase from Bothrops asper snake venom that exerts multiple tissue-damaging activities. Protein Sci. 2003;12(10):2273–81.PubMedCrossRefPubMedCentralGoogle Scholar
  65. Wlodawer A, Minor W, Dauter Z, Jaskolski M. Protein crystallography for non-crystallographers, or how to get the best (but not more) from published macromolecular structures. FEBS J. 2008;275(1):1–21.PubMedCrossRefGoogle Scholar
  66. Wlodawer A, Minor W, Dauter Z, Jaskolski M. Protein crystallography for aspiring crystallographers or how to avoid pitfalls and traps in macromolecular structure determination. FEBS J. 2013;280(22):5705–36.PubMedCrossRefGoogle Scholar
  67. Yamazaki Y, Morita T. Snake venom components affecting blood coagulation and the vascular system: structural similarities and marked diversity. Curr Pharm Des. 2007;13(28):2872–86.PubMedCrossRefGoogle Scholar
  68. Zhang Y, Wisner A, Xiong Y, Bon C. A novel plasminogen activator from snake venom. Purification, characterization, and molecular cloning. J Biol Chem. 1995;270(17):10246–55.PubMedCrossRefGoogle Scholar
  69. Zhu Z, Gong P, Teng M, Niu L. Purification, N-terminal sequencing, partial characterization, crystallization and preliminary crystallographic analysis of two glycosylated serine proteinases from Agkistrodon acutus venom. Acta Crystallogr D Biol Crystallogr. 2003;59(Pt 3):547–50.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  • M. A. Coronado
    • 1
  • F. R. de Moraes
    • 1
  • A. Ullah
    • 1
  • R. Masood
    • 1
  • V. S. Santana
    • 1
  • R. Mariutti
    • 1
  • H. Brognaro
    • 1
  • D. Georgieva
    • 2
  • M. T. Murakami
    • 3
  • C. Betzel
    • 2
  • R. K. Arni
    • 1
  1. 1.Department of Physics, IBILCE/UNESPMulti User Center for Biomolecular InnovationSão Jose do Rio Preto-SPBrazil
  2. 2.Institute of Biochemistry and Molecular BiologyUniversity of Hamburg, Laboratory of Structural Biology of Infection and Inflammation, c/o DESYHamburgGermany
  3. 3.National Laboratory for BiosciencesNational Center for Research in Energy and MaterialsCampinasBrazil

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