6AX7 image
Entry Detail
PDB ID:
6AX7
Keywords:
Title:
The crystal structure of a lysyl hydroxylase from Acanthamoeba polyphaga mimivirus
Biological Source:
PDB Version:
Deposition Date:
2017-09-06
Release Date:
2018-02-21
Method Details:
Experimental Method:
Resolution:
2.00 Å
R-Value Free:
0.21
R-Value Work:
0.18
R-Value Observed:
0.18
Space Group:
P 43 21 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Procollagen lysyl hydroxylase and glycosyltransferase
Chain IDs:A, B
Chain Length:235
Number of Molecules:2
Biological Source:Acanthamoeba polyphaga mimivirus
Ligand Molecules
Primary Citation
Pro-metastatic collagen lysyl hydroxylase dimer assemblies stabilized by Fe2+-binding.
Nat Commun 9 512 512 (2018)
PMID: 29410444 DOI: 10.1038/s41467-018-02859-z

Abstact

Collagen lysyl hydroxylases (LH1-3) are Fe2+- and 2-oxoglutarate (2-OG)-dependent oxygenases that maintain extracellular matrix homeostasis. High LH2 levels cause stable collagen cross-link accumulations that promote fibrosis and cancer progression. However, developing LH antagonists will require structural insights. Here, we report a 2 Å crystal structure and X-ray scattering on dimer assemblies for the LH domain of L230 in Acanthamoeba polyphaga mimivirus. Loop residues in the double-stranded β-helix core generate a tail-to-tail dimer. A stabilizing hydrophobic leucine locks into an aromatic tyrosine-pocket on the opposite subunit. An active site triad coordinates Fe2+. The two active sites flank a deep surface cleft that suggest dimerization creates a collagen-binding site. Loss of Fe2+-binding disrupts the dimer. Dimer disruption and charge reversal in the cleft increase Km and reduce LH activity. Ectopic L230 expression in tumors promotes collagen cross-linking and metastasis. These insights suggest inhibitor targets for fibrosis and cancer.

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Primary Citation of related structures