6I02

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

Summary for 6I02

• Entry DOI: 10.2210/pdb6i02/pdb
• Related: 6HZZ 6I01
• Descriptor: D-glucuronyl C5-epimerase, 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, ... (14 entities in total)
• Functional Keywords: c5-epimerase, heparan sulfate, isomerase
• Biological source: Homo sapiens (Human)
• Total number of polymer chains: 2
• Total formula weight: 129298.73

Authors

Debarnot, C.,Monneau, Y.R.,Roig-Zamboni, V.,Le Narvor, C.,Goulet, A.,Fadel, F.,Vives, R.R.,Bonnaffe, D.,Lortat-Jacob, H.,Bourne, Y. (deposition date: 2018-10-24, release date: 2019-04-03, Last modification date: 2024-10-23)

Primary citation

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.
Substrate binding mode and catalytic mechanism of human heparan sulfate d-glucuronyl C5 epimerase.
Proc.Natl.Acad.Sci.USA, 116:6760-6765, 2019

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 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) substrate or a (IdoA-GlcNS) 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 -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.

PubMed: 30872481
DOI: 10.1073/pnas.1818333116

Experimental method

X-RAY DIFFRACTION (2.45 Å)