9NEV

Acanthamoeba Polyphaga Mimivirus L230

Summary for 9NEV

• Entry DOI: 10.2210/pdb9nev/pdb
• Descriptor: Procollagen lysyl hydroxylase and glycosyltransferase (2 entities in total)
• Functional Keywords: viral protein, l230
• Biological source: Acanthamoeba polyphaga mimivirus
• Total number of polymer chains: 2
• Total formula weight: 54557.51

Authors

Chen, T.,Buhlheller, C.,Guo, H. (deposition date: 2025-02-20, release date: 2025-06-04)

Primary citation

Chen, T.,Buhlheller, C.,Guo, H.
Structure of an Fe 2+ -binding-deficient mimiviral collagen lysyl hydroxylase.
Acta Crystallogr.,Sect.F, 81:235-240, 2025

PubMed Abstract: Collagen lysyl hydroxylases catalyze the hydroxylation of collagen lysine residues during collagen synthesis in animals and mimiviruses. Lysyl hydroxylation is crucial for collagen fibrogenesis and function. We previously demonstrated that recombinant mimiviral and human collagen lysyl hydroxylases, isolated from bacterial and mammalian cells, have Fe in their active sites, suggesting that lysyl hydroxylases have a high affinity for Fe. We found that Fe binding stabilizes lysyl hydroxylase dimers, although the underlying mechanism remains unclear. Crystal structure analysis of mimiviral lysyl hydroxylase revealed that Fe is coordinated by a 2His-1Asp (His825/His877/Asp827) triad, with a nearby highly conserved histidine residue (His869) involved in an alternative 2His-1Asp triad (His869/His877/Asp827). This unique structural architecture suggests that the alternative 2His-1Asp triad may also bind Fe. To investigate whether the alternative 2His-1Asp triad binds Fe and how Fe binding regulates lysyl hydroxylase dimerization, we crystallized the mimiviral lysyl hydroxylase mutant His825Ala, which lacks one 2His-1Asp (His825/His877/Asp827) triad but retains the alternative triad (His869/His877/Asp827). Despite providing Fe during crystallization, we found no electron density near the alternative 2His-1Asp triad in the His825Ala mutant, indicating that the alternative 2His-1Asp triad does not bind Fe with high affinity. Although the His825Ala mutant forms a dimer similar to the wild-type enzyme, conformational changes occur in residues near Ala825, including Leu873, which is critical for dimerization. These structural findings provide new insights into the function and regulation of collagen lysyl hydroxylases.

PubMed: 40314237
DOI: 10.1107/S2053230X25003735

Experimental method

X-RAY DIFFRACTION (2.3 Å)