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6vxe

From Proteopedia

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Crystal structure of hydroxyproline dehydratase (HypD) from Clostridioides difficile with substrate trans-4-hydroxy-L-proline bound

Structural highlights

6vxe is a 8 chain structure with sequence from Clostridioides difficile 70-100-2010. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.464Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.^[1]

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^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Levin BJ, Huang YY, Peck SC, Wei Y, Martinez-Del Campo A, Marks JA, Franzosa EA, Huttenhower C, Balskus EP. A prominent glycyl radical enzyme in human gut microbiomes metabolizes trans-4-hydroxy-l-proline. Science. 2017 Feb 10;355(6325). pii: 355/6325/eaai8386. doi:, 10.1126/science.aai8386. PMID:28183913 doi:http://dx.doi.org/10.1126/science.aai8386
↑ Backman LR, Huang YY, Andorfer MC, Gold B, Raines RT, Balskus EP, Drennan CL. Molecular basis for catabolism of the abundant metabolite trans-4-hydroxy-L-proline by a microbial glycyl radical enzyme. Elife. 2020 Mar 17;9. pii: 51420. doi: 10.7554/eLife.51420. PMID:32180548 doi:http://dx.doi.org/10.7554/eLife.51420

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6vxe"

Categories: Clostridioides difficile 70-100-2010 | Large Structures | Backman LRF | Drennan CL

@@ Line 3: / Line 3: @@
 <StructureSection load='6vxe' size='340' side='right'caption='[[6vxe]], [[Resolution|resolution]] 2.46&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6vxe]] is a 8 chain structure. 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 [http://proteopedia.org/fgij/fg.htm?mol=6VXE FirstGlance]. <br>
+<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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HYP:4-HYDROXYPROLINE'>HYP</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]] 2.464&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Trans-4-hydroxy-L-proline_dehydratase Trans-4-hydroxy-L-proline dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.172 4.2.1.172] </span></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'>[http://proteopedia.org/fgij/fg.htm?mol=6vxe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vxe OCA], [http://pdbe.org/6vxe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vxe RCSB], [http://www.ebi.ac.uk/pdbsum/6vxe PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vxe ProSAT]</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=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 ==
-[[http://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>
+[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 ==
@@ Line 19: / Line 19: @@
 </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: Trans-4-hydroxy-L-proline dehydratase]]
+[[Category: Backman LRF]]
-[[Category: Backman, L R.F]]
+[[Category: Drennan CL]]
-[[Category: Drennan, C L]]
-[[Category: Glycyl radical enzyme]]
-[[Category: Hydroxyproline dehydratase]]
-[[Category: Lyase]]

6vxe

From Proteopedia

Current revision

Crystal structure of hydroxyproline dehydratase (HypD) from Clostridioides difficile with substrate trans-4-hydroxy-L-proline bound

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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