|
|
| Line 3: |
Line 3: |
| | <StructureSection load='6hzz' size='340' side='right'caption='[[6hzz]], [[Resolution|resolution]] 2.52Å' scene=''> | | <StructureSection load='6hzz' size='340' side='right'caption='[[6hzz]], [[Resolution|resolution]] 2.52Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6hzz]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HZZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6HZZ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6hzz]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HZZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6HZZ FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.52Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GLCE, KIAA0836 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Heparosan-N-sulfate-glucuronate_5-epimerase Heparosan-N-sulfate-glucuronate 5-epimerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.3.17 5.1.3.17] </span></td></tr>
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6hzz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hzz OCA], [https://pdbe.org/6hzz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6hzz RCSB], [https://www.ebi.ac.uk/pdbsum/6hzz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6hzz ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6hzz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hzz OCA], [http://pdbe.org/6hzz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6hzz RCSB], [http://www.ebi.ac.uk/pdbsum/6hzz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6hzz ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/GLCE_HUMAN GLCE_HUMAN]] Converts D-glucuronic acid residues adjacent to N-sulfate sugar residues to L-iduronic acid residues, both in maturing heparan sulfate (HS) and heparin chains. This is important for further modifications that determine the specificity of interactions between these glycosaminoglycans and proteins.<ref>PMID:20118238</ref> | + | [https://www.uniprot.org/uniprot/GLCE_HUMAN GLCE_HUMAN] Converts D-glucuronic acid residues adjacent to N-sulfate sugar residues to L-iduronic acid residues, both in maturing heparan sulfate (HS) and heparin chains. This is important for further modifications that determine the specificity of interactions between these glycosaminoglycans and proteins.<ref>PMID:20118238</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| Line 24: |
Line 23: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Heparosan-N-sulfate-glucuronate 5-epimerase]] | + | [[Category: Homo sapiens]] |
| - | [[Category: Human]]
| + | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Bonnaffe, D]] | + | [[Category: Bonnaffe D]] |
| - | [[Category: Bourne, Y]] | + | [[Category: Bourne Y]] |
| - | [[Category: Debarnot, C]] | + | [[Category: Debarnot C]] |
| - | [[Category: Fadel, F]] | + | [[Category: Fadel F]] |
| - | [[Category: Goulet, A]] | + | [[Category: Goulet A]] |
| - | [[Category: Lortat-Jacob, H]] | + | [[Category: Le Narvor C]] |
| - | [[Category: Monneau, Y R]] | + | [[Category: Lortat-Jacob H]] |
| - | [[Category: Narvor, C Le]] | + | [[Category: Monneau YR]] |
| - | [[Category: Roig-Zamboni, V]] | + | [[Category: Roig-Zamboni V]] |
| - | [[Category: Vives, R R]] | + | [[Category: Vives RR]] |
| - | [[Category: C5-epimerase]]
| + | |
| - | [[Category: Heparan sulfate]]
| + | |
| - | [[Category: Isomerase]]
| + | |
| Structural highlights
6hzz is a 2 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 2.52Å |
| Ligands: | , , , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
GLCE_HUMAN Converts D-glucuronic acid residues adjacent to N-sulfate sugar residues to L-iduronic acid residues, both in maturing heparan sulfate (HS) and heparin chains. This is important for further modifications that determine the specificity of interactions between these glycosaminoglycans and proteins.[1]
Publication Abstract from PubMed
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.
Substrate binding mode and catalytic mechanism of human heparan sulfate d-glucuronyl C5 epimerase.,Debarnot C, Monneau YR, Roig-Zamboni V, Delauzun V, Le Narvor C, Richard E, Henault J, Goulet A, Fadel F, Vives RR, Priem B, Bonnaffe D, Lortat-Jacob H, Bourne Y Proc Natl Acad Sci U S A. 2019 Mar 14. pii: 1818333116. doi:, 10.1073/pnas.1818333116. PMID:30872481[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Li K, Bethea HN, Liu J. Using engineered 2-O-sulfotransferase to determine the activity of heparan sulfate C5-epimerase and its mutants. J Biol Chem. 2010 Apr 9;285(15):11106-13. doi: 10.1074/jbc.M109.081059. Epub 2010, Jan 29. PMID:20118238 doi:http://dx.doi.org/10.1074/jbc.M109.081059
- ↑ Debarnot C, Monneau YR, Roig-Zamboni V, Delauzun V, Le Narvor C, Richard E, Henault J, Goulet A, Fadel F, Vives RR, 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 U S A. 2019 Mar 14. pii: 1818333116. doi:, 10.1073/pnas.1818333116. PMID:30872481 doi:http://dx.doi.org/10.1073/pnas.1818333116
|
