2wvu

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of a Michaelis complex of alpha-L-fucosidase GH29 from Bacteroides thetaiotaomicron with the synthetic substrate 4- nitrophenyl-alpha-L-fucose

Structural highlights

2wvu is a 4 chain structure with sequence from Bacteroides thetaiotaomicron VPI-5482. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.95Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q8A3I4_BACTN

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The enzymatic hydrolysis of alpha-l-fucosides is of importance in cancer, bacterial infections, and fucosidosis, a neurodegenerative lysosomal storage disorder. Here we show a series of snapshots along the reaction coordinate of a glycoside hydrolase family GH29 alpha-l-fucosidase unveiling a Michaelis (ES) complex in a (1)C(4) (chair) conformation and a covalent glycosyl-enzyme intermediate in (3)S(1) (skew-boat). First principles metadynamics simulations on isolated alpha-l-fucose strongly support a (1)C(4)<-->(3)H(4)<-->(3)S(1) conformational itinerary for the glycosylation step of the reaction mechanism and indicate a strong "preactivation" of the (1)C(4) complex to nucleophilic attack as reflected by free energy, C1-O1/O5-C1 bond length elongation/reduction, C1-O1 bond orientation, and positive charge development around the anomeric carbon. Analysis of an imino sugar inhibitor is consistent with tight binding of a chair-conformed charged species.

Analysis of the Reaction Coordinate of alpha-l-Fucosidases: A Combined Structural and Quantum Mechanical Approach.,Lammerts van Bueren A, Fayers-Kerr J, Luo B, Zhang Y, Sollogoub M, Bleriot Y, Rovira C, Davies GJ J Am Chem Soc. 2010 Jan 21. PMID:20092273^[1]

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

References

↑ Lammerts van Bueren A, Fayers-Kerr J, Luo B, Zhang Y, Sollogoub M, Bleriot Y, Rovira C, Davies GJ. Analysis of the Reaction Coordinate of alpha-l-Fucosidases: A Combined Structural and Quantum Mechanical Approach. J Am Chem Soc. 2010 Jan 21. PMID:20092273 doi:10.1021/ja908908q

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2wvu"

@@ Line 3: / Line 3: @@
 <StructureSection load='2wvu' size='340' side='right'caption='[[2wvu]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2wvu]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bactn Bactn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WVU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2WVU FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2wvu]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron_VPI-5482 Bacteroides thetaiotaomicron VPI-5482]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WVU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2WVU FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=JFZ:4-nitrophenyl+6-deoxy-alpha-L-galactopyranoside'>JFZ</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]] 1.95&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2wvt|2wvt]], [[2wvs|2wvs]], [[2wvv|2wvv]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=JFZ:4-nitrophenyl+6-deoxy-alpha-L-galactopyranoside'>JFZ</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=2wvu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2wvu OCA], [https://pdbe.org/2wvu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2wvu RCSB], [https://www.ebi.ac.uk/pdbsum/2wvu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2wvu ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q8A3I4_BACTN Q8A3I4_BACTN]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 31: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Bactn]]
+[[Category: Bacteroides thetaiotaomicron VPI-5482]]
 [[Category: Large Structures]]
-[[Category: Ardevol, A]]
+[[Category: Ardevol A]]
-[[Category: Bleriot, Y]]
+[[Category: Bleriot Y]]
-[[Category: Bueren, A Lammerts van]]
+[[Category: Davies GJ]]
-[[Category: Davies, G J]]
+[[Category: Fayers-Kerr J]]
-[[Category: Fayers-Kerr, J]]
+[[Category: Lammerts van Bueren A]]
-[[Category: Luo, B]]
+[[Category: Luo B]]
-[[Category: Rovira, C]]
+[[Category: Rovira C]]
-[[Category: Sollogoub, M]]
+[[Category: Sollogoub M]]
-[[Category: Zhang, Y]]
+[[Category: Zhang Y]]
-[[Category: Alpha-l-fucose]]
-[[Category: Glycoside hydrolase family 29]]
-[[Category: Hydrolase]]

2wvu

From Proteopedia

Current revision

Crystal structure of a Michaelis complex of alpha-L-fucosidase GH29 from Bacteroides thetaiotaomicron with the synthetic substrate 4- nitrophenyl-alpha-L-fucose

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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