Open AccessRecurring main‐chain anion‐binding motifs in short polypeptides: nests
Author(s) -
MilnerWhite E. James,
Nissink J. Willem M.,
Allen Frank H.,
Duddy William J.
Publication year - 2004
Publication title -
acta crystallographica section d
Language(s) - English
Resource type - Journals
ISSN - 1399-0047
DOI - 10.1107/s0907444904021390
Subject(s) - tripeptide , peptide , nest (protein structural motif) , amino acid , carboxylate , alanine , chemistry , stereochemistry , hydrogen bond , structural motif , pentapeptide repeat , peptide sequence , molecule , crystallography , biochemistry , organic chemistry , gene
A novel tripeptide motif called a nest has recently been described in proteins with the function of binding anionic, or partially anionic, atoms such as carbonyl O atoms. In the present work, a search for nests in small polypeptides stored in the Cambridge Structural Database is reported. 37 unique examples were found: over half form part of hydrogen‐bond arrangements resembling those in proteins, such as Schellman/paperclip loop motifs, various types of β‐turn and Asx‐turns or Ser/Thr‐turns, while a third are in novel situations, some involving binding to anionic groups from other molecules within the crystal complex. An example is the antibiotic vancomycin, which incorporates a prominent nest forming part of a peptide‐binding site. This nest binds the carboxylate of the C‐terminal d ‐alanine of the bacterial cell‐wall precursor peptide, thereby inhibiting the final step of bacterial cell‐wall synthesis. As in proteins, a number of nests occur in short peptides with an alternating glycine/ l ‐amino‐acid sequence but, uniquely to non‐ribosomally synthesized short peptides, several nests within them are constructed from alternating d ‐ and l ‐amino acids, and such sequences seem to specially favour nests.