9NEV image
Deposition Date 2025-02-20
Release Date 2025-06-04
Last Version Date 2025-06-04
Entry Detail
PDB ID:
9NEV
Keywords:
Title:
Acanthamoeba Polyphaga Mimivirus L230
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
2.30 Å
R-Value Free:
0.25
R-Value Work:
0.20
Space Group:
P 43 21 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Procollagen lysyl hydroxylase and glycosyltransferase
Gene (Uniprot):MIMI_L230
Mutations:H825A
Chain IDs:A, B
Chain Length:235
Number of Molecules:2
Biological Source:Acanthamoeba polyphaga mimivirus
Primary Citation
Structure of an Fe 2+ -binding-deficient mimiviral collagen lysyl hydroxylase.
Acta Crystallogr.,Sect.F 81 235 240 (2025)
PMID: 40314237 DOI: 10.1107/S2053230X25003735

Abstact

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 Fe2+ in their active sites, suggesting that lysyl hydroxylases have a high affinity for Fe2+. We found that Fe2+ binding stabilizes lysyl hydroxylase dimers, although the underlying mechanism remains unclear. Crystal structure analysis of mimiviral lysyl hydroxylase revealed that Fe2+ 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 Fe2+. To investigate whether the alternative 2His-1Asp triad binds Fe2+ and how Fe2+ 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 Fe2+ 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 Fe2+ 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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures