8ONE image
Deposition Date 2023-04-02
Release Date 2023-07-19
Last Version Date 2024-11-13
Entry Detail
PDB ID:
8ONE
Keywords:
Title:
Crystal Structure of full-length Human Lysyl Hydroxylase LH3 - Asp190Ser mutant - Cocrystal with Fe2+, Mn2+, UDP-Glucose
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.30 Å
R-Value Free:
0.22
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
C 2 2 21
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3
Gene (Uniprot):PLOD3
Mutagens:Asp190Ser
Chain IDs:A
Chain Length:719
Number of Molecules:1
Biological Source:Homo sapiens
Primary Citation
Identification of Regulatory Molecular "Hot Spots" for LH/PLOD Collagen Glycosyltransferase Activity.
Int J Mol Sci 24 ? ? (2023)
PMID: 37446392 DOI: 10.3390/ijms241311213

Abstact

Hydroxylysine glycosylations are post-translational modifications (PTMs) essential for the maturation and homeostasis of fibrillar and non-fibrillar collagen molecules. The multifunctional collagen lysyl hydroxylase 3 (LH3/PLOD3) and the collagen galactosyltransferase GLT25D1 are the human enzymes that have been identified as being responsible for the glycosylation of collagen lysines, although a precise description of the contribution of each enzyme to these essential PTMs has not yet been provided in the literature. LH3/PLOD3 is thought to be capable of performing two chemically distinct collagen glycosyltransferase reactions using the same catalytic site: an inverting beta-1,O-galactosylation of hydroxylysines (Gal-T) and a retaining alpha-1,2-glucosylation of galactosyl hydroxylysines (Glc-T). In this work, we have combined indirect luminescence-based assays with direct mass spectrometry-based assays and molecular structure studies to demonstrate that LH3/PLOD3 only has Glc-T activity and that GLT25D1 only has Gal-T activity. Structure-guided mutagenesis confirmed that the Glc-T activity is defined by key residues in the first-shell environment of the glycosyltransferase catalytic site as well as by long-range contributions from residues within the same glycosyltransferase (GT) domain. By solving the molecular structures and characterizing the interactions and solving the molecular structures of human LH3/PLOD3 in complex with different UDP-sugar analogs, we show how these studies could provide insights for LH3/PLOD3 glycosyltransferase inhibitor development. Collectively, our data provide new tools for the direct investigation of collagen hydroxylysine PTMs and a comprehensive overview of the complex network of shapes, charges, and interactions that enable LH3/PLOD3 glycosyltransferase activities, expanding the molecular framework and facilitating an improved understanding and manipulation of glycosyltransferase functions in biomedical applications.

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