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. 1994 Jan;3(1):118–125. doi: 10.1002/pro.5560030115

Positions of His-64 and a bound water in human carbonic anhydrase II upon binding three structurally related inhibitors.

G M Smith 1, R S Alexander 1, D W Christianson 1, B M McKeever 1, G S Ponticello 1, J P Springer 1, W C Randall 1, J J Baldwin 1, C N Habecker 1
PMCID: PMC2142482  PMID: 8142888

Abstract

The 3-dimensional structure of human carbonic anhydrase II (HCAII; EC 4.2.1.1) complexed with 3 structurally related inhibitors, 1a, 1b, and 1c, has been determined by X-ray crystallographic methods. The 3 inhibitors (1a = C8H12N2O4S3) vary only in the length of the substituent on the 4-amino group: 1a, proton; 1b, methyl; and 1c, ethyl. The binding constants (Ki's) for 1a, 1b, and 1c to HCAII are 1.52, 1.88, and 0.37 nM, respectively. These structures were solved to learn if any structural cause could be found for the difference in binding. In the complex with inhibitors 1a and 1b, electron density can be observed for His-64 and a bound water molecule in the native positions. When inhibitor 1c is bound, the side chain attached to the 4-amino group is positioned so that His-64 can only occupy the alternate position and the bound water is absent. While a variety of factors contribute to the observed binding constants, the major reason 1c binds tighter to HCAII than does 1a or 1b appears to be entropy: the increase in entropy when the bound water molecule is released contributes to the increase in binding and overcomes the small penalty for putting the His-64 side chain in a higher energy state.

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Selected References

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  1. Baldwin J. J., Ponticello G. S., Anderson P. S., Christy M. E., Murcko M. A., Randall W. C., Schwam H., Sugrue M. F., Springer J. P., Gautheron P. Thienothiopyran-2-sulfonamides: novel topically active carbonic anhydrase inhibitors for the treatment of glaucoma. J Med Chem. 1989 Dec;32(12):2510–2513. doi: 10.1021/jm00132a003. [DOI] [PubMed] [Google Scholar]
  2. Bernstein F. C., Koetzle T. F., Williams G. J., Meyer E. F., Jr, Brice M. D., Rodgers J. R., Kennard O., Shimanouchi T., Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol. 1977 May 25;112(3):535–542. doi: 10.1016/s0022-2836(77)80200-3. [DOI] [PubMed] [Google Scholar]
  3. Bott R., Subramanian E., Davies D. R. Three-dimensional structure of the complex of the Rhizopus chinensis carboxyl proteinase and pepstatin at 2.5-A resolution. Biochemistry. 1982 Dec 21;21(26):6956–6962. doi: 10.1021/bi00269a052. [DOI] [PubMed] [Google Scholar]
  4. Brünger A. T., Krukowski A., Erickson J. W. Slow-cooling protocols for crystallographic refinement by simulated annealing. Acta Crystallogr A. 1990 Jul 1;46(Pt 7):585–593. doi: 10.1107/s0108767390002355. [DOI] [PubMed] [Google Scholar]
  5. Hendrickson W. A. Stereochemically restrained refinement of macromolecular structures. Methods Enzymol. 1985;115:252–270. doi: 10.1016/0076-6879(85)15021-4. [DOI] [PubMed] [Google Scholar]
  6. James M. N., Sielecki A. R. Structure and refinement of penicillopepsin at 1.8 A resolution. J Mol Biol. 1983 Jan 15;163(2):299–361. doi: 10.1016/0022-2836(83)90008-6. [DOI] [PubMed] [Google Scholar]
  7. Krebs J. F., Fierke C. A., Alexander R. S., Christianson D. W. Conformational mobility of His-64 in the Thr-200----Ser mutant of human carbonic anhydrase II. Biochemistry. 1991 Sep 24;30(38):9153–9160. doi: 10.1021/bi00102a005. [DOI] [PubMed] [Google Scholar]
  8. Liljas A., Kannan K. K., Bergstén P. C., Waara I., Fridborg K., Strandberg B., Carlbom U., Järup L., Lövgren S., Petef M. Crystal structure of human carbonic anhydrase C. Nat New Biol. 1972 Feb 2;235(57):131–137. doi: 10.1038/newbio235131a0. [DOI] [PubMed] [Google Scholar]
  9. Maren T. H. Carbonic anhydrase: chemistry, physiology, and inhibition. Physiol Rev. 1967 Oct;47(4):595–781. doi: 10.1152/physrev.1967.47.4.595. [DOI] [PubMed] [Google Scholar]
  10. Osborne W. R., Tashian R. E. An improved method for the purification of carbonic anhydrase isozymes by affinity chromatography. Anal Biochem. 1975 Mar;64(1):297–303. doi: 10.1016/0003-2697(75)90434-0. [DOI] [PubMed] [Google Scholar]
  11. Pocker Y., Sarkanen S. Carbonic anhydrase: structure catalytic versatility, and inhibition. Adv Enzymol Relat Areas Mol Biol. 1978;47:149–274. doi: 10.1002/9780470122921.ch3. [DOI] [PubMed] [Google Scholar]
  12. Ponticello G. S., Freedman M. B., Habecker C. N., Lyle P. A., Schwam H., Varga S. L., Christy M. E., Randall W. C., Baldwin J. J. Thienothiopyran-2-sulfonamides: a novel class of water-soluble carbonic anhydrase inhibitors. J Med Chem. 1987 Apr;30(4):591–597. doi: 10.1021/jm00387a002. [DOI] [PubMed] [Google Scholar]
  13. Prugh J. D., Hartman G. D., Mallorga P. J., McKeever B. M., Michelson S. R., Murcko M. A., Schwam H., Smith R. L., Sondey J. M., Springer J. P. New isomeric classes of topically active ocular hypotensive carbonic anhydrase inhibitors: 5-substituted thieno[2,3-b]thiophene-2-sulfonamides and 5-substituted thieno[3,2-b]thiophene-2-sulfonamides. J Med Chem. 1991 Jun;34(6):1805–1818. doi: 10.1021/jm00110a008. [DOI] [PubMed] [Google Scholar]
  14. Rich D. H. Pepstatin-derived inhibitors of aspartic proteinases. A close look at an apparent transition-state analogue inhibitor. J Med Chem. 1985 Mar;28(3):263–273. doi: 10.1021/jm00381a001. [DOI] [PubMed] [Google Scholar]
  15. Tu C. K., Silverman D. N., Forsman C., Jonsson B. H., Lindskog S. Role of histidine 64 in the catalytic mechanism of human carbonic anhydrase II studied with a site-specific mutant. Biochemistry. 1989 Sep 19;28(19):7913–7918. doi: 10.1021/bi00445a054. [DOI] [PubMed] [Google Scholar]
  16. Weber A. E., Halgren T. A., Doyle J. J., Lynch R. J., Siegl P. K., Parsons W. H., Greenlee W. J., Patchett A. A. Design and synthesis of P2-P1'-linked macrocyclic human renin inhibitors. J Med Chem. 1991 Sep;34(9):2692–2701. doi: 10.1021/jm00113a005. [DOI] [PubMed] [Google Scholar]

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