Skip Navigation

This Article
Right arrow Abstract Freely available
Right arrow Print PDF (91K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (14)
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Degtyarenko, K. N.
Right arrow Articles by Findlay, J. B.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Degtyarenko, K. N.
Right arrow Articles by Findlay, J. B.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research Pages 233-236  

PROMISE: a database of bioinorganic motifs
Acknowledgements
References

PROMISE: a database of bioinorganic motifs

PROMISE: a database of bioinorganic motifs

K. N. Degtyarenko*, A. C. T. North1 and J. B. C. Findlay1

EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and 1School of Biochemistry and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK

Received September 25, 1998; Accepted September 29, 1998

ABSTRACT

The PROMISE (prosthetic centres and metal ions in protein active sites) database aims to present comprehensive sequence, structural, functional and bibliographic information on metalloproteins and other complex proteins, with an emphasis on active site structure and function. The database is available on the WorldWide Web at http://bioinf.leeds.ac.uk/promise/

PROMISE aims to be a comprehensive information source on bioinorganic motifs in proteins. Its focus is on protein active site structure and on the relationships between polypeptide and prosthetic centre, combining the relevant sequence, 3-D structural and physico-chemical information (1,2). Bioinorganic motifs provide a basis for classification of complex proteins, alternative and complementary to those employed in other `secondary' protein databases (see ref. 1 for comparison of PROMISE with other databases).

As of 15 September 1998, PROMISE version 2.0 contained six major groups (diiron-carboxylate proteins, haem proteins, iron-sulphur proteins, molybdopterin-containing proteins, mononuclear iron proteins and chlorophyll-containing proteins) comprising nine intermediate class entries and 56 protein family entries, each with an associated bibliographic entry (a total of 5403 references). Table 1 presents a full list of entries in PROMISE.

A number of novel bioinorganic motifs and prosthetic groups reported during the last few years have been included in PROMISE 2.0 (Fig. 1). Many entries have been revised, sometimes radically, to reflect the new data. For example, the recent X-ray structure of `prismane' protein has revealed that it does not contain an [Fe6S6] (prismane) cluster (Fig. 2a); instead, it contains an [Fe4S4] cubane cluster and a novel `hybrid' cluster with an unusual mixture of bridging ligands and coordinations (Fig. 2b) (5). Similarly, an [Fe8S8] model for the P-cluster of nitrogenase molybdenum-iron (MoFe) protein (Fig. 2c) was discarded when it was found that the P-cluster exists as an [Fe8S7] cluster in both oxidised and reduced states (Fig. 2d and e) (7). The [Fe8S8] model appears to have resulted from the inappropriate modelling of a mixture of the two P-cluster redox states by a single structure.

PROMISE is available on the WorldWide Web from URL: http://bioinf.leeds.ac.uk/promise/ or http://metallo.scripps.edu/PROMISE/ . Use of Netscape version 2.0 or higher is recommended. The SRS browser (3) provides simple and fast textual search through the whole PROMISE database. Any feedback and corrections will be gratefully received.

ACKNOWLEDGEMENTS

This work has been supported by Astra Charnwood, Glaxo Wellcome, Pfizer, Zeneca and the BBSRC under the UK DTI/BBSRC Biotechnology LINK Programme, and by the School of Biochemistry and Molecular Biology, University of Leeds. We thank Drs Nobuo Tanaka (Tokyo Institute of Technology), Sanghwa Han (Kangwon National University, Chunchon, South Korea), Kutbuddin S. Doctor (Johns Hopkins University) and Thorsten Ritz (Beckman Institute, University of Illinois at Urbana-Champaign) for their comments and corrections to the PROMISE entries. We are grateful to Jesus M. Castagnetto for his enthusiasm and efforts to establish the PROMISE mirror site at the Scripps Research Institute.

Table 1. Contents of PROMISE version 2.0
[dagger]The numbers in the columns correspond to the numbers of literature references in the associated bibliographic entries.
*Entries added in the last year.


Figure 1. Examples of novel prosthetic groups and bioinorganic motifs: (a) haem P460 of hydroxylamine oxidoreductase (8); (b) cytochrome cd1 nitrite reductase (9); (c) naphthalene 1,2-dioxygenase (10); (d) desulfoferrodoxin (11).


Figure 2. (a) [Fe6S6] model for iron cluster in prismane protein (4); (b) `hybrid' cluster in prismane protein as revealed by X-ray crystallography and spectroscopy (5); (c) [Fe8S8] model for P-cluster of nitrogenase molybdenum-iron protein (6); (d) [Fe8S7]N, model for reduced P-cluster (7); (e) [Fe8S7]OX, model for oxidised P-cluster (7).

