1ppy: Difference between revisions

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Revision as of 14:27, 20 March 2008

File:1ppy.gif

, resolution 1.95Å

Ligands:

Gene:

PAND OR B0131 OR C0160 OR Z0142 OR ECS0135 OR SF0128 (Escherichia coli)

Activity:

Aspartate 1-decarboxylase, with EC number 4.1.1.11

Coordinates:

save as pdb, mmCIF, xml

Native precursor of pyruvoyl dependent Aspartate decarboxylase

OverviewOverview

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-->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.

About this StructureAbout this Structure

1PPY is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.

ReferenceReference

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

Page seeded by OCA on Thu Mar 20 13:27:28 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:1ppy.gif|left|200px]]<br /><applet load="1ppy" size="350" color="white" frame="true" align="right" spinBox="true"
+[[Image:1ppy.gif|left|200px]]
-caption="1ppy, resolution 1.95&Aring;" />
-'''Native precursor of pyruvoyl dependent Aspartate decarboxylase'''<br />
+ {{Structure
+|PDB= 1ppy |SIZE=350|CAPTION= <scene name='initialview01'>1ppy</scene>, resolution 1.95&Aring;
+|SITE=
+|LIGAND= <scene name='pdbligand=SO4:SULFATE ION'>SO4</scene>
+|ACTIVITY= [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]
+|GENE= 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])
+}}
+'''Native precursor of pyruvoyl dependent Aspartate decarboxylase'''
 ==Overview==
@@ Line 7: / Line 16: @@
 ==About this Structure==
-PPY 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 <scene name='pdbligand=SO4:'>SO4</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. 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://oca.weizmann.ac.il/oca-bin/ocashort?id=1PPY OCA].
+PPY is a [[Single protein]] structure of 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].
 ==Reference==
-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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=14633979 14633979]
+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:[http://www.ncbi.nlm.nih.gov/pubmed/14633979 14633979]
 [[Category: Aspartate 1-decarboxylase]]
 [[Category: Escherichia coli]]
@@ Line 30: / Line 39: @@
 [[Category: pantothenate pathway]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:31:16 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 13:27:28 2008''