Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: SAXS, gel filtration, homology

Macromolecule Content

• Total Structure Weight: 84.11 kDa 
• Atom Count: 5914 
• Residue Count: 679 
• Unique protein chains: 1

6FXM

Crystal Structure of full-length Human Lysyl Hydroxylase LH3 - Cocrystal with Mn2+

• DOI: 10.2210/pdb6FXM/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2018-03-09 Released: 2018-08-22 
• Deposition Author(s): Scietti, L., Chiapparino, A., De Giorgi, F., Fumagalli, M., Khoriauli, L., Nergadze, S., Basu, S., Olieric, V., Banushi, B., Giulotto, E., Gissen, P., Forneris, F.
• Funding Organization(s): The Giovanni Armenise-Harvard Foundation, Cariplo Foundation, AIRC, European Commission MSCA-IF, European Union - BIOSTRUCT

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.252 
• R-Value Work: 0.229 
• R-Value Observed: 0.230 

Literature

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.

(2018) Nat Commun 9: 3163-3163

• PubMed: 30089812 
• DOI: 10.1038/s41467-018-05631-5
• Primary Citation of Related Structures:  
  6FXY, 6FXX, 6FXR, 6FXT, 6FXK, 6FXM


• PubMed Abstract: 
  

Lysyl hydroxylases catalyze hydroxylation of collagen lysines, and sustain essential roles in extracellular matrix (ECM) maturation and remodeling. Malfunctions in these enzymes cause severe connective tissue disorders. Human lysyl hydroxylase 3 (LH3/PLOD3) bears multiple enzymatic activities, as it catalyzes collagen lysine hydroxylation and also their subsequent glycosylation. Our understanding of LH3 functions is currently hampered by lack of molecular structure information. Here, we present high resolution crystal structures of full-length human LH3 in complex with cofactors and donor substrates. The elongated homodimeric LH3 architecture shows two distinct catalytic sites at the N- and C-terminal boundaries of each monomer, separated by an accessory domain. The glycosyltransferase domain displays distinguishing features compared to other known glycosyltransferases. Known disease-related mutations map in close proximity to the catalytic sites. Collectively, our results provide a structural framework characterizing the multiple functions of LH3, and the molecular mechanisms of collagen-related diseases involving human lysyl hydroxylases.

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Organizational Affiliation: 

The Armenise-Harvard Laboratory of Structural Biology, Department of Biology and Biotechnology, University of Pavia, Via Ferrata 9/A, 27100, Pavia, Italy. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3	A	718	Homo sapiens	Mutation(s): 0  Gene Names: PLOD3 EC: 1.14.11.4 (PDB Primary Data), 2.4.1.50 (UniProt), 2.4.1.66 (UniProt)
Find proteins for O60568 (Homo sapiens) Explore O60568  Go to UniProtKB:  O60568
NIH Common Fund Data Resources
PHAROS:  O60568 GTEx:  ENSG00000106397

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
AKG	A	2-OXOGLUTARIC ACID C5 H6 O5 KPGXRSRHYNQIFN-UHFFFAOYSA-N
GOL	A	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FE2	A	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N
MN	A	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.252 
• R-Value Work: 0.229 
• R-Value Observed: 0.230 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.27	α = 90
b = 99.949	β = 90
c = 225.138	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
SHARP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-03-09 
• Released Date: 2018-08-22 
Deposition Author(s): Scietti, L., Chiapparino, A., De Giorgi, F., Fumagalli, M., Khoriauli, L., Nergadze, S., Basu, S., Olieric, V., Banushi, B., Giulotto, E., Gissen, P., Forneris, F.

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Funding Organization	Location	Grant Number
The Giovanni Armenise-Harvard Foundation	United States	Career Development Award
Cariplo Foundation	Italy	2015-0768 - COME TRUE
AIRC	Italy	20075
European Commission MSCA-IF	Italy	745934 - COTETHERS
European Union - BIOSTRUCT	Italy	7551, 10205

Revision History 

• Version 1.0: 2018-08-22
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary