1uhd: Difference between revisions
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==Crystal structure of aspartate decarboxylase, pyruvoly group bound form== | ==Crystal structure of aspartate decarboxylase, pyruvoly group bound form== | ||
<StructureSection load='1uhd' size='340' side='right' caption='[[1uhd]], [[Resolution|resolution]] 2.00Å' scene=''> | <StructureSection load='1uhd' size='340' side='right'caption='[[1uhd]], [[Resolution|resolution]] 2.00Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1uhd]] is a 2 chain structure with sequence from [ | <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=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2Å</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=' | <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> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | == 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 == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/uh/1uhd_consurf.spt"</scriptWhenChecked> | <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/ | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </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/ | </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="clear:both"></div> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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==See Also== | ==See Also== | ||
*[[Aspartate decarboxylase|Aspartate decarboxylase]] | *[[Aspartate decarboxylase|Aspartate decarboxylase]] | ||
*[[Aspartate decarboxylase 3D structures|Aspartate decarboxylase 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Helicobacter pylori]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Han | [[Category: Han BW]] | ||
[[Category: Kwon | [[Category: Kwon A-R]] | ||
[[Category: Lee | [[Category: Lee BI]] | ||
[[Category: Suh | [[Category: Suh SW]] | ||
Latest revision as of 03:33, 21 November 2024
Crystal structure of aspartate decarboxylase, pyruvoly group bound formCrystal structure of aspartate decarboxylase, pyruvoly group bound form
Structural highlights
FunctionPAND_HELPY Catalyzes the pyruvoyl-dependent decarboxylation of aspartate to produce beta-alanine (By similarity).[HAMAP-Rule:MF_00446] 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 PubMedl-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. 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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