2vhl

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[[Image:2vhl.jpg|left|200px]]
[[Image:2vhl.jpg|left|200px]]
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{{Structure
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<!--
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|PDB= 2vhl |SIZE=350|CAPTION= <scene name='initialview01'>2vhl</scene>, resolution 2.050&Aring;
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The line below this paragraph, containing "STRUCTURE_2vhl", creates the "Structure Box" on the page.
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|SITE= <scene name='pdbsite=AC1:Glp+Binding+Site+For+Chain+A'>AC1</scene>, <scene name='pdbsite=AC2:Pig+Binding+Site+For+Chain+A'>AC2</scene>, <scene name='pdbsite=AC3:Fe+Binding+Site+For+Chain+A'>AC3</scene>, <scene name='pdbsite=AC4:Fe+Binding+Site+For+Chain+A'>AC4</scene>, <scene name='pdbsite=AC5:Glp+Binding+Site+For+Chain+B'>AC5</scene>, <scene name='pdbsite=AC6:Pig+Binding+Site+For+Chain+B'>AC6</scene>, <scene name='pdbsite=AC7:Fe+Binding+Site+For+Chain+B'>AC7</scene> and <scene name='pdbsite=AC8:Fe+Binding+Site+For+Chain+B'>AC8</scene>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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|LIGAND= <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GLP:GLUCOSAMINE+6-PHOSPHATE'>GLP</scene>, <scene name='pdbligand=PIG:2-[2-(2-HYDROXY-ETHOXY)-ETHOXY]-ETHANOL'>PIG</scene>
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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|ACTIVITY= <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>
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or leave the SCENE parameter empty for the default display.
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|GENE=
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-->
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|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=cd00854 NagA]</span>
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{{STRUCTURE_2vhl| PDB=2vhl | SCENE= }}
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|RELATEDENTRY=
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2vhl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vhl OCA], [http://www.ebi.ac.uk/pdbsum/2vhl PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2vhl RCSB]</span>
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}}
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'''THE THREE-DIMENSIONAL STRUCTURE OF THE N-ACETYLGLUCOSAMINE-6-PHOSPHATE DEACETYLASE FROM BACILLUS SUBTILIS'''
'''THE THREE-DIMENSIONAL STRUCTURE OF THE N-ACETYLGLUCOSAMINE-6-PHOSPHATE DEACETYLASE FROM BACILLUS SUBTILIS'''
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==About this Structure==
==About this Structure==
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2VHL is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. This structure supersedes the now removed PDB entry 1UN7. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VHL OCA].
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2VHL is a [[Single protein]] structure of sequence from [http://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].
==Reference==
==Reference==
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[[Category: Vincent, F.]]
[[Category: Vincent, F.]]
[[Category: Yates, D.]]
[[Category: Yates, D.]]
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[[Category: bacillus subtili]]
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[[Category: Bacillus subtili]]
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[[Category: carbohydrate metabolism]]
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[[Category: Carbohydrate metabolism]]
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[[Category: deacetylase]]
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[[Category: Deacetylase]]
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[[Category: hydrolase]]
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[[Category: Hydrolase]]
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[[Category: n- acetyleglucosamine-6-phosphate]]
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[[Category: N- acetyleglucosamine-6-phosphate]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 18:49:33 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 2 11:32:29 2008''
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Revision as of 15:49, 4 May 2008

Image:2vhl.jpg

Template:STRUCTURE 2vhl

THE THREE-DIMENSIONAL STRUCTURE OF THE N-ACETYLGLUCOSAMINE-6-PHOSPHATE DEACETYLASE FROM BACILLUS SUBTILIS


Overview

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.

About this Structure

2VHL is a Single protein structure of sequence from Bacillus subtilis. This structure supersedes the now removed PDB entry 1un7. Full crystallographic information is available from OCA.

Reference

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 Page seeded by OCA on Sun May 4 18:49:33 2008

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