An extracellular calcium-binding domain in bacteria with a distant relationship to EF-hands

FEMS Microbiology Letters

Volumn 221, Issue 1, 2003, Pages 103-110

  Rigden, Daniel J ^a   Jedrzejas, Mark J ^b   Galperin, Michael Y ^c  

^a EMBRAPA RECURSOS GENÉTICOS E BIOTECNOLOGIA   (Brazil)

^b CHILDREN S HOSPITAL OAKLAND RESEARCH INSTITUTE   (United States)

^c NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

Calcium binding site; Calmodulin; Cell envelope; Evolution; Genome analysis; Nuclease; Protein domain; S layer

Indexed keywords

BACTERIAL PROTEIN; CALMODULIN;

AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; CALCIUM BINDING; CONTROLLED STUDY; EXTRACELLULAR CALCIUM; GRAM NEGATIVE BACTERIUM; GRAM POSITIVE BACTERIUM; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN MOTIF; PROTEIN STRUCTURE; SEQUENCE ANALYSIS;

BACILLUS SUBTILIS;

EID: 0037432703     PISSN: 03781097     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0378-1097(03)00160-5     Document Type: Article

References (46)

1. Silver S., Phung L.T. Bacterial heavy metal resistance: new surprises. Annu. Rev. Microbiol. 50:1996;753-789.
2. Harrison M.D., Jones C.E., Solioz M., Dameron C.T. Intracellular copper routing: the role of copper chaperones. Trends Biochem. Sci. 25:2000;29-32.
3. Jordan I.K., Natale D.A., Koonin E.V., Galperin M.Y. Independent evolution of heavy metal-associated domains in copper chaperones and copper-transporting ATPases. J. Mol. Evol. 53:2001;622-633.
4. Andrews S.C. Iron storage in bacteria. Adv. Microb. Physiol. 40:1998;281-351.
5. Silver, S. (1977) Calcium transport in microorganisms. In: Microorganisms and Minerals (Weinberg, E.D., Ed.), pp. 49-103. Marcel Dekker Publ., New York.
6. Smith R.J. Calcium and bacteria. Adv. Microb. Physiol. 37:1995;83-133.
7. Baumann U., Wu S., Flaherty K.M., McKay D.B. Three-dimensional structure of the alkaline protease of Pseudomonas aeruginosa: a two-domain protein with a calcium binding parallel beta roll motif. EMBO J. 12:1993;3357-3364.
8. Kawasaki H., Nakayama S., Kretsinger R.H. Classification and evolution of EF-hand proteins. Biometals. 11:1998;277-295.
9. 2+ binding. Biometals. 11:1998;297-318.
10. Lewit-Bentley A., Rety S. EF-hand calcium-binding proteins. Curr. Opin. Struct. Biol. 10:2000;637-643.
11. Swan D.G., Hale R.S., Dhillon N., Leadlay P.F. A bacterial calcium-binding protein homologous to calmodulin. Nature. 329:1987;84-85.
12. Xi C., Schoeters E., Vanderleyden J., Michiels J. Symbiosis-specific expression of Rhizobium etli casA encoding a secreted calmodulin-related protein. Proc. Natl. Acad. Sci. USA. 97:2000;11114-11119.
13. Aitio H., Annila A., Heikkinen S., Thulin E., Drakenberg T., Kilpelainen I. NMR assignments, secondary structure, and global fold of calerythrin, an EF-hand calcium-binding protein from Saccharopolyspora erythraea. Protein Sci. 8:1999;2580-2588.
14. Yang K. Prokaryotic calmodulins: recent developments and evolutionary implications. J. Mol. Microbiol. Biotechnol. 3:2001;457-459.
15. 2+ in bacteria: a role for EF-hand proteins? Trends Microbiol. 10:2002;87-93.
16. van Asselt E.J., Dijkstra A.J., Kalk K.H., Takacs B., Keck W., Dijkstra B.W. Crystal structure of Escherichia coli lytic transglycosylase Slt35 reveals a lysozyme-like catalytic domain with an EF-hand. Struct. Fold. Des. 7:1999;1167-1180.
17. Vyas N.K., Vyas M.N., Quiocho F.A. A novel calcium binding site in the galactose-binding protein of bacterial transport and chemotaxis. Nature. 327:1987;635-638.
18. Petosa C., Collier R.J., Klimpel K.R., Leppla S.H., Liddington R.C. Crystal structure of the anthrax toxin protective antigen. Nature. 385:1997;833-838.
19. Lytle B.L., Volkman B.F., Westler W.M., Heckman M.P., Wu J.H. Solution structure of a type I dockerin domain, a novel prokaryotic, extracellular calcium-binding domain. J. Mol. Biol. 307:2001;745-753.
20. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zheng Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST - A new generation of protein database search programs. Nucleic Acids Res. 25:1997;3389-3402.
