The expanding diversity of serine hydrolases

Current Opinion in Structural Biology

Volumn 17, Issue 6, 2007, Pages 683-690

  Botos, Istvan ^a   Wlodawer, Alexander ^b  

^a NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES   (United States)

^b NATIONAL CANCER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DIPEPTIDYL PEPTIDASE IV; ENDOPEPTIDASE LA; SEPRASE; SERINE PROTEINASE;

BIODIVERSITY; CATALYSIS; CELL MEMBRANE; ENZYME ACTIVATION; ENZYME BINDING; ENZYME STRUCTURE; PRIORITY JOURNAL; REVIEW;

CATALYTIC DOMAIN; HYDROLASES; MODELS, MOLECULAR; PROTEIN CONFORMATION; SERINE;

EID: 36549068790     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.sbi.2007.08.003     Document Type: Review

References (35)

1. Barrett A.J., Rawlings N.D., and Woessner J.F. Handbook of Proteolytic Enzymes (1998), Academic Press, London
2. Tang J., Yu C.L., Williams S.R., Springman E., Jeffery D., Sprengeler P.A., Estevez A., Sampang J., Shrader W., Spencer J., et al. Expression, crystallization, and three-dimensional structure of the catalytic domain of human plasma kallikrein. J Biol Chem 280 (2005) 41077-41089
3. Laxmikanthan G., Blaber S.I., Bernett M.J., Scarisbrick I.A., Juliano M.A., and Blaber M. 1.70 Å X-ray structure of human apo kallikrein 1: structural changes upon peptide inhibitor/substrate binding. Proteins 58 (2005) 802-814
4. Debela M., Magdolen V., Grimminger V., Sommerhoff C., Messerschmidt A., Huber R., Friedrich R., Bode W., and Goettig P. Crystal structures of human tissue kallikrein 4: activity modulation by a specific zinc binding site. J Mol Biol 362 (2006) 1094-1107
5. Wang F., Wang C., Li M., Zhang J.P., Gui L.L., An X.M., and Chang W.R. Crystal structure of earthworm fibrinolytic enzyme component B: a novel, glycosylated two-chained trypsin. J Mol Biol 348 (2005) 671-685
6. Prasad L., Leduc Y., Hayakawa K., and Delbaere L.T.J. The structure of a universally employed enzyme: V8 protease from Staphylococcus aureus. Acta Crystallogr D60 (2007) 256-259
7. Popowicz G.M., Dubin G., Stec-Niemczyk J., Czarny A., Dubin A., Potempa J., and Holak T.A. Functional and structural characterization of Spl proteases from Staphylococcus aureus. J Mol Biol 358 (2006) 270-279
8. Zhu Z., Liang Z., Zhang T., Zhu Z., Xu W., Teng M., and Niu L. Crystal structures and amidolytic activities of two glycosylated snake venom serine proteinases. J Biol Chem 280 (2005) 10524-10529
9. Murakami M.T., and Arni R.K. 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 280 (2005) 39309-39315
10. Papagrigoriou E., McEwan P.A., Walsh P.N., and Emsley J. Crystal structure of the factor XI zymogen reveals a pathway for transactivation. Nat Struct Mol Biol 13 (2006) 557-558
11. Piao S., Kim S., Kim J.H., Park J.W., Lee B.L., and Ha N.C. Crystal structure of the serine protease domain of prophenoloxidase activating factor-I. J Biol Chem 282 (2007) 10783-10791. First crystal structure of the serine protease domain of easter-type proteases. The results reveal that the serine protease domain has a surface patch similar to the fibrinogen recognition exosite of thrombin.
12. Piao S., Song Y.L., Kim J.H., Park S.Y., Park J.W., Lee B.L., Oh B.H., and Ha N.C. Crystal structure of a clip-domain serine protease and functional roles of the clip domains. EMBO J 24 (2005) 4404-4414
13. Milder F.J., Gomes L., Schouten A., Janssen B.J., Huizinga E.G., Romijn R.A., Hemrika W., Roos A., Daha M.R., and Gros P. Factor B structure provides insights into activation of the central protease of the complement system. Nat Struct Mol Biol 14 (2007) 224-228. This crystal structure of human factor B reveals how the five-domain proenzyme is kept securely inactive.
14. Krishnan V., Xu Y., Macon K., Volanakis J.E., and Narayana S.V. The crystal structure of C2a, the catalytic fragment of classical pathway C3 and C5 convertase of human complement. J Mol Biol 367 (2007) 224-233
15. Gál P., Harmat V., Kocsis A., Bián T., Barna L., Ambrus G., Végh B., Balczer J., Sim R.B., Náray-Szabó G., and Závodszky P. A true autoactivating enzyme. Structural insight into mannose-binding lectin-associated serine protease-2 activations. J Biol Chem 280 (2005) 33435-33444
16. Otto B.R., Sijbrandi R., Luirink J., Oudega B., Heddle J.G., Mizutani K., Park S.Y., and Tame J.R. Crystal structure of hemoglobin protease, a heme binding autotransporter protein from pathogenic Escherichia coli. J Biol Chem 280 (2005) 17339-17345. This serine protease autotransporter degrades hemoglobin and delivers heme to the symbiotic E. coli and B. fragilis. The structure of the whole passenger domain is the first structure from this class of serine proteases and the largest parallel β-helical structure solved.
17. Erbel P., Schiering N., D'Arcy A., Renatus M., Kroemer M., Lim S.P., Yin Z., Keller T.H., Vasudevan S.G., and Hommel U. Structural basis for the activation of flaviviral NS3 proteases from dengue and West Nile virus. Nat Struct Mol Biol 13 (2006) 372-373. These NS3 protease structures are in a catalytically relevant conformation. A previous NS3 structure, in the absence of NS2B shows substantial differences.
