Abstract
The large HAD (haloacid dehalogenase) superfamily of hydrolases comprises P-type ATPases, phosphatases, epoxide hydrolases and L-2-haloacid dehalogenases. A comparison of the three-dimensional structure of L-2-haloacid dehalogenase with that of the response regulator protein CheY allowed the assignment of a conserved pair of aspartate residues as the Mg2+-binding site in the P-type ATPase and phosphatase members of the superfamily. From the resulting model of the active site, a conserved serine/threonine residue is suggested to be involved in phosphate binding, and a mechanism comprising a phosphoaspartate intermediate is postulated.
Full Text
The Full Text of this article is available as a PDF (180.1 KB).
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Aravind L., Galperin M. Y., Koonin E. V. The catalytic domain of the P-type ATPase has the haloacid dehalogenase fold. Trends Biochem Sci. 1998 Apr;23(4):127–129. doi: 10.1016/s0968-0004(98)01189-x. [DOI] [PubMed] [Google Scholar]
- Asano S., Tega Y., Konishi K., Fujioka M., Takeguchi N. Functional expression of gastric H+,K(+)-ATPase and site-directed mutagenesis of the putative cation binding site and catalytic center. J Biol Chem. 1996 Feb 2;271(5):2740–2745. doi: 10.1074/jbc.271.5.2740. [DOI] [PubMed] [Google Scholar]
- Auer M., Scarborough G. A., Kühlbrandt W. Three-dimensional map of the plasma membrane H+-ATPase in the open conformation. Nature. 1998 Apr 23;392(6678):840–843. doi: 10.1038/33967. [DOI] [PubMed] [Google Scholar]
- Bellsolell L., Prieto J., Serrano L., Coll M. Magnesium binding to the bacterial chemotaxis protein CheY results in large conformational changes involving its functional surface. J Mol Biol. 1994 May 13;238(4):489–495. doi: 10.1006/jmbi.1994.1308. [DOI] [PubMed] [Google Scholar]
- Collet J. F., Gerin I., Rider M. H., Veiga-da-Cunha M., Van Schaftingen E. Human L-3-phosphoserine phosphatase: sequence, expression and evidence for a phosphoenzyme intermediate. FEBS Lett. 1997 May 26;408(3):281–284. doi: 10.1016/s0014-5793(97)00438-9. [DOI] [PubMed] [Google Scholar]
- Collet J. F., Stroobant V., Pirard M., Delpierre G., Van Schaftingen E. A new class of phosphotransferases phosphorylated on an aspartate residue in an amino-terminal DXDX(T/V) motif. J Biol Chem. 1998 Jun 5;273(23):14107–14112. doi: 10.1074/jbc.273.23.14107. [DOI] [PubMed] [Google Scholar]
- Dahms A. S., Kanazawa T., Boyer P. D. Source of the oxygen in the C-O-P linkage of the acyl phosphate in transport adenosine triphosphatases. J Biol Chem. 1973 Oct 10;248(19):6592–6595. [PubMed] [Google Scholar]
- Emsley J., King S. L., Bergelson J. M., Liddington R. C. Crystal structure of the I domain from integrin alpha2beta1. J Biol Chem. 1997 Nov 7;272(45):28512–28517. doi: 10.1074/jbc.272.45.28512. [DOI] [PubMed] [Google Scholar]
- Guha S. K., Rose Z. B. The synthesis of mannose 1-phosphate in brain. Arch Biochem Biophys. 1985 Nov 15;243(1):168–173. doi: 10.1016/0003-9861(85)90785-4. [DOI] [PubMed] [Google Scholar]
