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A structural census of metabolic networks for E. coli
1Biomolecular Modelling Laboratory, Imperial Cancer Research Fund, 44 Lincoln's Inn Fields, London WC2A 3PX, UK.
Journal of Molecular Biology
|November 9, 2001
Summary
This study surveyed Escherichia coli metabolic networks, finding most enzymes have known structures. Many proteins with matching domains require experimental structure determination, indicating a need for further research.
Area of Science:
- Biochemistry
- Structural Biology
- Bioinformatics
Background:
- Metabolic networks are crucial for cellular function.
- Understanding protein structures within these networks is key to comprehending biological processes.
- The KEGG database provides a valuable resource for studying metabolic pathways.
Purpose of the Study:
- To conduct a structural survey of Escherichia coli proteins within metabolic networks.
- To assess the structural coverage of these metabolic networks.
- To identify proteins that are targets for experimental structure determination.
Main Methods:
- Utilized the KEGG database (LIGAND release 19) for protein and metabolic network data.
- Defined and calculated a measure of structural coverage for each network.
- Employed SCOP domain matching to identify proteins with known structural similarities.
Main Results:
- 21 out of 24 analyzed Escherichia coli metabolic networks showed over 50% structural coverage.
- 50% of proteins with matching SCOP domains had below 30% sequence identity, marking them as targets for experimental studies.
- Alpha/beta and alpha+beta folds predominate among metabolic enzymes, with coenzyme binding domains being the most common superfamily.
Conclusions:
- Significant structural coverage exists for Escherichia coli metabolic networks.
- There is a clear need for experimental structure determination for many proteins.
- Enzyme structure in metabolic pathways is dominated by specific fold types and shows pathway specificity.