REFERENCES

1. Degtyarenko,K.N., North,A.C.T. and Findlay,J.B.C. (1997) Protein Engng., 10, 183-186.

2. Degtyarenko,K.N., North,A.C.T., Perkins,D.N. and Findlay,J.B.C. (1998) Nucleic Acids Res., 26, 376-381. MEDLINE Abstract

3. Etzold,T., Ulyanov,A. and Argos,P. (1996) Methods Enzymol., 266, 114-128. MEDLINE Abstract

4. Bertini,I., Ciurli,S. and Luchinat,C. (1995) Structure Bonding, 83, 1-53.

5. Arendsen,A., Hadden,J., Card,G., McAlpine,A.S., Bailey,S., Zaitsev,V., Duke,E.H.M., Lindley,P., Kröckel,M., Trautwein,A.X., Feiters,M.C., Charnock,J.M., Garner,C.D., Marritt,S.J., Thomson,A.J., Kooter,I.M., Johnson,M.K., van den Berg,W.A.M., van Dongen,W.M.A.M. and Hagen,W.R. (1998) J. Biol. Inorg. Chem., 3, 81-95.

6. Kim,J. and Rees,D.C. (1992) Nature, 360, 553-560.

7. Peters,J.W., Stowell,M.H., Soltis,S.M., Finnegan,M.G., Johnson,M.K. and Rees,D.C. (1997) Biochemistry, 36, 1181-1187. MEDLINE Abstract

8. Igarashi,N., Moriyama,H., Fujiwara,T., Fukumori,Y. and Tanaka,N. (1997) Nature Struct. Biol., 4, 276-284.

9. Fülöp,V., Moir,J.W.B., Ferguson,S.J. and Hajdu,J. (1995) Cell, 81, 369-377. MEDLINE Abstract

10. Kauppi,B., Lee,K., Carredano,E., Parales,R.E., Gibson,D.T., Eklund,H. and Ramaswamy,S. (1998) Structure, 6, 571-586. MEDLINE Abstract

11. Coelho,A.V., Matias,P.M., Fülöp,V., Thompson,A., Gonzalez,A. and Carrondo,M.A. (1997) J. Biol. Inorg. Chem., 2, 680-689.

*To whom correspondence should be addressed. Tel: +44 1223 494659; Fax: +44 1223 494468; Email: kirill@ebi.ac.uk

This page is run by Oxford University Press, Great Clarendon Street, Oxford OX2 6DP, as part of the OUP Journals
Comments and feedback: www-admin{at}oup.co.uk
Last modification: 9 Dec 1998
Copyright©Oxford University Press, 1998.
Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 BioinformaticsHome page
C. Andreini, I. Bertini, G. Cavallaro, G. L. Holliday, and J. M. Thornton
Metal-MACiE: a database of metals involved in biological catalysis
Bioinformatics, August 15, 2009; 25(16): 2088 - 2089.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
C. J. Reedy, M. M. Elvekrog, and B. R. Gibney
Development of a heme protein structure electrochemical function database
Nucleic Acids Res., January 11, 2008; 36(suppl_1): D307 - D313.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
I. Bertini and A. Rosato
Bioinorganic Chemistry Special Feature: Bioinorganic chemistry in the postgenomic era
PNAS, April 1, 2003; 100(7): 3601 - 3604.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. M. Castagnetto, S. W. Hennessy, V. A. Roberts, E. D. Getzoff, J. A. Tainer, and M. E. Pique
MDB: the Metalloprotein Database and Browser at The Scripps Research Institute
Nucleic Acids Res., January 1, 2002; 30(1): 379 - 382.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
B. M. Lange, M. R. Wildung, E. J. Stauber, C. Sanchez, D. Pouchnik, and R. Croteau
Probing essential oil biosynthesis and secretion by functional evaluation of expressed sequence tags from mint glandular trichomes
PNAS, March 14, 2000; 97(6): 2934 - 2939.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. Goto, T. Nishioka, and M. Kanehisa
LIGAND: chemical database of enzyme reactions
Nucleic Acids Res., January 1, 2000; 28(1): 380 - 382.
[Abstract] [Full Text] [PDF]

This Article
Right arrow Abstract Freely available
Right arrow Print PDF (91K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (14)
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Degtyarenko, K. N.
Right arrow Articles by Findlay, J. B.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Degtyarenko, K. N.
Right arrow Articles by Findlay, J. B.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?