6FXY

Crystal Structure of full-length Human Lysyl Hydroxylase LH3 - Cocrystal with Fe2+, Mn2+, UDP-Gal - Structure from long-wavelength S-SAD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.138 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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

  • DOI: 10.1038/s41467-018-05631-5
  • Primary Citation of Related Structures:  

  • 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 ...

    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.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3
A
718Homo sapiensMutation(s): 0 
Gene Names: PLOD3
Find proteins for O60568 (Homo sapiens)
Go to Gene View: PLOD3
Go to UniProtKB:  O60568
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

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A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
AKG
Query on AKG

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A
2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
UDP
Query on UDP

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A
URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
 Ligand Interaction
FE2
Query on FE2

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A
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.138 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.194 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 97.040α = 90.00
b = 100.105β = 90.00
c = 224.743γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
CRANK2phasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The Giovanni Armenise-Harvard FoundationUnited StatesCareer Development Award
Cariplo FoundationItaly2015-0768 - COME TRUE
AIRCItaly20075
European Commission MSCA-IFItaly745934 - COTETHERS
European Union - BIOSTRUCTItaly7551, 10205

Revision History 

  • Version 1.0: 2018-08-22
    Type: Initial release