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HydDB: A web tool for hydrogenase classification and analysis.

Dan Søndergaard¹, Christian N S Pedersen¹, Chris Greening^2,3

¹Aarhus University, Bioinformatics Research Centre, C.F. Møllers Allé 8, Aarhus DK-8000, Denmark.

Scientific Reports

|September 28, 2016

Summary

This summary is machine-generated.

Related Concept Videos

Hydrogen Bonds

Hydrogen Bonds

Hydrogen bonds are weak attractions between atoms that have formed other chemical bonds. One of these atoms is electronegative, like oxygen, and has a partial negative charge. The other is a hydrogen atom that has bonded with another electronegative atom and has a partial positive charge.
Hydrogen Bonds Control the World!
Because hydrogen has very weak electronegativity when it binds with a strongly electronegative atom, such as oxygen or nitrogen, electrons in the bond are unequally shared....

Hydrogen Bonds

Hydrogen Bonds

A hydrogen bond is formed when a weakly positive hydrogen atom already bonded to one electronegative atom (for example, the oxygen in the water molecule) is attracted to another electronegative atom from another polar molecule, such as water (H2O), hydrogen fluoride (HF), or ammonia (NH3). The huge electronegativity difference between the H atom (2.1) and the atom to which it is bonded (4.0 for an F atom, 3.5 for an O atom, or 3.0 for an N atom), combined with the very small size of an H atom...

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Researchers developed HydDB, a web tool for classifying hydrogenase enzymes. This tool predicts enzyme function from primary sequence, aiding the study of ancient energy conservation mechanisms across diverse life forms.

Area of Science:

Biochemistry
Microbiology
Bioinformatics

Background:

Hydrogenases are ancient metalloenzymes central to H2 metabolism and energy conservation.
These enzymes are widespread across microbial phyla and ecosystems.
A comprehensive classification system is needed for structural and functional analysis.

Purpose of the Study:

To develop a classification system and web tool (HydDB) for hydrogenase analysis.
To enable prediction of hydrogenase function based on primary sequence.
To provide a resource for exploring hydrogenase diversity and information.

Main Methods:

Developed an expanded classification scheme defining 38 hydrogenase classes (including 11 new ones).
Utilized k-nearest neighbors' algorithms and CD-ROM referencing for sequence classification.

Related Experiment Videos

Integrated a database of 3248 annotated hydrogenase catalytic subunits and associated information.

Main Results:

Demonstrated reliable prediction of hydrogenase content and function in diverse newly-sequenced organisms.
The HydDB tool accurately classifies hydrogenase primary sequences.
Identified 11 new hydrogenase classes with distinct biological functions.

Conclusions:

Hydrogenase function can be reliably predicted from primary sequence alone.
HydDB provides a valuable resource for researchers studying hydrogenases and microbial metabolism.
The classification system expands our understanding of hydrogenase diversity and biological roles.