The Directory of P450-containing Systems in 1996
Péter
Fábián
and kirill{at}icgeb.trieste.it
1,
*
Institute for Biochemistry, Agricultural Biotechnology Center,
Gödöllö
, PO Box 411, 2100,
Hungary
and
1
Department of Biochemistry and Molecular Biology, University of Leeds,
Leeds
LS2 9JT,
UK
Received August 19, 1996;
Revised and Accepted October 8, 1996
ABSTRACT
The Directory of P450-containing Systems on WorldWide Web has been designed to facilitate access
to electronic resources for all researchers working in the field of P450-containing and related enzyme systems. Currently, it contains the most up-to-date list of sequences of both the P450 superfamily and
proteins mediating electron transfer to P450, i.e. NADPH:P450 reductases,
specific NAD(P)H:ferredoxin reductases, cytochrome
b
5 reductases, ferredoxins and cytochromes
b
5, and their homologues. All the referenced sequences are provided with
accession numbers and links to major sequence databanks: PIR, SWISS-PROT, EMBL/GenBank and PRF. An associated database of steroid substrates
and products of P450-dependent reactions has also been developed.
BACKGROUND
CONTENTS
The home page of DPS (Fig.
1
) provides access to all associated hypertext documents.
The `core' of DPS is systematic information on protein and nucleic acid
sequences of the P450 superfamily as well as other components of P450-containing systems and their homologues. A typical DPS entry is shown in
Figure
2
. It contains accession numbers for known sequences of relevant proteins in PIR
(
7
), SWISS-PROT (
8
), EMBL (
9
) and PRF/SEQDB (
10
) databases. Only complete or reasonably complete sequences are being referenced
in DPS; as a rule, ESTs are not considered. All the accession numbers are
linked to the corresponding databases: `clicking' the code retrieves the
sequence. This allows the user to get the most up-to-date versions of sequences as soon as they appear in major
databases. The search for new sequences is conducted automatically by a perl
script (see reference
6
for more details). In addition, DPS has links to other databases such as
PROSITE (
11
), PRINTS (
12
), BLOCKS (
13
), ProDom (
14
), Prot-Fam at MIPS (
7
),
Entrez
Taxonomy Database at NCBI (
15
), ENZYME (
16
), LIGAND (
17
) and OMIM (
18
). The tables of P450 sequences are being continuously updated in accordance
with the P450 nomenclature recommendations (
19
). As of September 1, 1996 DPS contained reference data on 927 genes from 256
different species (Table
1
). A special page is dedicated to genes with a known exon/intron structure.
PRINTS entries for structural domains of P450-containing systems
For all the components/domains of P450 systems, the corresponding fingerprints
have been constructed, which can be used to identify the new members of these
protein superfamilies, even if the overall amino acid sequence identities are
at or below the limit of significance (
6
). The fingerprint entries are integrated in the PRINTS database (
12
). As of July 1, 1996 the PRINTS database contained 14 relevant entries.
OMIM entries related to P450-containing systems
MOLSCRIPT images of known 3D structures
The names of the two last sections are self-explanatory. The former represents a table containing links to 54 entries
of the Online Mendelian Inheritance in Man (OMIM) database (
18
). The latter provides an interface to drawings produced with the program
MOLSCRIPT (
22
); the images can be retrieved both in PostScript and GIF format.
AVAILABILITY
DPS is currently available on the WorldWide Web servers of the International
Centre for Genetic Engineering and Biotechnology, Trieste, Italy at <http://www.icgeb.trieste.it/p450/ > and the Agricultural Biotechnology Center,
Gödöllö, Hungary at <http://p450.abc.hu >.
ACKNOWLEDGEMENTS
This project was launched during the authors' fellowship at the Protein
Structure and Function Laboratory of the International Centre for Genetic
Engineering and Biotechnology, Trieste, Italy. We are grateful to David R.
Nelson of University of Tennessee at Memphis for his assistance with P450
nomenclature.
REFERENCES
1 NC-IUB (Nomenclature Committee of the International Union of Biochemistry) (1991) Eur. J. Biochem., 200, 599-611.
11 Bairoch, A., Bucher, P. and Hofmann, K. (1996) Nucleic Acids Res., 24, 189-196.
12 Attwood, T.K., Beck, M.E., Bleasby, A.J., Degtyarenko, K. and Parry-Smith, D.J. (1996) Nucleic Acids Res., 24, 182-188.
13 Pietrokovski, S., Henikoff, J.G. and Henikoff, S. (1996) Nucleic Acids Res., 24, 197-200.
14 Sonnhammer, E.L.L. and Kahn, D. (1994) Protein Sci., 3, 482-492.
15 Benson, D.A., Boguski, M., Lipman, D.J. and Ostell, J. (1996) Nucleic Acids Res., 24, 1-5.
16 Bairoch, A. (1996) Nucleic Acids Res., 24, 221-222.
17 Suyama, M., Ogiwara, A., Nishioka, T. and Oda, J. (1993) CABIOS, 9, 9-15.
18 Pearson, P., Francomano, C., Foster, P., Bocchini, C., Li, P. and McKusick, V. (1994) Nucleic Acids Res., 22, 3470-3473.
19 Nelson, D.R., www server <http://drnelson.utmem.edu/nelsonhomepage.html>
20 Ruckpaul, K. and Rein, H. (eds) (1990) Frontiers in Biotransformation, Vol. 3: Molecular Mechanisms of Adrenal Steroidogenesis and Aspects of Regulation and Application. Taylor & Francis, London.
21 Kazic, T. (1995) In:Collier, H. (ed.), Proceedings of the 1995 International Chemical Informatics Conference, Nimes, France. Infonortics Ltd. Calne, UK, pp. 48-61.
22 Kraulis, P.J. (1991) J. Appl. Crystallogr., 24, 946-950.
