› 6fxt

X-ray diffraction
2.5Å resolution

Crystal Structure of full-length Human Lysyl Hydroxylase LH3 - Cocrystal with Fe2+, Mn2+, UDP-Glc

Released:
DOI: 10.2210/pdb6fxt/pdb
PDB entry 6fxt coloured by chain, front view.
PDB entry 6fxt coloured by chain, side view.
PDB entry 6fxt coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Molecular architecture of the multifunctional collagen lysyl hydroxylase and glycosyltransferase LH3.
Scietti L, Chiapparino A, De Giorgi F, Fumagalli M, Khoriauli L, Nergadze S, Basu S, Olieric V, Cucca L, Banushi B, Profumo A, Giulotto E, Gissen P, Forneris F
Nat Commun 9 3163 (2018)
PMID: 30089812

Function and Biology Details

Reactions catalysed: 
L-lysine-[procollagen] + 2-oxoglutarate + O(2) = (2S,5R)-5-hydroxy-L-lysine-[procollagen] + succinate + CO(2)
UDP-alpha-D-galactose + [procollagen]-(2S,5R)-5-hydroxy-L-lysine = UDP + [procollagen]-(2S,5R)-5-O-(beta-D-galactosyl)-5-hydroxy-L-lysine
UDP-alpha-D-glucose + [procollagen]-(2S,5R)-5-O-(beta-D-galactosyl)-5-hydroxy-L-lysine = UDP + [procollagen]-(2S,5R)-5-O-(alpha-D-glucosyl-(1->2)-beta-D-galactosyl)-5-hydroxy-L-lysine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-130034 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3 Chain: A
Molecule details ›
Chain: A
Length: 718 amino acids
Theoretical weight: 82.78 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: O60568 (Residues: 25-738; Coverage: 100%)
Gene name: PLOD3
Sequence domains: 2OG-Fe(II) oxygenase superfamily

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
6 bound ligands:
Ligand GOL 2 x GOL
Ligand AKG 1 x AKG
Ligand UDP 1 x UDP
Ligand FE2 2 x FE2
Ligand MN 1 x MN
Ligand NAG 1 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE MASSIF-3
Spacegroup: C2221
Unit cell:
a: 97.744Å b: 100.472Å c: 225.394Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.218 0.216 0.248
Expression system: Homo sapiens

Quick links

Citations

5 review citations

Global view of human protein glycosylation pathways and functions.
Schjoldager et al. (2020)
4 more

2 mentions without citation

Molecular architecture of the multifunctional collagen lysyl hydroxylase and glycosyltransferase LH3.
Scietti et al. (2018)
1 more