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2p53

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Revision as of 07:27, 10 September 2015

Crystal structure of N-acetyl-D-glucosamine-6-phosphate deacetylase D273N mutant complexed with N-acetyl phosphonamidate-d-glucosamine-6-phosphate

Structural highlights

2p53 is a 2 chain structure with sequence from Ecoli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Related:	1ymy, 2p50
Gene:	nagA, b0677, JW0663 (ECOLI)
Activity:	N-acetylglucosamine-6-phosphate deacetylase, with EC number 3.5.1.25
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum

Function

[NAGA_ECOLI] Catalyzes the deacetylation of N-acetyl-D-glucosamine-6-phosphate. In vitro, can also hydrolyze substrate analogs such as N-thioacetyl-D-glucosamine-6-phosphate, N-trifluoroacetyl-D-glucosamine-6-phosphate, N-acetyl-D-glucosamine-6-sulfate, N-acetyl-D-galactosamine-6-phosphate, and N-formyl-D-glucosamine-6-phosphate.^[1]

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

NagA catalyzes the hydrolysis of N-acetyl-d-glucosamine-6-phosphate to d-glucosamine-6-phosphate and acetate. X-ray crystal structures of NagA from Escherichia coli were determined to establish the number and ligation scheme for the binding of zinc to the active site and to elucidate the molecular interactions between the protein and substrate. The three-dimensional structures of the apo-NagA, Zn-NagA, and the D273N mutant enzyme in the presence of a tight-binding N-methylhydroxyphosphinyl-d-glucosamine-6-phosphate inhibitor were determined. The structure of the Zn-NagA confirms that this enzyme binds a single divalent cation at the beta-position in the active site via ligation to Glu-131, His-195, and His-216. A water molecule completes the ligation shell, which is also in position to be hydrogen bonded to Asp-273. In the structure of NagA bound to the tight binding inhibitor that mimics the tetrahedral intermediate, the methyl phosphonate moiety has displaced the hydrolytic water molecule and is directly coordinated to the zinc within the active site. The side chain of Asp-273 is positioned to activate the hydrolytic water molecule via general base catalysis and to deliver this proton to the amino group upon cleavage of the amide bond of the substrate. His-143 is positioned to help polarize the carbonyl group of the substrate in conjunction with Lewis acid catalysis by the bound zinc. The inhibitor is bound in the alpha-configuration at the anomeric carbon through a hydrogen bonding interaction of the hydroxyl group at C-1 with the side chain of His-251. The phosphate group of the inhibitor attached to the hydroxyl at C-6 is ion paired with Arg-227 from the adjacent subunit. NagA from Thermotoga maritima was shown to require a single divalent cation for full catalytic activity.

Structural diversity within the mononuclear and binuclear active sites of N-acetyl-D-glucosamine-6-phosphate deacetylase.,Hall RS, Brown S, Fedorov AA, Fedorov EV, Xu C, Babbitt PC, Almo SC, Raushel FM Biochemistry. 2007 Jul 10;46(27):7953-62. Epub 2007 Jun 13. PMID:17567048^[2]

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

References

↑ Hall RS, Xiang DF, Xu C, Raushel FM. N-Acetyl-D-glucosamine-6-phosphate deacetylase: substrate activation via a single divalent metal ion. Biochemistry. 2007 Jul 10;46(27):7942-52. Epub 2007 Jun 13. PMID:17567047 doi:http://dx.doi.org/10.1021/bi700543x
↑ Hall RS, Brown S, Fedorov AA, Fedorov EV, Xu C, Babbitt PC, Almo SC, Raushel FM. Structural diversity within the mononuclear and binuclear active sites of N-acetyl-D-glucosamine-6-phosphate deacetylase. Biochemistry. 2007 Jul 10;46(27):7953-62. Epub 2007 Jun 13. PMID:17567048 doi:10.1021/bi700544c

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/2p53"

@@ Line 2: / Line 2: @@
 <StructureSection load='2p53' size='340' side='right' caption='[[2p53]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2p53]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2P53 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2P53 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2p53]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2P53 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2P53 FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NNG:2-DEOXY-2-{[(S)-HYDROXY(METHYL)PHOSPHORYL]AMINO}-6-O-PHOSPHONO-ALPHA-D-GLUCOPYRANOSE'>NNG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1ymy|1ymy]], [[2p50|2p50]]</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nagA, b0677, JW0663 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nagA, b0677, JW0663 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2p53 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p53 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2p53 RCSB], [http://www.ebi.ac.uk/pdbsum/2p53 PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2p53 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p53 OCA], [http://pdbe.org/2p53 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2p53 RCSB], [http://www.ebi.ac.uk/pdbsum/2p53 PDBsum]</span></td></tr>
 </table>
 == Function ==
@@ Line 29: / Line 29: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2p53" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Escherichia coli]]
+[[Category: Ecoli]]
 [[Category: N-acetylglucosamine-6-phosphate deacetylase]]
 [[Category: Almo, S C]]

2p53

From Proteopedia

Revision as of 07:27, 10 September 2015

Crystal structure of N-acetyl-D-glucosamine-6-phosphate deacetylase D273N mutant complexed with N-acetyl phosphonamidate-d-glucosamine-6-phosphate

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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