This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

1yrr

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 08:51, 20 January 2021

Crystal Structure Of The N-Acetylglucosamine-6-Phosphate Deacetylase From Escherichia Coli K12 at 2.0 A Resolution

Structural highlights

1yrr is a 2 chain structure with sequence from "bacillus_coli"_migula_1895 "bacillus coli" migula 1895. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Gene:	nagA ("Bacillus coli" Migula 1895)
Activity:	N-acetylglucosamine-6-phosphate deacetylase, with EC number 3.5.1.25
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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

We report the crystal structure of the apoenzyme of N-acetylglucosamine-6-phosphate (GlcNAc6P) deacetylase from Escherichia coli (EcNAGPase) and the spectrometric evidence of the presence of Zn2+ in the native protein. The GlcNAc6P deacetylase is an enzyme of the amino sugar catabolic pathway that catalyzes the conversion of the GlcNAc6P into glucosamine 6-phosphate (GlcN6P). The crystal structure was phased by the single isomorphous replacement with anomalous scattering (SIRAS) method using low-resolution (2.9 A) iodine anomalous scattering and it was refined against a native dataset up to 2.0 A resolution. The structure is similar to two other NAGPases whose structures are known from Thermotoga maritima (TmNAGPase) and Bacillus subtilis (BsNAGPase); however, it shows a phosphate ion bound at the metal-binding site. Compared to these previous structures, the apoenzyme shows extensive conformational changes in two loops adjacent to the active site. The E. coli enzyme is a tetramer and its dimer-dimer interface was analyzed. The tetrameric structure was confirmed in solution by small-angle X-ray scattering data. Although no metal ions were detected in the present structure, experiments of photon-induced X-ray emission (PIXE) spectra and of inductively coupled plasma emission spectroscopy (ICP-AES) with enzyme that was neither exposed to chelating agents nor metal ions during purification, revealed the presence of 1.4 atoms of Zn per polypeptide chain. Enzyme inactivation by metal-sequestering agents and subsequent reactivation by the addition of several divalent cations, demonstrate the role of metal ions in EcNAGPase structure and catalysis.

Structural analysis of N-acetylglucosamine-6-phosphate deacetylase apoenzyme from Escherichia coli.,Ferreira FM, Mendoza-Hernandez G, Castaneda-Bueno M, Aparicio R, Fischer H, Calcagno ML, Oliva G J Mol Biol. 2006 Jun 2;359(2):308-21. Epub 2006 Mar 29. PMID:16630633^[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
↑ Ferreira FM, Mendoza-Hernandez G, Castaneda-Bueno M, Aparicio R, Fischer H, Calcagno ML, Oliva G. Structural analysis of N-acetylglucosamine-6-phosphate deacetylase apoenzyme from Escherichia coli. J Mol Biol. 2006 Jun 2;359(2):308-21. Epub 2006 Mar 29. PMID:16630633 doi:10.1016/j.jmb.2006.03.024

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/1yrr"

@@ Line 1: / Line 1: @@
 ==Crystal Structure Of The N-Acetylglucosamine-6-Phosphate Deacetylase From Escherichia Coli K12 at 2.0 A Resolution==
-<StructureSection load='1yrr' size='340' side='right' caption='[[1yrr]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+<StructureSection load='1yrr' size='340' side='right'caption='[[1yrr]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1yrr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YRR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YRR FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1yrr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YRR OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1YRR FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nagA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=1yrr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yrr OCA], [http://pdbe.org/1yrr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yrr RCSB], [http://www.ebi.ac.uk/pdbsum/1yrr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1yrr ProSAT]</span></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=1yrr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yrr OCA], [http://pdbe.org/1yrr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yrr RCSB], [http://www.ebi.ac.uk/pdbsum/1yrr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1yrr ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 35: / Line 35: @@
 </StructureSection>
 [[Category: Bacillus coli migula 1895]]
+[[Category: Large Structures]]
 [[Category: N-acetylglucosamine-6-phosphate deacetylase]]
 [[Category: Aparicio, R]]

1yrr

From Proteopedia

Revision as of 08:51, 20 January 2021

Crystal Structure Of The N-Acetylglucosamine-6-Phosphate Deacetylase From Escherichia Coli K12 at 2.0 A Resolution

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox