Common ring motifs in proteins involving asparagine or glutamine amide groups hydrogen-bonded to main-chain atoms.
We report the frequent occurrence in proteins of motifs consisting of either 9-membered or 11-membered rings that involve the side-chain amide groups of asparagine and glutamine residues. The syn CO and NH groups of these amide groups are hydrogen-bonded to the main-chain NH and CO groups of other amino acid residues. The main-chain part of both the 9-membered and 11-membered rings has the conformation of a beta-strand. One such ring motifs occurs, on average, in half of all the proteins we examined. Similar conformations are found for most examples of the 9-membered and 11-membered rings. One of the 11-membered rings is distinct, compared to the others, in that its main-chain part has a mirror-image conformation. Another of the 11-membered rings occurs at the interior of the variable domains of some antibodies and assists in linking the two beta-sheets. We observe one 9-membered ring structure in a dihydrofolate reductase complex in which the amide in the nicotinamide group of the ligand NADP is bound to the enzyme. Groups that can form hydrogen bonds in a similar way to amide groups occur in several nucleotide bases; we find one example of a 9-membered ring involving adenine and main-chain atoms in the FAD-protein complex of glutathione reductase. Both have conformations like those of the other 9-membered rings.
Department of Biochemistry, University of Glasgow, Scotland, U.K.
J Y
JY
Le Questel
D G
DG
Morris
P H
PH
Maccallum
R
R
Poet
E J
EJ
Milner-White
D000577:Amides / Q000737:chemistry*; D001216:Asparagine / Q000737:chemistry*; D005973:Glutamine / Q000737:chemistry*; D006860:Hydrogen Bonding; D011487:Protein Conformation; D014961:X-Ray Diffraction
D000577:Amides; D005973:Glutamine; D001216:Asparagine