21. Letunic I., Goodstadt L., Dickens N.J., Doerks T., Schultz J., Mott R., Ciccarelli F., Copley R.R., Ponting C.P., Bork P. Recent improvements to the SMART domain-based sequence annotation resource. Nucleic Acids Res. 30:2002;242-244.
22. Bateman A., Birney E., Cerruti L., Durbin R., Etwiller L., Eddy S.R., Griffiths-Jones S., Howe K.L., Marshall M., Sonnhammer E.L. The Pfam protein families database. Nucleic Acids Res. 30:2002;276-280.
23. Nielsen H., Engelbrecht J., Brunak S., von Heijne G. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng. 10:1997;1-6.
24. Jones D.T. Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292:1999;195-202.
25. Pollastri G., Przybylski D., Rost B., Baldi P. Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles. Proteins. 47:2002;228-235.
26. Koonin, E.V. and Galperin, M.Y. (2002) Sequence - Evolution - Function. Computational Approaches in Comparative Genomics. Kluwer Academic Publishers, Boston, MA.
27. Brown N.P., Leroy C., Sander C. MView: a web-compatible database search or multiple alignment viewer. Bioinformatics. 14:1998;380-381.
28. Hynes T.R., Fox R.O. The crystal structure of staphylococcal nuclease refined at 1.7 A resolution. Proteins. 10:1991;92-105.
29. Sakamoto J.J., Sasaki M., Tsuchido T. Purification and characterization of a Bacillus subtilis 168 nuclease, YokF, involved in chromosomal DNA degradation and cell death caused by thermal shock treatments. J. Biol. Chem. 276:2001;47046-47051.
30. Sleytr U.B., Beveridge T.J. Bacterial S-layers. Trends Microbiol. 7:1999;253-260.
31. Kosugi A., Murashima K., Tamaru Y., Doi R.H. Cell-surface-anchoring role of N-terminal surface layer homology domains of Clostridium cellulovorans EngE. J. Bacteriol. 184:2002;884-888.
32. Walker S.G., Karunaratne D.N., Ravenscroft N., Smit J. Characterization of mutants of Caulobacter crescentus defective in surface attachment of the paracrystalline surface layer. J. Bacteriol. 176:1994;6312-6323.
33. Aravind L. An evolutionary classification of the metallo-beta-lactamase fold proteins. In Silico Biol. 1:1999;69-91.
34. Hahn J., Inamine G., Kozlov Y., Dubnau D. Characterization of comE, a late competence operon of Bacillus subtilis required for the binding and uptake of transforming DNA. Mol. Microbiol. 10:1993;99-111.
35. Jekel M., Wackernagel W. The periplasmic endonuclease I of Escherichia coli has amino-acid sequence homology to the extracellular DNases of Vibrio cholerae and Aeromonas hydrophila. Gene. 154:1995;55-59.
36. Schindelin H., Jiang W., Inouye M., Heinemann U. Crystal structure of CspA, the major cold shock protein of Escherichia coli. Proc. Natl. Acad. Sci. USA. 91:1994;5119-5123.
37. Weber M.H., Fricke I., Doll N., Marahiel M.A. CSDBase: an interactive database for cold shock domain-containing proteins and the bacterial cold shock response. Nucleic Acids Res. 30:2002;375-378.
38. Sommerville J. Activities of cold-shock domain proteins in translation control. Bioessays. 21:1999;319-325.
39. Sigrist C.J., Cerutti L., Hulo N., Gattiker A., Falquet L., Pagni M., Bairoch A., Bucher P. PROSITE: a documented database using patterns and profiles as motif descriptors. Brief Bioinform. 3:2002;265-274.
40. Grishin N.V. Fold change in evolution of protein structures. J. Struct. Biol. 134:2001;167-185.
41. Denessiouk K.A., Rantanen V.V., Johnson M.S. Adenine recognition: a motif present in ATP-, CoA-, NAD-, NADP-, and FAD-dependent proteins. Proteins. 44:2001;282-291.
42. Rodrigues J.J., Ferreira H.B., Farias S.E., Zaha A. A protein with a novel calcium-binding domain associated with calcareous corpuscles in Echinococcus granulosus. Biochem. Biophys. Res. Commun. 237:1997;451-456.
43. Cox J.A., Bairoch A. Sequence similarities in calcium-binding proteins. Nature. 331:1988;491.
44. Crooks, G.E., Hon, G., Chandonia, J.M. and Brenner, S.E. (2003) WebLogo: A sequence logo generator. Genome Res. 13, (in press).
45. Sali A., Blundell T.L. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234:1993;779-815.
46. Meador W.E., Means A.R., Quiocho F.A. Target enzyme recognition by calmodulin: 2.4 A structure of a calmodulin-peptide complex. Science. 257:1992;1251-1255.