1ppy: Difference between revisions
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== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1ppy]] is a 2 chain structure with sequence 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=1PPY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PPY FirstGlance]. <br> | <table><tr><td colspan='2'>[[1ppy]] is a 2 chain structure with sequence 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=1PPY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PPY FirstGlance]. <br> | ||
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>< | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | ||
<tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSX:S-OXY+CYSTEINE'>CSX</scene></td></tr> | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSX:S-OXY+CYSTEINE'>CSX</scene></td></tr> | ||
<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1aw8|1aw8]], [[1pqe|1pqe]], [[1pqf|1pqf]], [[1pqh|1pqh]], [[1pt0|1pt0]], [[1pt1|1pt1]], [[1pyq|1pyq]], [[1pyu|1pyu]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1aw8|1aw8]], [[1pqe|1pqe]], [[1pqf|1pqf]], [[1pqh|1pqh]], [[1pt0|1pt0]], [[1pt1|1pt1]], [[1pyq|1pyq]], [[1pyu|1pyu]]</td></tr> | ||
<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PAND OR B0131 OR C0160 OR Z0142 OR ECS0135 OR SF0128 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr> | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PAND OR B0131 OR C0160 OR Z0142 OR ECS0135 OR SF0128 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr> | ||
<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr> | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr> | ||
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ppy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ppy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ppy RCSB], [http://www.ebi.ac.uk/pdbsum/1ppy PDBsum]</span></td></tr> | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ppy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ppy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ppy RCSB], [http://www.ebi.ac.uk/pdbsum/1ppy PDBsum]</span></td></tr> | ||
<table> | </table> | ||
== Function == | |||
[[http://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 == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
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[[Category: Aspartate 1-decarboxylase]] | [[Category: Aspartate 1-decarboxylase]] | ||
[[Category: Escherichia coli]] | [[Category: Escherichia coli]] | ||
[[Category: Abell, C | [[Category: Abell, C]] | ||
[[Category: Blundell, T L | [[Category: Blundell, T L]] | ||
[[Category: Chirgadze, D Y | [[Category: Chirgadze, D Y]] | ||
[[Category: Kilkenny, M L | [[Category: Kilkenny, M L]] | ||
[[Category: Lobley, C M.C | [[Category: Lobley, C M.C]] | ||
[[Category: Matak-Vinkovic, D | [[Category: Matak-Vinkovic, D]] | ||
[[Category: Schmitzberger, F | [[Category: Schmitzberger, F]] | ||
[[Category: Smith, A G | [[Category: Smith, A G]] | ||
[[Category: Vinkovic, M | [[Category: Vinkovic, M]] | ||
[[Category: Webb, M E | [[Category: Webb, M E]] | ||
[[Category: Witty, M | [[Category: Witty, M]] | ||
[[Category: Decarboxylase]] | [[Category: Decarboxylase]] | ||
[[Category: Intramolecular protein self-processing]] | [[Category: Intramolecular protein self-processing]] | ||
[[Category: Lyase]] | [[Category: Lyase]] | ||
[[Category: Pantothenate pathway]] | [[Category: Pantothenate pathway]] | ||
Revision as of 18:06, 25 December 2014
Native precursor of pyruvoyl dependent Aspartate decarboxylaseNative precursor of pyruvoyl dependent Aspartate decarboxylase
Structural highlights
Function[PAND_ECOLI] Catalyzes the pyruvoyl-dependent decarboxylation of aspartate to produce beta-alanine.[1] 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 PubMedAspartate 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-->Ser, His11-->Ala, Ser25-->Ala, Ser25-->Cys and Ser25-->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-->Ala or Ser-->Thr mutants alone may lead to erroneous interpretations of the mechanism. 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[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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