6I02

Structure of human D-glucuronyl C5 epimerase in complex with product


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Substrate binding mode and catalytic mechanism of human heparan sulfate d-glucuronyl C5 epimerase.

Debarnot, C.Monneau, Y.R.Roig-Zamboni, V.Delauzun, V.Le Narvor, C.Richard, E.Henault, J.Goulet, A.Fadel, F.Vives, R.R.Priem, B.Bonnaffe, D.Lortat-Jacob, H.Bourne, Y.

(2019) Proc.Natl.Acad.Sci.USA 116: 6760-6765

  • DOI: 10.1073/pnas.1818333116
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Heparan sulfate (HS) is a linear, complex polysaccharide that modulates the biological activities of proteins through binding sites made by a series of Golgi-localized enzymes. Of these, glucuronyl C5-epimerase (Glce) catalyzes C5-epimerization of th ...

    Heparan sulfate (HS) is a linear, complex polysaccharide that modulates the biological activities of proteins through binding sites made by a series of Golgi-localized enzymes. Of these, glucuronyl C5-epimerase (Glce) catalyzes C5-epimerization of the HS component, d-glucuronic acid (GlcA), into l-iduronic acid (IdoA), which provides internal flexibility to the polymer and forges protein-binding sites to ensure polymer function. Here we report crystal structures of human Glce in the unbound state and of an inactive mutant, as assessed by real-time NMR spectroscopy, bound with a (GlcA-GlcNS) n substrate or a (IdoA-GlcNS) n product. Deep infiltration of the oligosaccharides into the active site cleft imposes a sharp kink within the central GlcNS-GlcA/IdoA-GlcNS trisaccharide motif. An extensive network of specific interactions illustrates the absolute requirement of N -sulfate groups vicinal to the epimerization site for substrate binding. At the epimerization site, the GlcA/IdoA rings are highly constrained in two closely related boat conformations, highlighting ring-puckering signatures during catalysis. The structure-based mechanism involves the two invariant acid/base residues, Glu499 and Tyr578, poised on each side of the target uronic acid residue, thus allowing reversible abstraction and readdition of a proton at the C5 position through a neutral enol intermediate, reminiscent of mandelate racemase. These structures also shed light on a convergent mechanism of action between HS epimerases and lyases and provide molecular frameworks for the chemoenzymatic synthesis of heparin or HS analogs.


    Organizational Affiliation

    Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, 13288 Marseille, France.,Centre de Recherches sur les Macromolécules Végétales, CNRS, University Grenoble Alpes, 38041 Grenoble, France.,Institut de Chimie Moléculaire et des Matériaux d'Orsay, University Paris Sud, CNRS, Université Paris-Saclay, 91405 Orsay, France.,Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, 13288 Marseille, France; Yves.Bourne@afmb.univ-mrs.fr.,Institut de Biologie Structurale, University Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives, CNRS, 38044 Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
D-glucuronyl C5-epimerase
A, B
527Homo sapiensMutation(s): 1 
Gene Names: GLCE (KIAA0836)
EC: 5.1.3.17
Find proteins for O94923 (Homo sapiens)
Go to Gene View: GLCE
Go to UniProtKB:  O94923
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GNS
Query on GNS

Download SDF File 
Download CCD File 
A, B
N-SULFO-ALPHA-D-GLUCOSAMINE
C6 H13 N O8 S
PRDZVHCOEWJPOB-UKFBFLRUSA-N
 Ligand Interaction
IDR
Query on IDR

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Download CCD File 
A, B
L-IDURONIC ACID
C6 H10 O7
AEMOLEFTQBMNLQ-VCSGLWQLSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

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Download CCD File 
A, B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

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Download CCD File 
A, B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
P6G
Query on P6G

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Download CCD File 
A
HEXAETHYLENE GLYCOL
POLYETHYLENE GLYCOL PEG400
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
MES
Query on MES

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Download CCD File 
A
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.173 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 99.811α = 90.00
b = 99.811β = 90.00
c = 260.488γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French Infrastructure for Integrated Structural BiologyFranceANR-10-INBS-05
French National Research AgencyFranceANR-10-LABX-49-01
French National Research AgencyFranceANR-10-LABX-33

Revision History 

  • Version 1.0: 2019-04-03
    Type: Initial release
  • Version 1.1: 2019-04-17
    Type: Data collection, Database references