1yrr

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(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...)
Current revision (08:59, 14 February 2024) (edit) (undo)
 
(14 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1yrr.gif|left|200px]]<br /><applet load="1yrr" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1yrr, resolution 2.00&Aring;" />
 
-
'''Crystal Structure Of The N-Acetylglucosamine-6-Phosphate Deacetylase From Escherichia Coli K12 at 2.0 A Resolution'''<br />
 
-
==Overview==
+
==Crystal Structure Of The N-Acetylglucosamine-6-Phosphate Deacetylase From Escherichia Coli K12 at 2.0 A Resolution==
-
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.
+
<StructureSection load='1yrr' size='340' side='right'caption='[[1yrr]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
-
 
+
== Structural highlights ==
-
==About this Structure==
+
<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>
-
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].
+
</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>
-
 
+
<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>
-
==Reference==
+
<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>
-
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]
+
</table>
 +
== Function ==
 +
[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>
 +
== Evolutionary Conservation ==
 +
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yr/1yrr_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</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].
 +
<div style="clear:both"></div>
 +
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
-
[[Category: N-acetylglucosamine-6-phosphate deacetylase]]
+
[[Category: Large Structures]]
-
[[Category: Single protein]]
+
[[Category: Aparicio R]]
-
[[Category: Aparicio, R.]]
+
[[Category: Calcagno ML]]
-
[[Category: Calcagno, M.L.]]
+
[[Category: Ferreira FM]]
-
[[Category: Ferreira, F.M.]]
+
[[Category: Mendoza-Hernandez G]]
-
[[Category: Mendoza-Hernandez, G.]]
+
[[Category: Oliva G]]
-
[[Category: Oliva, G.]]
+
-
[[Category: GOL]]
+
-
[[Category: PO4]]
+
-
[[Category: (beta/alpha)8 barrel]]
+
-
[[Category: beta sandwich]]
+
-
 
+
-
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 07:00:32 2007''
+

Current revision

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

PDB ID 1yrr

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1yrr"
Personal tools