Anatomy of enzyme channels
Lukáš Pravda1, Karel Berka2, Radka Svobodová Vařeková3
1National Centre for Biomolecular Research, Faculty of Science and CEITEC, Central European Institute of Technology, Masaryk University Brno, Kamenice 5, Brno-Bohunice, 625 00, Czech Republic. xpravda@ncbr.muni.cz.
BMC Bioinformatics
|November 19, 2014
Summary
Most enzymes have buried active sites accessed through channels. Over 64% of enzymes feature multiple long channels, suggesting these pathways are crucial for enzyme substrate interactions.
Area of Science:
- Biochemistry
- Structural Biology
- Enzymology
Background:
- Enzyme active sites are often connected to the external environment via protein channels.
- Limited knowledge exists regarding the prevalence and common structural features of these enzyme channels.
Purpose of the Study:
- To investigate the frequency and characteristics of channels providing access to enzyme active sites.
- To understand the structural role of channels in enzyme function.
Main Methods:
- Analysis of 4,306 enzyme structures.
- Identification and characterization of long channels (>15 Å) leading to active sites.
Main Results:
- Over 64% of analyzed enzymes possess two or more long channels.
- The typical length of these channels is 28 Å.
- Channel amino acid composition differs significantly from active site, surface, and interior.
Conclusions:
- The majority of enzymes have buried active sites.
- Enzyme channels control substrate access and product egress.
- Channels likely play a critical role in determining enzyme substrate specificity.
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