1uhd: Difference between revisions

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-[[Image:1uhd.jpg|left|200px]]<br /><applet load="1uhd" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1uhd, resolution 2.00&Aring;" />
-'''Crystal structure of aspartate decarboxylase, pyruvoly group bound form'''<br />
-==Overview==
+==Crystal structure of aspartate decarboxylase, pyruvoly group bound form==
-l-Aspartate alpha-decarboxylase (ADC), encoded by the panD gene, catalyzes, the conversion of l-aspartate into beta-alanine. In the microorganisms, beta-alanine is required for the synthesis of pantothenate (vitamin B(5)), which is the precursor of 4'-phosphopantetheine and coenzyme A. We have, determined the crystal structure of Helicobacter pylori ADC, a tetrameric, enzyme, in two forms: the apo structure at 2.0 A resolution and the, isoasparagine complex structure at 1.55 A resolution. All subunits of the, tetramer are self-processed at the Gly24-Ser25 linkage, producing the, smaller beta chain (residues 1-24) and the larger alpha chain (residues, 25-117). Each subunit contains nine beta-strands and three alpha-helices;, it is folded into the double-psi beta-barrel structure. In the apo, structure, the new amino terminus of the alpha chain, Ser25, is converted, into a pyruvoyl group. In the isoasparagine complex structure, the, substrate analog is covalently attached to the pyruvoyl group. This, structure represents the enzyme-substrate Schiff base intermediate that, was proposed to form prior to the decarboxylation step in the catalytic, cycle of ADC. Thus our study provides direct structural evidence for the, reaction mechanism of ADC.
+<StructureSection load='1uhd' size='340' side='right'caption='[[1uhd]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1uhd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicobacter_pylori Helicobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UHD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UHD FirstGlance]. <br>
+</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=PYR:PYRUVIC+ACID'>PYR</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1uhd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uhd OCA], [https://pdbe.org/1uhd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1uhd RCSB], [https://www.ebi.ac.uk/pdbsum/1uhd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1uhd ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PAND_HELPY PAND_HELPY] Catalyzes the pyruvoyl-dependent decarboxylation of aspartate to produce beta-alanine (By similarity).[HAMAP-Rule:MF_00446]
+== 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/uh/1uhd_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1uhd ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+l-Aspartate alpha-decarboxylase (ADC), encoded by the panD gene, catalyzes the conversion of l-aspartate into beta-alanine. In the microorganisms, beta-alanine is required for the synthesis of pantothenate (vitamin B(5)), which is the precursor of 4'-phosphopantetheine and coenzyme A. We have determined the crystal structure of Helicobacter pylori ADC, a tetrameric enzyme, in two forms: the apo structure at 2.0 A resolution and the isoasparagine complex structure at 1.55 A resolution. All subunits of the tetramer are self-processed at the Gly24-Ser25 linkage, producing the smaller beta chain (residues 1-24) and the larger alpha chain (residues 25-117). Each subunit contains nine beta-strands and three alpha-helices; it is folded into the double-psi beta-barrel structure. In the apo structure, the new amino terminus of the alpha chain, Ser25, is converted into a pyruvoyl group. In the isoasparagine complex structure, the substrate analog is covalently attached to the pyruvoyl group. This structure represents the enzyme-substrate Schiff base intermediate that was proposed to form prior to the decarboxylation step in the catalytic cycle of ADC. Thus our study provides direct structural evidence for the reaction mechanism of ADC.
-==About this Structure==
+Crystal structure of the schiff base intermediate prior to decarboxylation in the catalytic cycle of aspartate alpha-decarboxylase.,Lee BI, Suh SW J Mol Biol. 2004 Jun 25;340(1):1-7. PMID:15184017<ref>PMID:15184017</ref>
-UHD is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Helicobacter_pylori Helicobacter pylori]. Active as [http://en.wikipedia.org/wiki/Aspartate_1-decarboxylase Aspartate 1-decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.11 4.1.1.11] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1UHD OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Crystal structure of the schiff base intermediate prior to decarboxylation in the catalytic cycle of aspartate alpha-decarboxylase., Lee BI, Suh SW, J Mol Biol. 2004 Jun 25;340(1):1-7. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15184017 15184017]
+</div>
-[[Category: Aspartate 1-decarboxylase]]
+<div class="pdbe-citations 1uhd" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Aspartate decarboxylase|Aspartate decarboxylase]]
+*[[Aspartate decarboxylase 3D structures|Aspartate decarboxylase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Helicobacter pylori]]
-[[Category: Protein complex]]
+[[Category: Large Structures]]
-[[Category: Han, B.W.]]
+[[Category: Han BW]]
-[[Category: Kwon, A.R.]]
+[[Category: Kwon A-R]]
-[[Category: Lee, B.I.]]
+[[Category: Lee BI]]
-[[Category: Suh, S.W.]]
+[[Category: Suh SW]]
-[[Category: double-psi beta barrel]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 04:07:40 2007''