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. 2010 Jan 7:11:12.
doi: 10.1186/1471-2105-11-12.

SKPDB: a structural database of shikimate pathway enzymes

Helen A Arcuri  1 , Geraldo Fd Zafalon, Evandro A Marucci, Carlos E Bonalumi, Nelson Jf da Silveira, José M Machado, Walter F de Azevedo Jr, Mário S Palma
Affiliations

SKPDB: a structural database of shikimate pathway enzymes

Helen A Arcuri et al. BMC Bioinformatics. .

Abstract

Background: The functional and structural characterisation of enzymes that belong to microbial metabolic pathways is very important for structure-based drug design. The main interest in studying shikimate pathway enzymes involves the fact that they are essential for bacteria but do not occur in humans, making them selective targets for design of drugs that do not directly impact humans.

Description: The ShiKimate Pathway DataBase (SKPDB) is a relational database applied to the study of shikimate pathway enzymes in microorganisms and plants. The current database is updated regularly with the addition of new data; there are currently 8902 enzymes of the shikimate pathway from different sources. The database contains extensive information on each enzyme, including detailed descriptions about sequence, references, and structural and functional studies. All files (primary sequence, atomic coordinates and quality scores) are available for downloading. The modeled structures can be viewed using the Jmol program.

Conclusions: The SKPDB provides a large number of structural models to be used in docking simulations, virtual screening initiatives and drug design. It is freely accessible at http://lsbzix.rc.unesp.br/skpdb/.

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Figures

Figure 1
Figure 1
The sequence of seven metabolic steps in the shikimate pathway, from phosphoenolpyruvate and erythrose 4-phosphate to chorismate, adapted from the site: http://www.chem.qmul.ac.uk/iubmb/enzyme/reaction/misc/shikim.html.
Figure 2
Figure 2
The flowchart describing all steps of comparative modeling in large scale, used in the model predictions for SKPDB, adapted from [27].
Figure 3
Figure 3
The construction of the SKPDB database.
Figure 4
Figure 4
This diagram describes the entity relationships for database tables.
Figure 5
Figure 5
Homepage of SKPDB.
Figure 6
Figure 6
The page for the shikimate pathway.
Figure 7
Figure 7
This page is shown when the user searches by name of enzyme, or by organism, or by name of enzyme AND organism.
Figure 8
Figure 8
The resulting page when the structure of the enzyme was predicted by molecular modeling.
Figure 9
Figure 9
The resulting page when the structure of the enzyme was experimentally determined.
Figure 10
Figure 10
The page "Model Info" has information about model predicted by molecular modeling.
Figure 11
Figure 11
The page "Template Info" has information about template used during molecular modeling.
Figure 12
Figure 12
The page "Model Analysis" has analysis of the models available dynamically in relation to the results of the generated model.
See this image and copyright information in PMC

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