1YM8

crystal structure of GZZ shows up puckering of the proline ring in the Xaa position.

Summary for 1YM8

• Entry DOI: 10.2210/pdb1ym8/pdb
• Related: 1G9W 1ITT 1K6F 1V4F 1V6Q 1V7H
• Descriptor: collagen gly-4(R)hyp-4(R)hyp (2 entities in total)
• Functional Keywords: collagen; triple helix; proline pucker, structural protein
• Total number of polymer chains: 6
• Total formula weight: 15405.28

Authors

Schumacher, M.A.,Mizuno, K.,Bachinger, H.P. (deposition date: 2005-01-20, release date: 2005-04-19, Last modification date: 2023-08-23)

Primary citation

Schumacher, M.,Mizuno, K.,Bachinger, H.P.
The crystal structure of the collagen-like polypeptide (glycyl-4(R)-hydroxyprolyl-4(R)-hydroxyprolyl)9 at 1.55 A resolution shows up-puckering of the proline ring in the Xaa position.
J.Biol.Chem., 280:20397-20403, 2005

PubMed Abstract: The collagen triple helix is characterized by the repeating sequence motif Gly-Xaa-Yaa, where Xaa and Yaa are typically proline and (2S,4R)-4-hydroxyproline (4(R)Hyp), respectively. Previous analyses have revealed that H-(Pro-4(R)Hyp-Gly)(10)-OH forms a stable triple helix, whereas H-(4(R)Hyp-Pro-Gly)(10)-OH does not. Several theories have been put forth to explain the importance of proline puckering and conformation in triple helix formation; however, the details of how they affect triple helix stability are unknown. Underscoring this, we recently demonstrated that the polypeptide Ac-(Gly-4(R)Hyp-4(R)Hyp)(10)-NH(2) forms a triple helix that is more stable than Ac-(Gly-Pro-4(R)Hyp)(10)-NH(2). Here we report crystal the structure of the H-(Gly-4(R)Hyp-4(R)Hyp)(9)-OH peptide at 1.55 A resolution. The puckering of the Yaa position 4(R)Hyp in this structure is up (Cgamma exo), as has been found in other collagen peptide structures. Notably, however, the 4(R)Hyp in the Xaa position also takes the up pucker, which is distinct from all other collagen structures. Regardless of the notable difference in the Xaa proline puckering, our structure still adopts a 7/2 superhelical symmetry similar to that observed in other collagen structures. Thus, the basis for the observed differences in the thermodynamic data of the triple helix<--> coil transition between our peptide and other triple helical peptides likely results from contributions from the unfolded state. Indeed, the unfolded state of the H-(Gly-4(R)Hyp-4(R)Hyp)(9)-OH peptide seems to be stabilized by a preformed polyproline II helix in each strand, which could be explained by the presence of a unique repeating intra-strand water-mediated bridge observed in the H-(Gly-4(R)Hyp-4(R)Hyp)(9)-OH structure, as well as a higher amount of trans peptide bonds.

PubMed: 15784619
DOI: 10.1074/jbc.M501453200

Experimental method

X-RAY DIFFRACTION (1.55 Å)