3ADM

Crystal structure of (Pro-Pro-Gly)4-Hyp-Ser-Gly-(Pro-Pro-Gly)4

Summary for 3ADM

• Entry DOI: 10.2210/pdb3adm/pdb
• Related: 3A08 3A0A 3A0M 3A19 3A1H 3ABN
• Descriptor: collagen-like peptide (2 entities in total)
• Functional Keywords: collagen, triple helix, model peptide, structural protein
• Total number of polymer chains: 6
• Total formula weight: 13713.06

Authors

Okuyama, K.,Miyama, K.,Masakiyo, K.,Mizuno, K.,Bachinger, H.P. (deposition date: 2010-01-22, release date: 2011-01-19, Last modification date: 2023-11-01)

Primary citation

Okuyama, K.,Miyama, K.,Morimoto, T.,Masakiyo, K.,Mizuno, K.,Bachinger, H.P.
Stabilization of triple-helical structures of collagen peptides containing a Hyp-Thr-Gly, Hyp-Val-Gly, or Hyp-Ser-Gly sequence.
Biopolymers, 95:628-640, 2011

PubMed Abstract: The single-crystal structures of three collagen-like host-guest peptides, (Pro-Pro-Gly)(4) -Hyp-Yaa-Gly-(Pro-Pro-Gly)(4) [Yaa = Thr, Val, Ser; Hyp = (4R)-4-hydroxyproline] were analyzed at atomic resolution. These peptides adopted a 7/2-helical structure similar to that of the (Pro-Pro-Gly)(9) peptide. The stability of these triple helices showed a similar tendency to that observed in Ac-(Gly-Hyp-Yaa)(10) -NH(2) (Yaa = Thr, Val, Ser) peptides. On the basis of their detailed structures, the differences in the triple-helical stabilities of the peptides containing a Hyp-Thr-Gly, Hyp-Val-Gly, or Hyp-Ser-Gly sequence were explained in terms of van der Waals interactions and dipole-dipole interaction between the Hyp residue in the X position and the Yaa residue in the Y position involved in the Hyp(X):Yaa(Y) stacking pair. This idea also explains the inability of Ac-(Gly-Hyp-alloThr)(10) -NH(2) and Ac-(Gly-Hyp-Ala)(10) -NH(2) peptides to form triple helices. In the Hyp(X):Thr(Y), Hyp(X):Val(Y), and Hyp(X):Ser(Y) stacking pairs, the proline ring of the Hyp residues adopts an up-puckering conformation, in agreement with the residual preference of Hyp, but in disagreement with the positional preference of X in the Gly-Xaa-Yaa sequence.

PubMed: 21442606
DOI: 10.1002/bip.21625

Experimental method

X-RAY DIFFRACTION (1.18 Å)