18. Gayathri P., Satheshkumar P.S., Prasad K., Nair S., Savithri H.S., and Murthy M.R. Crystal structure of the serine protease domain of Sesbania mosaic virus polyprotein and mutational analysis of residues forming the S1-binding pocket. Virology 346 (2006) 440-451
19. Aertgeerts K., Levin I., Shi L., Snell G.P., Jennings A., Prasad G.S., Zhang Y., Kraus M.L., Salakian S., Sridhar V., et al. Structural and kinetic analysis of the substrate specificity of human fibroblast activation protein alpha. J Biol Chem 280 (2005) 19441-19444
20. Ito K., Nakajima Y., Xu Y., Yamada N., Onohara Y., Ito T., Matsubara F., Kabashima T., Nakayama K., and Yoshimoto T. Crystal structure and mechanism of tripeptidyl activity of prolyl tripeptidyl aminopeptidase from Porphyromonas gingivalis. J Mol Biol 362 (2006) 228-240
21. Shan L., Mathews I.I., and Khosla C. Structural and mechanistic analysis of two prolyl endopeptidases: role of interdomain dynamics in catalysis and specificity. Proc Natl Acad Sci USA 102 (2005) 3599-3604
22. Paton A.W., Beddoe T., Thorpe C.M., Whisstock J.C., Wilce M.C., Rossjohn J., Talbot U.M., and Paton J.C. AB5 subtilase cytotoxin inactivates the endoplasmic reticulum chaperone BiP. Nature 443 (2006) 548-552
23. Helland R., Larsen A.N., Smalås A.O., and Willassen N.P. The 1.8 Å crystal structure of a proteinase K-like enzyme from a psychrotroph Serratia species. FEBS J 273 (2006) 61-71
24. Arnórsdóttir J., Kristjánsson M.M., and Ficner R. Crystal structure of a subtilisin-like serine proteinase from a psychrotrophic Vibrio species reveals structural aspects of cold adaptation. FEBS J 272 (2005) 832-845. This is the first structure of a cold-adapted subtilase. Some of the structural determinants of cold adaptation are described.
25. Xu Q., Guo H.B., Wlodawer A., Nakayama T., and Guo H. The QM/MM molecular dynamics and free energy simulations of the acylation reaction catalyzed by the serine-carboxyl peptidase kumamolisin-As. Biochemistry 46 (2007) 3784-3792
26. Siezen R.J., Renckens B., and Boekhorst J. Evolution of prokaryotic subtilases: genome-wide analysis reveals novel subfamilies with different catalytic residues. Proteins 67 (2007) 681-694
27. Im Y.J., Na Y., Kang G.B., Rho S.H., Kim M.K., Lee J.H., Chung C.H., and Eom S.H. The active site of a lon protease from Methanococcus jannaschii distinctly differs from the canonical catalytic Dyad of Lon proteases. J Biol Chem 279 (2004) 53451-53457
28. Botos I., Melnikov E.E., Cherry S., Kozlov S., Makhovskaya O.V., Tropea J.E., Gustchina A., Rotanova T.V., and Wlodawer A. Atomic-resolution crystal structure of the proteolytic domain of Archaeoglobus fulgidus lon reveals the conformational variability in the active sites of lon proteases. J Mol Biol 351 (2005) 144-157. The structures of a native B-type Lon protease and of several mutants reveal differences in the conformation of the active-site residues, compared with known Lon structures. The results confirm that B-type Lon employs a Ser-Lys dyad for catalysis. Substrate binding might stabilize the productive conformation of the active site.
29. Yokoyama H., Matsui E., Akiba T., Harata K., and Matsui I. Molecular structure of a novel membrane protease specific for a stomatin homolog from the hyperthermophilic archaeon Pyrococcus horikoshii. J Mol Biol 358 (2006) 1152-1164
30. Feldman A.R., Lee J., Delmas B., and Paetzel M. Crystal structure of a novel viral protease with a serine/lysine catalytic dyad mechanism. J Mol Biol 358 (2006) 1378-1389. This is the first crystal structure of a viral protease that utilizes a mechanism previously seen in bacterial Ser-Lys dyad proteases.
31. Wang Y., Zhang Y., and Ha Y. Crystal structure of a rhomboid family intramembrane protease. Nature 444 (2006) 179-180. The first crystal structure of the intramembrane protease GlpG that cleaves transmembrane domains of other membrane proteins. GlpG uses a Ser-His dyad for catalysis instead of the classic Ser-His-Asn triad, located in the interior of the protein. This active site is laterally accessible by substrate through a V-shaped opening, gated by a loop.
32. Wu Z., Yan N., Feng L., Oberstein A., Yan H., Baker R.P., Gu L., Jeffrey P.D., Urban S., and Shi Y. Structural analysis of a rhomboid family intramembrane protease reveals a gating mechanism for substrate entry. Nat Struct Mol Biol 13 (2006) 1084-1091. This crystal structure captures both the open and the closed conformations of transmembrane GlpG protease, supporting the proposed gating mechanism. Despite its water-excluding transmembrane environment, GlpG manipulates water to hydrolyze the peptide bonds of substrates.
33. Ben-Shem A., Fass D., and Bibi E. Structural basis for intramembrane proteolysis by rhomboid serine proteases. Proc Natl Acad Sci USA 104 (2007) 462-466
34. DeLano W.L. The PyMOL Molecular Graphics System (2002), DeLano Scientific, San Carlos, CA
35. Lemieux M.J., Fischer S.J., Cherney M.M., Bateman K.S., and James M.N. The crystal structure of the rhomboid peptidase from Haemophilus influenzae provides insight into intramembrane proteolysis. Proc Natl Acad Sci USA 104 (2007) 750-754