Chapter 9

Where to Start

Stroud, R. M. 1974. A family of protein-cutting proteins. Sci. Am. 231(1):74–88.

Kraut, J. 1977. Serine proteases: Structure and mechanism of catalysis. Annu. Rev. Biochem. 46:331–358.

Lindskog, S. 1997. Structure and mechanism of carbonic anhydrase. Pharmacol. Ther. 74:1–20.

Jeltsch, A., Alves, J., Maass, G., and Pingoud, A. 1992. On the catalytic mechanism of EcoRI and EcoRV: A detailed proposal based on biochemical results, structural data and molecular modelling. FEBS Lett. 304:4–8.

Bauer, C. B., Holden, H. M., Thoden, J. B., Smith, R., and Rayment, I. 2000. X-ray structures of the apo and MgATP-bound states of Dictyostelium discoideum myosin motor domain. J. Biol. Chem. 275:38494–38499.

Lolis, E., and Petsko, G. A. 1990. Transition-state analogues in protein crystallography: Probes of the structural source of enzyme catalysis. Annu. Rev. Biochem. 59:597–630.

Books

Fersht, A. 1999. Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding. W. H. Freeman and Company.

B8

Silverman, R. B. 2000. The Organic Chemistry of Enzyme-Catalyzed Reactions. Academic Press.

Page, M., and Williams, A. 1997. Organic and Bio-organic Mechanisms. Addison Wesley Longman.

Chymotrypsin and Other Serine Proteases

Fastrez, J., and Fersht, A. R. 1973. Demonstration of the acyl-enzyme mechanism for the hydrolysis of peptides and anilides by chymotrypsin. Biochemistry 12:2025–2034.

Sigler, P. B., Blow, D. M., Matthews, B. W., and Henderson, R. 1968. Structure of crystalline-chymotrypsin II: A preliminary report including a hypothesis for the activation mechanism. J. Mol. Biol. 35:143–164.

Kossiakoff, A. A., and Spencer, S. A. 1981. Direct determination of the protonation states of aspartic acid-102 and histidine-57 in the tetrahedral intermediate of the serine proteases: Neutron structure of trypsin. Biochemistry 20:6462–6474.

Carter, P., and Wells, J. A. 1988. Dissecting the catalytic triad of a serine protease. Nature 332:564–568.

Carter, P., and Wells, J. A. 1990. Functional interaction among catalytic residues in subtilisin BPN′. Proteins 7:335–342.

Koepke, J., Ermler, U., Warkentin, E., Wenzl, G., and Flecker, P. 2000. Crystal structure of cancer chemopreventive Bowman-Birk inhibitor in ternary complex with bovine trypsin at 2.3 Å resolution: Structural basis of Janus-faced serine protease inhibitor specificity. J. Mol. Biol. 298:477–491.

Gaboriaud, C., Rossi, V., Bally, I., Arlaud, G. J., and Fontecilla-Camps, J. C. 2000. Crystal structure of the catalytic domain of human complement C1s: A serine protease with a handle. EMBO J. 19:1755–1765.

Bachovchin D. A., and Cravatt B. F. 2012. The pharmacological landscape and therapeutic potential of serine hydrolases. Nature Reviews Drug Discovery. 11:52–68.

Other Proteases

Vega, S., Kang, L. W., Velazquez-Campoy, A., Kiso, Y., Amzel, L. M., and Freire, E. 2004. A structural and thermodynamic escape mechanism from a drug resistant mutation of the HIV-1 protease. Proteins 55:594–602.

Kamphuis, I. G., Kalk, K. H., Swarte, M. B., and Drenth, J. 1984. Structure of papain refined at 1.65 Å resolution. J. Mol. Biol. 179:233–256.

Kamphuis, I. G., Drenth, J., and Baker, E. N. 1985. Thiol proteases: Comparative studies based on the high-resolution structures of papain and actinidin, and on amino acid sequence information for cathepsins B and H, and stem bromelain. J. Mol. Biol. 182:317–329.

Sivaraman, J., Nagler, D. K., Zhang, R., Menard, R., and Cygler, M. 2000. Crystal structure of human procathepsin X: A cysteine protease with the proregion covalently linked to the active site cysteine. J. Mol. Biol. 295:939–951.

Davies, D. R. 1990. The structure and function of the aspartic proteinases. Annu. Rev. Biophys. Biophys. Chem. 19:189–215.

Dorsey, B. D., Levin, R. B., McDaniel, S. L., Vacca, J. P., Guare, J. P., Darke, P. L., Zugay, J. A., Emini, E. A., Schleif, W. A., Quintero, J. C., et al. 1994. L-735,524: The design of a potent and orally bio-available HIV protease inhibitor. J. Med. Chem. 37:3443–3451.

Chen, Z., Li, Y., Chen, E., Hall, D. L., Darke, P. L., Culberson, C., Shafer, J. A., and Kuo, L. C. 1994. Crystal structure at 1.9-Å resolution of human immunodeficiency virus (HIV) II protease complexed with L-735,524, an orally bioavailable inhibitor of the HIV proteases. J. Biol. Chem. 269:26344–26348.

