1pyu: Difference between revisions

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{{Seed}}
[[Image:1pyu.png|left|200px]]


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==Processed Aspartate Decarboxylase Mutant with Ser25 mutated to Cys==
The line below this paragraph, containing "STRUCTURE_1pyu", creates the "Structure Box" on the page.
<StructureSection load='1pyu' size='340' side='right'caption='[[1pyu]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[1pyu]] is a 4 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=1PYU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PYU FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#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=SO4:SULFATE+ION'>SO4</scene></td></tr>
{{STRUCTURE_1pyu|  PDB=1pyu  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1pyu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pyu OCA], [https://pdbe.org/1pyu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pyu RCSB], [https://www.ebi.ac.uk/pdbsum/1pyu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pyu ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/PAND_ECOLI PAND_ECOLI] Catalyzes the pyruvoyl-dependent decarboxylation of aspartate to produce beta-alanine.<ref>PMID:6767707</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/py/1pyu_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=1pyu ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Aspartate decarboxylase, which is translated as a pro-protein, undergoes intramolecular self-cleavage at Gly24-Ser25. We have determined the crystal structures of an unprocessed native precursor, in addition to Ala24 insertion, Ala26 insertion and Gly24--&gt;Ser, His11--&gt;Ala, Ser25--&gt;Ala, Ser25--&gt;Cys and Ser25--&gt;Thr mutants. Comparative analyses of the cleavage site reveal specific conformational constraints that govern self-processing and demonstrate that considerable rearrangement must occur. We suggest that Thr57 Ogamma and a water molecule form an 'oxyanion hole' that likely stabilizes the proposed oxyoxazolidine intermediate. Thr57 and this water molecule are probable catalytic residues able to support acid-base catalysis. The conformational freedom in the loop preceding the cleavage site appears to play a determining role in the reaction. The molecular mechanism of self-processing, presented here, emphasizes the importance of stabilization of the oxyoxazolidine intermediate. Comparison of the structural features shows significant similarity to those in other self-processing systems, and suggests that models of the cleavage site of such enzymes based on Ser--&gt;Ala or Ser--&gt;Thr mutants alone may lead to erroneous interpretations of the mechanism.


===Processed Aspartate Decarboxylase Mutant with Ser25 mutated to Cys===
Structural constraints on protein self-processing in L-aspartate-alpha-decarboxylase.,Schmitzberger F, Kilkenny ML, Lobley CM, Webb ME, Vinkovic M, Matak-Vinkovic D, Witty M, Chirgadze DY, Smith AG, Abell C, Blundell TL EMBO J. 2003 Dec 1;22(23):6193-204. PMID:14633979<ref>PMID:14633979</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1pyu" style="background-color:#fffaf0;"></div>


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==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_14633979}}, adds the Publication Abstract to the page
*[[Aspartate decarboxylase 3D structures|Aspartate decarboxylase 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 14633979 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_14633979}}
__TOC__
 
</StructureSection>
==About this Structure==
1PYU is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PYU OCA].
 
==Reference==
<ref group="xtra">PMID:14633979</ref><references group="xtra"/>
[[Category: Aspartate 1-decarboxylase]]
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Abell, C.]]
[[Category: Large Structures]]
[[Category: Blundell, T L.]]
[[Category: Abell C]]
[[Category: Chirgadze, D Y.]]
[[Category: Blundell TL]]
[[Category: Kilkenny, M L.]]
[[Category: Chirgadze DY]]
[[Category: Lobley, C M.C.]]
[[Category: Kilkenny ML]]
[[Category: Matak-Vinkovic, D.]]
[[Category: Lobley CMC]]
[[Category: Schmitzberger, F.]]
[[Category: Matak-Vinkovic D]]
[[Category: Smith, A G.]]
[[Category: Schmitzberger F]]
[[Category: Vinkovic, M.]]
[[Category: Smith AG]]
[[Category: Webb, M E.]]
[[Category: Vinkovic M]]
[[Category: Witty, M.]]
[[Category: Webb ME]]
[[Category: Aspartate decarboxylase]]
[[Category: Witty M]]
[[Category: Auto-processing]]
[[Category: Pyruvoyl]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 00:00:40 2009''
Retrieved from "https://proteopedia.org/1pyu"