- Hisano T., Hata Y., Fujii T., Liu J. Q., Kurihara T., Esaki N., Soda K. Crystal structure of L-2-haloacid dehalogenase from Pseudomonas sp. YL. An alpha/beta hydrolase structure that is different from the alpha/beta hydrolase fold. J Biol Chem. 1996 Aug 23;271(34):20322–20330. doi: 10.1074/jbc.271.34.20322. [DOI] [PubMed] [Google Scholar]
- Holm L., Sander C. Protein structure comparison by alignment of distance matrices. J Mol Biol. 1993 Sep 5;233(1):123–138. doi: 10.1006/jmbi.1993.1489. [DOI] [PubMed] [Google Scholar]
- Koonin E. V., Tatusov R. L. Computer analysis of bacterial haloacid dehalogenases defines a large superfamily of hydrolases with diverse specificity. Application of an iterative approach to database search. J Mol Biol. 1994 Nov 18;244(1):125–132. doi: 10.1006/jmbi.1994.1711. [DOI] [PubMed] [Google Scholar]
- Kurihara T., Liu J. Q., Nardi-Dei V., Koshikawa H., Esaki N., Soda K. Comprehensive site-directed mutagenesis of L-2-halo acid dehalogenase to probe catalytic amino acid residues. J Biochem. 1995 Jun;117(6):1317–1322. doi: 10.1093/oxfordjournals.jbchem.a124861. [DOI] [PubMed] [Google Scholar]
- Lee J. O., Rieu P., Arnaout M. A., Liddington R. Crystal structure of the A domain from the alpha subunit of integrin CR3 (CD11b/CD18). Cell. 1995 Feb 24;80(4):631–638. doi: 10.1016/0092-8674(95)90517-0. [DOI] [PubMed] [Google Scholar]
- Liu J. Q., Kurihara T., Miyagi M., Esaki N., Soda K. Reaction mechanism of L-2-haloacid dehalogenase of Pseudomonas sp. YL. Identification of Asp10 as the active site nucleophile by 18O incorporation experiments. J Biol Chem. 1995 Aug 4;270(31):18309–18312. [PubMed] [Google Scholar]
- Liu J. Q., Kurihara T., Miyagi M., Tsunasawa S., Nishihara M., Esaki N., Soda K. Paracatalytic inactivation of L-2-haloacid dehalogenase from Pseudomonas sp. YL by hydroxylamine. Evidence for the formation of an ester intermediate. J Biol Chem. 1997 Feb 7;272(6):3363–3368. doi: 10.1074/jbc.272.6.3363. [DOI] [PubMed] [Google Scholar]
- Lutsenko S., Kaplan J. H. Organization of P-type ATPases: significance of structural diversity. Biochemistry. 1995 Dec 5;34(48):15607–15613. doi: 10.1021/bi00048a001. [DOI] [PubMed] [Google Scholar]
- MacGregor E. A., Jespersen H. M., Svensson B. A circularly permuted alpha-amylase-type alpha/beta-barrel structure in glucan-synthesizing glucosyltransferases. FEBS Lett. 1996 Jan 15;378(3):263–266. doi: 10.1016/0014-5793(95)01428-4. [DOI] [PubMed] [Google Scholar]
- Munson K. B., Gutierrez C., Balaji V. N., Ramnarayan K., Sachs G. Identification of an extracytoplasmic region of H+,K(+)-ATPase labeled by a K(+)-competitive photoaffinity inhibitor. J Biol Chem. 1991 Oct 5;266(28):18976–18988. [PubMed] [Google Scholar]
- Møller J. V., Juul B., le Maire M. Structural organization, ion transport, and energy transduction of P-type ATPases. Biochim Biophys Acta. 1996 May 6;1286(1):1–51. doi: 10.1016/0304-4157(95)00017-8. [DOI] [PubMed] [Google Scholar]
