2vk6: Difference between revisions

Latest revision as of 10:01, 9 May 2024

THE STRUCTURE OF CLOSTRIDIUM PERFRINGENS NANI SIALIDASE AND ITS CATALYTIC INTERMEDIATES

Structural highlights

2vk6 is a 1 chain structure with sequence from Clostridium perfringens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.5Å
Ligands:	CA, DAN, MG, PG4
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q59310_CLOPF

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

Clostridium perfringens is a Gram-positive bacterium responsible for bacteremia, gas gangrene, and occasionally food poisoning. Its genome encodes three sialidases, nanH, nanI, and nanJ, that are involved in the removal of sialic acids from a variety of glycoconjugates and that play a role in bacterial nutrition and pathogenesis. Recent studies on trypanosomal (trans-) sialidases have suggested that catalysis in all sialidases may proceed via a covalent intermediate similar to that of other retaining glycosidases. Here we provide further evidence to support this suggestion by reporting the 0.97A resolution atomic structure of the catalytic domain of the C. perfringens NanI sialidase, and complexes with its substrate sialic acid (N-acetylneuramic acid) also to 0.97A resolution, with a transition-state analogue (2-deoxy-2,3-dehydro-N-acetylneuraminic acid) to 1.5A resolution, and with a covalent intermediate formed using a fluorinated sialic acid analogue to 1.2A resolution. Together, these structures provide high resolution snapshots along the catalytic pathway. The crystal structures suggested that NanI is able to hydrate 2-deoxy-2,3-dehydro-N-acetylneuraminic acid to N-acetylneuramic acid. This was confirmed by NMR, and a mechanism for this activity is suggested.

The structure of Clostridium perfringens NanI sialidase and its catalytic intermediates.,Newstead SL, Potter JA, Wilson JC, Xu G, Chien CH, Watts AG, Withers SG, Taylor GL J Biol Chem. 2008 Apr 4;283(14):9080-8. Epub 2008 Jan 24. PMID:18218621^[1]

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

References

↑ Newstead SL, Potter JA, Wilson JC, Xu G, Chien CH, Watts AG, Withers SG, Taylor GL. The structure of Clostridium perfringens NanI sialidase and its catalytic intermediates. J Biol Chem. 2008 Apr 4;283(14):9080-8. Epub 2008 Jan 24. PMID:18218621 doi:10.1074/jbc.M710247200

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OCA

[1] Newstead SL, Potter JA, Wilson JC, Xu G, Chien CH, Watts AG, Withers SG, Taylor GL. The structure of Clostridium perfringens NanI sialidase and its catalytic intermediates. J Biol Chem. 2008 Apr 4;283(14):9080-8. Epub 2008 Jan 24. PMID:18218621 doi:10.1074/jbc.M710247200

[1]

@@ Line 3: / Line 3: @@
 <StructureSection load='2vk6' size='340' side='right'caption='[[2vk6]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2vk6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_perfringens"_veillon_and_zuber_1898 "bacillus perfringens" veillon and zuber 1898]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VK6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VK6 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2vk6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridium_perfringens Clostridium perfringens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VK6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VK6 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DAN:2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC+ACID'>DAN</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</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]] 1.5&#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;'>[[2bf6|2bf6]], [[2vk5|2vk5]], [[2vk7|2vk7]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DAN:2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC+ACID'>DAN</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Exo-alpha-sialidase Exo-alpha-sialidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.18 3.2.1.18] </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=2vk6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vk6 OCA], [https://pdbe.org/2vk6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vk6 RCSB], [https://www.ebi.ac.uk/pdbsum/2vk6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vk6 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q59310_CLOPF Q59310_CLOPF]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 32: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Bacillus perfringens veillon and zuber 1898]]
+[[Category: Clostridium perfringens]]
-[[Category: Exo-alpha-sialidase]]
 [[Category: Large Structures]]
-[[Category: Chien, C H]]
+[[Category: Chien CH]]
-[[Category: Newstead, S L]]
+[[Category: Newstead SL]]
-[[Category: Potter, J A]]
+[[Category: Potter JA]]
-[[Category: Taylor, G L]]
+[[Category: Taylor GL]]
-[[Category: Watts, A G]]
+[[Category: Watts AG]]
-[[Category: Wilson, J C]]
+[[Category: Wilson JC]]
-[[Category: Withers, S G]]
+[[Category: Withers SG]]
-[[Category: Xu, G]]
+[[Category: Xu G]]
-[[Category: Clostridium perfringen]]
-[[Category: Glycosidase]]
-[[Category: Hydrolase]]
-[[Category: Sialic acid]]
-[[Category: Sialidase]]

2vk6: Difference between revisions

Latest revision as of 10:01, 9 May 2024

THE STRUCTURE OF CLOSTRIDIUM PERFRINGENS NANI SIALIDASE AND ITS CATALYTIC INTERMEDIATES

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

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Proteopedia Page Contributors and Editors (what is this?)

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