6vxe
From Proteopedia
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(New page: '''Unreleased structure''' The entry 6vxe is ON HOLD Authors: Description: Category: Unreleased Structures) |
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| - | '''Unreleased structure''' | ||
| - | + | ==Crystal structure of hydroxyproline dehydratase (HypD) from Clostridioides difficile with substrate trans-4-hydroxy-L-proline bound== | |
| + | <StructureSection load='6vxe' size='340' side='right'caption='[[6vxe]], [[Resolution|resolution]] 2.46Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[6vxe]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridioides_difficile_70-100-2010 Clostridioides difficile 70-100-2010]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VXE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6VXE FirstGlance]. <br> | ||
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.464Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HYP:4-HYDROXYPROLINE'>HYP</scene></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=6vxe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vxe OCA], [https://pdbe.org/6vxe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6vxe RCSB], [https://www.ebi.ac.uk/pdbsum/6vxe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6vxe ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/HYPD_CLODI HYPD_CLODI] Glycine radical enzyme that catalyzes the dehydration of the non-proteinogenic amino acid trans-4-hydroxy-L-proline (Hyp) to produce delta(1)-pyrroline-5-carboxylate (P5C). Is involved in the anaerobic degradation of 4-hydroxyproline.<ref>PMID:28183913</ref> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | The glycyl radical enzyme (GRE) superfamily utilizes a glycyl radical cofactor to catalyze difficult chemical reactions in a variety of anaerobic microbial metabolic pathways. Recently, a GRE, trans-4-hydroxy-L-proline (Hyp) dehydratase (HypD), was discovered that catalyzes the dehydration of Hyp to (S)-Delta(1)-pyrroline-5-carboxylic acid (P5C). This enzyme is abundant in the human gut microbiome and also present in prominent bacterial pathogens. However, we lack an understanding of how HypD performs its unusual chemistry. Here, we have solved the crystal structure of HypD from the pathogen Clostridioides difficile with Hyp bound in the active site. Biochemical studies have led to the identification of key catalytic residues and have provided insight into the radical mechanism of Hyp dehydration. | ||
| - | + | Molecular basis for catabolism of the abundant metabolite trans-4-hydroxy-L-proline by a microbial glycyl radical enzyme.,Backman LR, Huang YY, Andorfer MC, Gold B, Raines RT, Balskus EP, Drennan CL Elife. 2020 Mar 17;9. pii: 51420. doi: 10.7554/eLife.51420. PMID:32180548<ref>PMID:32180548</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | [[Category: | + | </div> |
| + | <div class="pdbe-citations 6vxe" style="background-color:#fffaf0;"></div> | ||
| + | |||
| + | ==See Also== | ||
| + | *[[HypA%2C HypB%2C HypC%2C HypD%2C HypE and HypF 3D structures|HypA%2C HypB%2C HypC%2C HypD%2C HypE and HypF 3D structures]] | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Clostridioides difficile 70-100-2010]] | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Backman LRF]] | ||
| + | [[Category: Drennan CL]] | ||
Current revision
Crystal structure of hydroxyproline dehydratase (HypD) from Clostridioides difficile with substrate trans-4-hydroxy-L-proline bound
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