9HTD

Peptide-substrate-binding (PSB) domain of human type II collagen prolyl 4-hydroxylase complexed with Pro-Hyp-Gly-Pro-Ala-Gly-Pro-Hyp-Gly.

Summary for 9HTD

• Entry DOI: 10.2210/pdb9htd/pdb
• Related: 6EVL 6EVM 6EVN 6EVO 6EVP
• Descriptor: Prolyl 4-hydroxylase subunit alpha-2, GLY-PRO-ALA-GLY-PRO-HYP-GLY, GLYCINE, ... (5 entities in total)
• Functional Keywords: collagen, tetratricopeptide, extracellular matrix, protein binding
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 2
• Total formula weight: 13094.42

Authors

Sulu, R.,Rahman, M.M.,Wierenga, R.K.,Koski, M.K. (deposition date: 2024-12-19, release date: 2025-09-24)

Primary citation

Rahman, M.M.,Sulu, R.,Adediran, B.,Tu, H.,Salo, A.M.,Murthy, S.,Myllyharju, J.,Wierenga, R.K.,Koski, M.K.
Binding Differences of the Peptide-Substrate-Binding Domain of Collagen Prolyl 4-Hydroxylases I and II for Proline- and Hydroxyproline-Rich Peptides.
Proteins, 93:1732-1746, 2025

PubMed Abstract: Collagen prolyl 4-hydroxylase (C-P4H) catalyzes the 4-hydroxylation of Y-prolines of the XYG-repeat of procollagen. C-P4Hs are tetrameric αβ enzymes. The α-subunit provides the N-terminal dimerization domain, the middle peptide-substrate-binding (PSB) domain, and the C-terminal catalytic (CAT) domain. There are three isoforms of the α-subunit, complexed with a β-subunit that is protein disulfide isomerase, forming C-P4H I-III. The PSB domain of the α-subunit binds proline-rich peptides, but its function with respect to the prolyl hydroxylation mechanism is unknown. An extended mode of binding of proline-rich peptides (PPII, polyproline type-II, conformation) to the PSB-I domain has previously been reported for the PPG-PPG-PPG and P9 peptides. Crystal structures now show that peptides with the motif PxGP (PPG-PRG-PPG, PPG-PAG-PPG) (where x, at Y-position 5, is not a proline) bind to the PSB-I domain differently, more deeply, in the peptide-binding groove. The latter mode of binding has previously been reported for structures of the PSB-II domain complexed with these PxGP-peptides. In addition, it is shown here by crystallographic binding studies that the POG-PAG-POG peptide (with 4-hydroxyprolines at Y-positions 2 and 8) also adopts the PxGP mode of binding to PSB-I as well as to PSB-II. Calorimetric binding studies show that the affinities of these peptides are lower for PSB-I than for PSB-II, with, respectively, K values of about 70 μM for PSB-I and 20 μM for PSB-II. The importance of these results for understanding the reaction mechanism of C-P4H, in particular concerning the function of the PSB domain, is discussed.

PubMed: 40386874
DOI: 10.1002/prot.26839

Experimental method

X-RAY DIFFRACTION (1.751 Å)