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| | <StructureSection load='2vhl' size='340' side='right'caption='[[2vhl]], [[Resolution|resolution]] 2.05Å' scene=''> | | <StructureSection load='2vhl' size='340' side='right'caption='[[2vhl]], [[Resolution|resolution]] 2.05Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2vhl]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1un7 1un7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VHL OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2VHL FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2vhl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1un7 1un7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VHL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VHL FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GLP:GLUCOSAMINE+6-PHOSPHATE'>GLP</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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]] 2.05Å</td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/N-acetylglucosamine-6-phosphate_deacetylase N-acetylglucosamine-6-phosphate deacetylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.25 3.5.1.25] </span></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GLP:GLUCOSAMINE+6-PHOSPHATE'>GLP</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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=2vhl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vhl OCA], [http://pdbe.org/2vhl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vhl RCSB], [http://www.ebi.ac.uk/pdbsum/2vhl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2vhl 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=2vhl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vhl OCA], [https://pdbe.org/2vhl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vhl RCSB], [https://www.ebi.ac.uk/pdbsum/2vhl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vhl ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/NAGA_BACSU NAGA_BACSU] |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Vibrio subtilis ehrenberg 1835]] | + | [[Category: Bacillus subtilis]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: N-acetylglucosamine-6-phosphate deacetylase]]
| + | [[Category: Davies GJ]] |
| - | [[Category: Davies, G J]] | + | [[Category: Garman E]] |
| - | [[Category: Garman, E]] | + | [[Category: Vincent F]] |
| - | [[Category: Vincent, F]] | + | [[Category: Yates D]] |
| - | [[Category: Yates, D]] | + | |
| - | [[Category: Bacillus subtili]]
| + | |
| - | [[Category: Carbohydrate metabolism]]
| + | |
| - | [[Category: Deacetylase]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: N- acetyleglucosamine-6-phosphate]]
| + | |
| Structural highlights
Function
NAGA_BACSU
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 enzyme N-acetylglucosamine-6-phosphate deacetylase, NagA, catalyzes the hydrolysis of the N-acetyl group of GlcNAc-6-P to yield glucosamine 6-phosphate and acetate, the first committed step in the biosynthetic pathway to amino-sugar-nucleotides. It is classified into carbohydrate esterase family CE-9 (see afmb.cnrs-mrs.fr/CAZY/). Here we report the cloning, expression, and three-dimensional structure (Protein Data Bank code 1un7) determination by x-ray crystallography of the Bacillus subtilis NagA at a resolution of 2.0 A. The structure presents two domains, a (beta/alpha)(8) barrel enclosing the active center and a small beta barrel domain. The structure is dimeric, and the substrate phosphate coordination at the active center is provided by an Arg/His pair contributed from the second molecule of the dimer. Both the overall structure and the active center bear a striking similarity to the urease superfamily with two metals involved in substrate binding and catalysis. PIXE (Proton-Induced x-ray Emission) data show that iron is the predominant metal in the purified protein. We propose a catalytic mechanism involving proton donation to the leaving group by aspartate, nucleophilic attack by an Fe-bridged hydroxide, and stabilization of the carbonyl oxygen by one of the two Fe atoms of the pair. We believe that this is the first sugar deacetylase to utilize this fold and catalytic mechanism.
The three-dimensional structure of the N-acetylglucosamine-6-phosphate deacetylase, NagA, from Bacillus subtilis: a member of the urease superfamily.,Vincent F, Yates D, Garman E, Davies GJ, Brannigan JA J Biol Chem. 2004 Jan 23;279(4):2809-16. Epub 2003 Oct 13. PMID:14557261[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Vincent F, Yates D, Garman E, Davies GJ, Brannigan JA. The three-dimensional structure of the N-acetylglucosamine-6-phosphate deacetylase, NagA, from Bacillus subtilis: a member of the urease superfamily. J Biol Chem. 2004 Jan 23;279(4):2809-16. Epub 2003 Oct 13. PMID:14557261 doi:10.1074/jbc.M310165200
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