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Related Experiment Videos

A structurally conserved water molecule in Rossmann dinucleotide-binding domains.

Christopher A Bottoms1, Paul E Smith, John J Tanner

  • 1Department of Chemistry, University of Missouri-Columbia, Columbia, MO 65211, USA.

Protein Science : a Publication of the Protein Society
|August 23, 2002
PubMed
Summary

A conserved water molecule plays a key role in how Rossmann fold enzymes recognize dinucleotides like NAD, NADP, and FAD. This water bridge is crucial for the classic Rossmann fold structure.

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Area of Science:

  • Structural Biology
  • Computational Biology
  • Enzymology

Background:

  • Rossmann fold domains are common protein structures that bind dinucleotides (NAD, NADP, FAD).
  • The role of solvent molecules, particularly water, in protein-ligand interactions is not fully understood.
  • Understanding dinucleotide recognition is vital for enzyme function and drug design.

Purpose of the Study:

  • To computationally investigate the role of solvent in dinucleotide recognition by Rossmann fold domains.
  • To identify conserved structural features, including water molecules, involved in binding.
  • To determine if these features are characteristic of the classic Rossmann fold motif.

Main Methods:

  • Computational comparison of 102 high-resolution crystal structures of enzyme-dinucleotide complexes.

Related Experiment Videos

  • Analysis of hydrogen bonding networks, including water-mediated interactions.
  • Examination of structural variations in non-classic Rossmann fold domains.

    • Main Results:

    • Enzyme binding sites typically contain 9-12 water molecules, mediating ~30% of protein-dinucleotide hydrogen bonds.
    • A structurally conserved water molecule was identified, bridging the dinucleotide pyrophosphate and the glycine-rich loop.
    • This conserved water molecule is present in classic Rossmann folds but absent in those with significant structural deviations.

    Conclusions:

    • A specific, conserved water molecule is integral to the recognition of dinucleotides by classic Rossmann fold domains.
    • This water molecule forms key hydrogen bonds, stabilizing the protein-dinucleotide complex.
    • Its presence appears to be a defining characteristic of the canonical Rossmann dinucleotide-binding fold.