The linked conservation of structure and function in a family of high diversity: The monomeric cupredoxins

Structure

Volumn 12, Issue 6, 2004, Pages 917-925

  Gough, Julian ^a   Chothia, Cyrus ^b  

^a RIKEN YOKOHAMA INSTITUTE   (Japan)

^b MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CARRIER PROTEIN; COPPER; CUPREDOXIN; IMMUNOGLOBULIN; MONOMER; PLASTOCYANIN; UNCLASSIFIED DRUG;

ARTICLE; BETA SHEET; BINDING SITE; BIODIVERSITY; CONSERVATION BIOLOGY; HYDROGEN BOND; PHOTOSYNTHESIS; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FUNCTION; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS;

AZURIN; BINDING SITES; COMPUTER SIMULATION; ELECTRON TRANSPORT; HYDROGEN BONDING; MODELS, MOLECULAR; OXYGEN CONSUMPTION; PHOTOSYNTHESIS; PLASTOCYANIN; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 2942589291     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2004.03.029     Document Type: Article

References (29)

1. Adman E.T. Copper protein structures. Adv. Protein Chem. 42:1991;145-197
2. Adman E.T., Stenkamp R.E., Sieker L.C., Jensen L.H. A Crystallographic model for azurin at 3 Å resolution. J. Mol. Biol. 123:1978;35-47
3. Baker E.N. Structure of azurin from Alcaligenes denitrificans refinement at 1.8 (Å) resolution and comparison of the two crystallographically independent molecules. J. Mol. Biol. 203:1988;1071-1095
4. Bond C.S., Blankenship R.E., Freeman H.C., Guss J.M., Maher M.J., Selvaraj F.M., Wilce M.C., Willingham K.M. Crystal structure of auracyanin, a "blue" copper protein from the green thermophilic photosynthetic bacterium Chloroflexus aurantiacus. J. Mol. Biol. 306:2001;47-67
5. Chothia C., Lesk A.M. The evolution of proteins formed by β-sheets. I. plastocyanin and azurin J. Mol. Biol. 160:1982;309-323
6. Chothia C., Gelfand I., Kister A. Structural determinants in the sequences of immunoglobulin variable domain. J. Mol. Biol. 278:1998;457-479
7. Colman P.M., Freeman H.C., Guss J.M., Murata M., Norris V.A., Ramshaw J.A.M., Venkatappa M.P. X-ray crystal structure analysis of plastocyanin at 2.7 Å resolution. Nature. 272:1978;319-324
8. Djebli A., Proctor P., Blake R.C. II, Shoham M. Crystallization and preliminary X-ray crystallographic studies of rusticyanin from Thiobacillus ferrooxidans. J. Mol. Biol. 227:1992;581-582
9. Durley R., Chen L., Lim L.W., Mathews F.S., Davidson V.L. Crystal structure analysis of amicyanin and apoamicyanin from Paracoccus denitrificans at 2.0 Å and 1.8 Å resolution. Protein Sci. 2:1993;739-752
10. Garrett T.P.J., Clingeleffer D.J., Guss J.M., Rogers S., Freeman H.C. The crystal structure of poplar apoplastocyanin at 1.8 Å resolution. J. Biol. Chem. 259:1983;2822-2825
11. Guss J.M., Freeman H.C. Structure of oxidized poplar plastocyanin at 1.6 Å resolution. J. Mol. Biol. 169:1983;521-563
12. Guss J.M., Bartunik H.D., Freeman H.C. Accuracy and precision in protein structure analysis. restrained least-squares refinement of poplar plastocyanin at 1.33 Å resolution Acta Crystallogr. B. 48:1992;790-811
13. Guss J.M., Merritt E.A., Phizackerley R.P., Freeman H.C. The structure of a phytocyanin, the basic blue protein from cucumber, refined at 1.8 Å resolution. J. Mol. Biol. 262:1996;686-705
14. Hart P.J., Nersissian A.M., Herrmann R.G., Nalbandyan R.M., Valentine J.S., Eisenberg D. A missing link in cupredoxins. crystal structure of cucumber stellacyanin at 1.6 Å resolution Protein Sci. 5:1996;2175-2183
15. Hill E.E., Morea V., Chothia C. Sequence conservation in families whose members have little or no sequence similarity. the four-helical cytokines and cytochromes J. Mol. Biol. 322:2002;205-233
16. Holm L., Sander C. Removing near-neighbour redundancy from large protein sequence collections. Bioinformatics. 14:1998;423-429
17. Lee B., Richards F.M. The interpretation of protein structures. estimation of static accessibility J. Mol. Biol. 55:1971;379-400
18. Leung Y.C., Chan C., Reader J.S., Willis A.C., van Spanning R.J., Ferguson S.J., Radford S.E. The pseudoazurin gene from Thiosphaera pantotropha. analysis of upstream putative regulatory sequences and overexpression in Escherichia coli Biochem. J. 321:1997;699-705
19. Miller S., Janin J., Lesk A.M., Chothia C. Interior and surface of monomeric proteins. J. Mol. Biol. 196:1987;641-656
20. Mirny L.A., Shakhnovich E.I. Universally conserved positions in protein folds. reading evolutionary signals about stability, folding kinetics and function J. Mol. Biol. 291:1999;177-196
21. Murphy M.E., Lindley P.F., Adman E.T. Structural comparison of cupredoxin domains. domain recycling to construct proteins with novel functions Protein Sci. 6:1997;761-770
22. Pearson W.R., Lipman D.J. Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. USA. 85:1988;2444-2448
23. Petratos K., Dauter Z., Wilson K.S. Refinement of the structure of pseudoazurin from Alcaligenes faecalis S6 at 1.55 Å resolution. Acta Crystallogr. B. 44:1988;628-636
24. Petratos K., Papadovasilaki M., Dauter Z. The crystal structure of apo-pseudoazurin from Alcaligenes Faecalis S6. FEBS Lett. 368:1995;432-434
25. Ryden L.G. Structure and evolution of the small blue proteins. Lontie R. Copper Proteins and Copper Enzymes Volume 1. 1984;183-214 CRC Press, Boca Raton FL
26. Shepard W.E.B., Kingston R.L., Anderson B.F., Baker E.N. Structure of apo-azurin at 1.8 Å resolution. Acta Crystallogr. D Biol. Crystallogr. 49:1993;331-342
27. Thompson J.D., Higgins D.G., Gibson T.J. Clustal w. improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Res. 22:1994;4673-4680
28. van Driessche G., Hu W., van der Werken G., Selvaraj F., McManus J.D., Blankenship R.E., van Beeumen J.J. Auracyanin, A from the thermopholoc green gliding bacterium Choroflexus aurantiacus represents an unusual class of small blue copper proteins. Protein Sci. 8:1999;947-957
29. Walter R.L., Ealick S.E., Friedman A.M., Blake R.C. II, Proctor P., Shoham M. Multiple wavelength anomalous diffraction (MAD) crystal structure of rusticyanin. a highly oxidizing cupredoxin with extreme acid stability J. Mol. Biol. 263:1996;730-751