NON-PROLINE CIS PEPTIDE BONDS IN PROTEINS
Manfred S. Weiss, Andreas Jabs, Rolf Hilgenfeld
Department of Structural Biology and Crystallography, Institute of Molecular Biotechnology, P.O.Box 100 183, D-07708 Jena, Germany
Keywords: Protein Structure, Peptide Bonds, cis Conformation
A non-redundant set of 571 crystallographically determined protein structures from the PDB [1] was analysed with respect to the cis peptide content. A total of 429 (0.3 %) peptide bonds were found to be in the cis conformation. About 90\% of these are of type Xaa-Pro, and the remaining 43 are of type Xaa-nonPro. We have examined these unusual peptide bonds and found that in most cases, they are located at or near the active site of enzymes. This strongly suggests a functional role for them.
Furthermore, it appears as if there is a strong resolution dependence of the cis peptide content in the database. At high resolution (i.e. <= 2.0 A) there are about four times the number of non-Pro cis peptide bonds observed than at medium and low resolution (i.e. > 2.5 A). This suggests that many such peptide bonds may have been overlooked.
From our own experience with the coagulation factor XIII [2] we have developed an algorithm to identify possible non-Pro cis peptide bonds in protein structures that may have been overlooked during the course of structure determination and refinement. Some results will be discussed.