8ONE | pdb_00008one

Crystal Structure of full-length Human Lysyl Hydroxylase LH3 - Asp190Ser mutant - Cocrystal with Fe2+, Mn2+, UDP-Glucose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.228 (Depositor), 0.239 (DCC) 
  • R-Value Work: 
    0.204 (Depositor) 
  • R-Value Observed: 
    0.205 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Identification of Regulatory Molecular "Hot Spots" for LH/PLOD Collagen Glycosyltransferase Activity.

Mattoteia, D.Chiapparino, A.Fumagalli, M.De Marco, M.De Giorgi, F.Negro, L.Pinnola, A.Faravelli, S.Roscioli, T.Scietti, L.Forneris, F.

(2023) Int J Mol Sci 24

  • DOI: https://doi.org/10.3390/ijms241311213
  • Primary Citation Related Structures: 
    8ONE

  • PubMed Abstract: 

    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.


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

Macromolecule Content 

  • Total Structure Weight: 84.61 kDa 
  • Atom Count: 6,125 
  • Modeled Residue Count: 696 
  • Deposited Residue Count: 719 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3719Homo sapiensMutation(s): 1 
Gene Names: PLOD3
EC: 1.14.11.4 (PDB Primary Data), 2.4.1.50 (PDB Primary Data), 2.4.1.66 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O60568 (Homo sapiens)
Explore O60568 
Go to UniProtKB:  O60568
PHAROS:  O60568
GTEx:  ENSG00000106397 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60568
Glycosylation
Glycosylation Sites: 1Go to GlyGen: O60568-1
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseB [auth L]2N/A
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UPG
(Subject of Investigation/LOI)

Query on UPG



Download:Ideal Coordinates CCD File
K [auth A]URIDINE-5'-DIPHOSPHATE-GLUCOSE
C15 H24 N2 O17 P2
HSCJRCZFDFQWRP-JZMIEXBBSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
G [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
AKG

Query on AKG



Download:Ideal Coordinates CCD File
C [auth A]2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
H [auth A],
I [auth A],
J [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
FE2

Query on FE2



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
MN

Query on MN



Download:Ideal Coordinates CCD File
F [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.228 (Depositor), 0.239 (DCC) 
  • R-Value Work:  0.204 (Depositor) 
  • R-Value Observed: 0.205 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.09α = 90
b = 100.181β = 90
c = 223.794γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The Giovanni Armenise-Harvard FoundationUnited StatesCDA 2013
Italian Association for Cancer ResearchItalyMFAG 20075
Italian Association for Cancer ResearchItalyBridge 27004
Mizutani Foundation for GlycoscienceJapan200039

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-19
    Type: Initial release
  • Version 1.1: 2023-07-26
    Changes: Database references
  • Version 1.2: 2023-08-09
    Changes: Derived calculations
  • Version 1.3: 2024-11-13
    Changes: Data collection, Structure summary