6yq4: Difference between revisions

Latest revision as of 13:33, 24 January 2024

Crystal structure of Fusobacterium nucleatum tannase

Structural highlights

6yq4 is a 3 chain structure with sequence from Fusobacterium nucleatum subsp. nucleatum ATCC 25586. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.399Å
Ligands:	GOL, MG, SPD
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q8RFS1_FUSNN

Publication Abstract from PubMed

Colorectal cancer pathogenesis and progression is associated with the presence of Fusobacterium nucleatum and the reduction of acetylated derivatives of spermidine, as well as dietary components such as tannin-rich foods. We show that a new tannase orthologue of F. nucleatum (TanBFnn ) has significant structural differences with its Lactobacillus plantarum counterpart affecting the flap covering the active site and the accessibility of substrates. Crystallographic and molecular dynamics analysis revealed binding of polyamines to a small cavity that connects the active site with the bulk solvent which interact with catalytically indispensable residues. As a result, spermidine and its derivatives, particularly N(8) -acetylated spermidine, inhibit the hydrolytic activity of TanBFnn and increase the toxicity of gallotannins to F. nucleatum. Our results support a model in which the balance between the detoxicant activity of TanBFnn and the presence of metabolic inhibitors can dictate either conducive or unfavourable conditions for the survival of F. nucleatum.

A structurally unique Fusobacterium nucleatum tannase provides detoxicant activity against gallotannins and pathogen resistance.,Mancheno JM, Atondo E, Tomas-Cortazar J, Luis Lavin J, Plaza-Vinuesa L, Martin-Ruiz I, Barriales D, Palacios A, Daniel Navo C, Sampedro L, Pena-Cearra A, Angel Pascual-Itoiz M, Castelo J, Carreras-Gonzalez A, Castellana D, Pellon A, Delgado S, Ruas-Madiedo P, de Las Rivas B, Abecia L, Munoz R, Jimenez-Oses G, Anguita J, Rodriguez H Microb Biotechnol. 2020 Dec 18. doi: 10.1111/1751-7915.13732. PMID:33336898^[1]

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

References

↑ Mancheno JM, Atondo E, Tomas-Cortazar J, Luis Lavin J, Plaza-Vinuesa L, Martin-Ruiz I, Barriales D, Palacios A, Daniel Navo C, Sampedro L, Pena-Cearra A, Angel Pascual-Itoiz M, Castelo J, Carreras-Gonzalez A, Castellana D, Pellon A, Delgado S, Ruas-Madiedo P, de Las Rivas B, Abecia L, Munoz R, Jimenez-Oses G, Anguita J, Rodriguez H. A structurally unique Fusobacterium nucleatum tannase provides detoxicant activity against gallotannins and pathogen resistance. Microb Biotechnol. 2020 Dec 18. doi: 10.1111/1751-7915.13732. PMID:33336898 doi:https://dx.doi.org/10.1111/1751-7915.13732

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OCA

[1] Mancheno JM, Atondo E, Tomas-Cortazar J, Luis Lavin J, Plaza-Vinuesa L, Martin-Ruiz I, Barriales D, Palacios A, Daniel Navo C, Sampedro L, Pena-Cearra A, Angel Pascual-Itoiz M, Castelo J, Carreras-Gonzalez A, Castellana D, Pellon A, Delgado S, Ruas-Madiedo P, de Las Rivas B, Abecia L, Munoz R, Jimenez-Oses G, Anguita J, Rodriguez H. A structurally unique Fusobacterium nucleatum tannase provides detoxicant activity against gallotannins and pathogen resistance. Microb Biotechnol. 2020 Dec 18. doi: 10.1111/1751-7915.13732. PMID:33336898 doi:https://dx.doi.org/10.1111/1751-7915.13732

[1]

@@ Line 3: / Line 3: @@
 <StructureSection load='6yq4' size='340' side='right'caption='[[6yq4]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6yq4]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Fusnn Fusnn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YQ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YQ4 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6yq4]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Fusobacterium_nucleatum_subsp._nucleatum_ATCC_25586 Fusobacterium nucleatum subsp. nucleatum ATCC 25586]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YQ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YQ4 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SPD:SPERMIDINE'>SPD</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]] 2.399&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">FN0616 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=190304 FUSNN])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SPD:SPERMIDINE'>SPD</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=6yq4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yq4 OCA], [https://pdbe.org/6yq4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yq4 RCSB], [https://www.ebi.ac.uk/pdbsum/6yq4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yq4 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q8RFS1_FUSNN Q8RFS1_FUSNN]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 21: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Fusnn]]
+[[Category: Fusobacterium nucleatum subsp. nucleatum ATCC 25586]]
 [[Category: Large Structures]]
-[[Category: Anguita, J]]
+[[Category: Anguita J]]
-[[Category: Mancheno, J M]]
+[[Category: Mancheno JM]]
-[[Category: Rodriguez, H]]
+[[Category: Rodriguez H]]
-[[Category: Colorectal cancer]]
-[[Category: Gallotannin]]
-[[Category: Hydrolase]]
-[[Category: Pathogen]]
-[[Category: Tannase]]

6yq4: Difference between revisions

Latest revision as of 13:33, 24 January 2024

Crystal structure of Fusobacterium nucleatum tannase

Structural highlights

Function

Publication Abstract from PubMed

References

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