1ym8 | pdb_00001ym8

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

spinqualitylabelsall models 1ym8, resolution 1.55Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 1ym8 is a 6 chain structure with sequence from Saimiriine gammaherpesvirus 2. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 1.55Å Ligands: HYP Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function Q80BK4_SHV2 Publication Abstract from PubMed 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. 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.,Schumacher M, Mizuno K, Bachinger HP J Biol Chem. 2005 May 27;280(21):20397-403. Epub 2005 Mar 22. PMID:15784619 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Collagen 3D structures

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