Ollis, D. L., Cheah, E., Cygler, M., Dijkstra, B., Frolow, F., Franken, S. M., Harel, M., Remington, S. J., Silman, I., Schrag, J., et al. 1992. The α/β hydrolase fold. Protein Eng. 5:197–211.

Carbonic Anhydrase

Lindskog, S., and Coleman, J. E. 1973. The catalytic mechanism of carbonic anhydrase. Proc. Natl. Acad. Sci. U.S.A. 70:2505–2508.

Kannan, K. K., Notstrand, B., Fridborg, K., Lovgren, S., Ohlsson, A., and Petef, M. 1975. Crystal structure of human erythrocyte carbonic anhydrase B: Three-dimensional structure at a nominal 2.2-Å resolution. Proc. Natl. Acad. Sci. U.S.A. 72:51–55.

Boriack-Sjodin, P. A., Zeitlin, S., Chen, H. H., Crenshaw, L., Gross, S., Dantanarayana, A., Delgado, P., May, J. A., Dean, T., and Christianson, D. W. 1998. Structural analysis of inhibitor binding to human carbonic anhydrase II. Protein Sci. 7:2483–2489.

Wooley, P. 1975. Models for metal ion function in carbonic anhydrase. Nature 258:677–682.

Jonsson, B. H., Steiner, H., and Lindskog, S. 1976. Participation of buffer in the catalytic mechanism of carbonic anhydrase. FEBS Lett. 64:310–314.

Sly, W. S., and Hu, P. Y. 1995. Human carbonic anhydrases and carbonic anhydrase deficiencies. Annu. Rev. Biochem. 64:375–401.

Maren, T. H. 1988. The kinetics of HCO3 synthesis related to fluid secretion, pH control, and CO2 elimination. Annu. Rev. Physiol. 50:695–717.

Roy, A., and Taraphder, S. 2010. Role of protein motions on proton transfer pathways in human carbonic anhydrase II. Biochim. Biophys. Acta 1804:352–361.

Restriction Enzymes

Selvaraj, S., Kono, H., and Sarai, A. 2002. Specificity of protein-DNA recognition revealed by structure-based potentials: Symmetric/asymmetric and cognate/non-cognate binding. J. Mol. Biol. 322:907–915.

Winkler, F. K., Banner, D. W., Oefner, C., Tsernoglou, D., Brown, R. S., Heathman, S. P., Bryan, R. K., Martin, P. D., Petratos, K., and Wilson, K. S. 1993. The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments. EMBO J. 12:1781–1795.

Kostrewa, D., and Winkler, F. K. 1995. Mg2+ binding to the active site of EcoRV endonuclease: A crystallographic study of complexes with substrate and product DNA at 2 Å resolution. Biochemistry 34:683–696.

Athanasiadis, A., Vlassi, M., Kotsifaki, D., Tucker, P. A., Wilson, K. S., and Kokkinidis, M. 1994. Crystal structure of PvuII endonuclease reveals extensive structural homologies to EcoRV. Nat. Struct. Biol. 1:469–475.

Sam, M. D., and Perona, J. J. 1999. Catalytic roles of divalent metal ions in phosphoryl transfer by EcoRV endonuclease. Biochemistry 38:6576–6586.

Jeltsch, A., and Pingoud, A. 1996. Horizontal gene transfer contributes to the wide distribution and evolution of type II restriction-modification systems. J. Mol. Evol. 42:91–96.

Advani S., Mishra P., Dubey S., and Thakur S. 2010. Categoric prediction of metal ion mechanisms in the active sites of 17 select type II restriction endonucleases. Biochem. Biophys. Res. Commun. 402:177–179.

Myosins

Grigorenko, B. L., Rogov, A. V., Topol, I. A., Burt, S. K., Martinez, H. M., and Nemukhin, A. V. 2007. Mechanism of the myosin catalyzed hydrolysis of ATP as rationalized by molecular modeling. Proc. Natl. Acad. Sci. U.S.A. 104:7057–7061.

Gulick, A. M., Bauer, C. B., Thoden, J. B., and Rayment, I. 1997. X-ray structures of the MgADP, MgATPγ S, and MgAMPPNP complexes of the Dictyostelium discoideum myosin motor domain. Biochemistry 36:11619–11628.

Kovacs, M., Malnasi-Csizmadia, A., Woolley, R. J., and Bagshaw, C. R. 2002. Analysis of nucleotide binding to Dictyostelium myosin II motor domains containing a single tryptophan near the active site. J. Biol. Chem. 277:28459–28467.

B9

Kuhlman, P. A., and Bagshaw, C. R. 1998. ATPase kinetics of the Dictyostelium discoideum myosin II motor domain. J. Muscle Res. Cell Motil. 19:491–504.

Smith, C. A., and Rayment, I. 1996. X-ray structure of the magnesium(II) ADP vanadate complex of the Dictyostelium discoideum myosin motor domain to 1.9 Å resolution. Biochemistry 35:5404–5417.

Yildiz A., Forkey J. N., McKinney S. A., Ha T., Goldman Y. E., and Selvin P. R. 2003. Myosin V walks hand-over-hand: Single fluorophore imaging with 1.5-nm localization. Science. 300:2061–2065.