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1yrr

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(New page: 200px<br /><applet load="1yrr" size="450" color="white" frame="true" align="right" spinBox="true" caption="1yrr, resolution 2.00&Aring;" /> '''Crystal Structure Of...)
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[[Image:1yrr.gif|left|200px]]<br /><applet load="1yrr" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1yrr, resolution 2.00&Aring;" />
 
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'''Crystal Structure Of The N-Acetylglucosamine-6-Phosphate Deacetylase From Escherichia Coli K12 at 2.0 A Resolution'''<br />
 
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==Overview==
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==Crystal Structure Of The N-Acetylglucosamine-6-Phosphate Deacetylase From Escherichia Coli K12 at 2.0 A Resolution==
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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.
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<StructureSection load='1yrr' size='340' side='right'caption='[[1yrr]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[1yrr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. 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 [https://proteopedia.org/fgij/fg.htm?mol=1YRR FirstGlance]. <br>
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1YRR is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with PO4 and GOL as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1YRR OCA].
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</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&#8491;</td></tr>
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<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>
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==Reference==
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1yrr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yrr OCA], [https://pdbe.org/1yrr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yrr RCSB], [https://www.ebi.ac.uk/pdbsum/1yrr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yrr ProSAT]</span></td></tr>
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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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16630633 16630633]
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/NAGA_ECOLI 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.<ref>PMID:17567047</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yr/1yrr_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1yrr ConSurf].
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<div style="clear:both"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: N-acetylglucosamine-6-phosphate deacetylase]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Aparicio R]]
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[[Category: Aparicio, R.]]
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[[Category: Calcagno ML]]
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[[Category: Calcagno, M.L.]]
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[[Category: Ferreira FM]]
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[[Category: Ferreira, F.M.]]
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[[Category: Mendoza-Hernandez G]]
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[[Category: Mendoza-Hernandez, G.]]
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[[Category: Oliva G]]
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[[Category: Oliva, G.]]
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[[Category: GOL]]
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[[Category: PO4]]
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[[Category: (beta/alpha)8 barrel]]
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[[Category: beta sandwich]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 07:00:32 2007''
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Current revision

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

PDB ID 1yrr

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