- Norman E. G., Colman B. Purification and Characterization of Phosphoglycolate Phosphatase from the Cyanobacterium Coccochloris peniocystis. Plant Physiol. 1991 Mar;95(3):693–698. doi: 10.1104/pp.95.3.693. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Pai E. F., Krengel U., Petsko G. A., Goody R. S., Kabsch W., Wittinghofer A. Refined crystal structure of the triphosphate conformation of H-ras p21 at 1.35 A resolution: implications for the mechanism of GTP hydrolysis. EMBO J. 1990 Aug;9(8):2351–2359. doi: 10.1002/j.1460-2075.1990.tb07409.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ridder I. S., Rozeboom H. J., Kalk K. H., Janssen D. B., Dijkstra B. W. Three-dimensional structure of L-2-haloacid dehalogenase from Xanthobacter autotrophicus GJ10 complexed with the substrate-analogue formate. J Biol Chem. 1997 Dec 26;272(52):33015–33022. doi: 10.1074/jbc.272.52.33015. [DOI] [PubMed] [Google Scholar]
- SKOU J. C. The influence of some cations on an adenosine triphosphatase from peripheral nerves. Biochim Biophys Acta. 1957 Feb;23(2):394–401. doi: 10.1016/0006-3002(57)90343-8. [DOI] [PubMed] [Google Scholar]
- Schimming S., Schwarz W. H., Staudenbauer W. L. Structure of the Clostridium thermocellum gene licB and the encoded beta-1,3-1,4-glucanase. A catalytic region homologous to Bacillus lichenases joined to the reiterated domain of clostridial cellulases. Eur J Biochem. 1992 Feb 15;204(1):13–19. doi: 10.1111/j.1432-1033.1992.tb16600.x. [DOI] [PubMed] [Google Scholar]
- Shigekawa M., Wakabayashi S., Nakamura H. Effect of divalent cation bound to the ATPase of sarcoplasmic reticulum. Activation of phosphoenzyme hydrolysis by Mg2+. J Biol Chem. 1983 Dec 10;258(23):14157–14161. [PubMed] [Google Scholar]
- Shirakihara Y., Evans P. R. Crystal structure of the complex of phosphofructokinase from Escherichia coli with its reaction products. J Mol Biol. 1988 Dec 20;204(4):973–994. doi: 10.1016/0022-2836(88)90056-3. [DOI] [PubMed] [Google Scholar]
- Stock A. M., Martinez-Hackert E., Rasmussen B. F., West A. H., Stock J. B., Ringe D., Petsko G. A. Structure of the Mg(2+)-bound form of CheY and mechanism of phosphoryl transfer in bacterial chemotaxis. Biochemistry. 1993 Dec 14;32(49):13375–13380. doi: 10.1021/bi00212a001. [DOI] [PubMed] [Google Scholar]
- Stock A. M., Mowbray S. L. Bacterial chemotaxis: a field in motion. Curr Opin Struct Biol. 1995 Dec;5(6):744–751. doi: 10.1016/0959-440x(95)80006-9. [DOI] [PubMed] [Google Scholar]
- Vandercammen A., François J., Hers H. G. Characterization of trehalose-6-phosphate synthase and trehalose-6-phosphate phosphatase of Saccharomyces cerevisiae. Eur J Biochem. 1989 Jul 1;182(3):613–620. doi: 10.1111/j.1432-1033.1989.tb14870.x. [DOI] [PubMed] [Google Scholar]
- Volz K. Structural conservation in the CheY superfamily. Biochemistry. 1993 Nov 9;32(44):11741–11753. doi: 10.1021/bi00095a001. [DOI] [PubMed] [Google Scholar]
- Wakabayashi S., Shigekawa M. Effect of metal bound to the substrate site on calcium release from the phosphoenzyme intermediate of sarcoplasmic reticulum ATPase. J Biol Chem. 1987 Aug 25;262(24):11524–11531. [PubMed] [Google Scholar]
- Zhang P., Toyoshima C., Yonekura K., Green N. M., Stokes D. L. Structure of the calcium pump from sarcoplasmic reticulum at 8-A resolution. Nature. 1998 Apr 23;392(6678):835–839. doi: 10.1038/33959. [DOI] [PubMed] [Google Scholar]