2zy2: Difference between revisions

Latest revision as of 22:30, 26 March 2025

dodecameric L-aspartate beta-decarboxylase

Structural highlights

2zy2 is a 1 chain structure with sequence from Pseudomonas sp. ATCC 19121. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.3Å
Ligands:	PLP
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ASDP_PSESP Bifunctional enzyme that has both L-aspartate decarboxylase and transaminase activity. Has high activity with L-aspartate, and much lower activity with D-aspartate, L-lysine and L-glutamine.^[1] ^[2]

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 PubMed

The type-I PLP enzyme l-aspartate beta-decarboxylase converts aspartate to alanine and CO(2). Similar to the homodimeric aminotransferases, its protein subunit comprises a large and a small domain, of 410 and 120 residues, respectively. The crystal structure reveals a dodecamer made of six identical dimers arranged in a truncated tetrahedron whose assembly involves tetramer and hexamer as intermediates. The additional helical motifs I and II participate in the oligomer formation. Triple mutations of S67R/Y68R/M69R or S67E/Y68E/M69E in motif I produced an inactive dimer. The PLP is bound covalently to Lys315 in the active site, while its phosphate group interacts with a neighboring Tyr134. Removal of the bulky side chain of Arg37, which overhangs the PLP group, improved the substrate affinity. Mutations in flexible regions produced the more active K17A and the completely inactive R487A. The structure also suggests that substrate binding triggers conformational changes essential for catalyzing the reaction.

Structure, assembly, and mechanism of a PLP-dependent dodecameric L-aspartate beta-decarboxylase.,Chen HJ, Ko TP, Lee CY, Wang NC, Wang AH Structure. 2009 Apr 15;17(4):517-29. PMID:19368885^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Wang NC, Lee CY. Molecular cloning of the aspartate 4-decarboxylase gene from Pseudomonas sp. ATCC 19121 and characterization of the bifunctional recombinant enzyme. Appl Microbiol Biotechnol. 2006 Nov;73(2):339-48. Epub 2006 Jun 8. PMID:16847601 doi:https://dx.doi.org/10.1007/s00253-006-0475-6
↑ Chen HJ, Ko TP, Lee CY, Wang NC, Wang AH. Structure, assembly, and mechanism of a PLP-dependent dodecameric L-aspartate beta-decarboxylase. Structure. 2009 Apr 15;17(4):517-29. PMID:19368885 doi:10.1016/j.str.2009.02.013
↑ Chen HJ, Ko TP, Lee CY, Wang NC, Wang AH. Structure, assembly, and mechanism of a PLP-dependent dodecameric L-aspartate beta-decarboxylase. Structure. 2009 Apr 15;17(4):517-29. PMID:19368885 doi:10.1016/j.str.2009.02.013

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Wang NC, Lee CY. Molecular cloning of the aspartate 4-decarboxylase gene from Pseudomonas sp. ATCC 19121 and characterization of the bifunctional recombinant enzyme. Appl Microbiol Biotechnol. 2006 Nov;73(2):339-48. Epub 2006 Jun 8. PMID:16847601 doi:https://dx.doi.org/10.1007/s00253-006-0475-6

[2] Chen HJ, Ko TP, Lee CY, Wang NC, Wang AH. Structure, assembly, and mechanism of a PLP-dependent dodecameric L-aspartate beta-decarboxylase. Structure. 2009 Apr 15;17(4):517-29. PMID:19368885 doi:10.1016/j.str.2009.02.013

[3] Chen HJ, Ko TP, Lee CY, Wang NC, Wang AH. Structure, assembly, and mechanism of a PLP-dependent dodecameric L-aspartate beta-decarboxylase. Structure. 2009 Apr 15;17(4):517-29. PMID:19368885 doi:10.1016/j.str.2009.02.013

[1]

[2]

[3]

@@ Line 3: / Line 3: @@
 <StructureSection load='2zy2' size='340' side='right'caption='[[2zy2]], [[Resolution|resolution]] 3.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2zy2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_sp._atcc_19121 Pseudomonas sp. atcc 19121]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZY2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZY2 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2zy2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_sp._ATCC_19121 Pseudomonas sp. ATCC 19121]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZY2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZY2 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.3&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2zy3|2zy3]], [[2zy4|2zy4]], [[2zy5|2zy5]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">asdP ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=206121 Pseudomonas sp. ATCC 19121])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Aspartate_4-decarboxylase Aspartate 4-decarboxylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.12 4.1.1.12] </span></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=2zy2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zy2 OCA], [https://pdbe.org/2zy2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zy2 RCSB], [https://www.ebi.ac.uk/pdbsum/2zy2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zy2 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/ASDP_PSESP ASDP_PSESP]] Bifunctional enzyme that has both L-aspartate decarboxylase and transaminase activity. Has high activity with L-aspartate, and much lower activity with D-aspartate, L-lysine and L-glutamine.<ref>PMID:16847601</ref> <ref>PMID:19368885</ref>
+[https://www.uniprot.org/uniprot/ASDP_PSESP ASDP_PSESP] Bifunctional enzyme that has both L-aspartate decarboxylase and transaminase activity. Has high activity with L-aspartate, and much lower activity with D-aspartate, L-lysine and L-glutamine.<ref>PMID:16847601</ref> <ref>PMID:19368885</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 17: / Line 15: @@
    <jmolCheckbox>
      <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zy/2zy2_consurf.spt"</scriptWhenChecked>
-     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
    </jmolCheckbox>
@@ Line 38: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Aspartate 4-decarboxylase]]
 [[Category: Large Structures]]
-[[Category: Pseudomonas sp. atcc 19121]]
+[[Category: Pseudomonas sp. ATCC 19121]]
-[[Category: Chen, H J]]
+[[Category: Chen H-J]]
-[[Category: Ko, T P]]
+[[Category: Ko T-P]]
-[[Category: Lee, C Y]]
+[[Category: Lee C-Y]]
-[[Category: Wang, A H.J]]
+[[Category: Wang AH-J]]
-[[Category: Wang, N C]]
+[[Category: Wang N-C]]
-[[Category: Aminotransferase]]
-[[Category: Lyase]]
-[[Category: Pyridoxal 5'-phosphate]]

2zy2: Difference between revisions

Latest revision as of 22:30, 26 March 2025

dodecameric L-aspartate beta-decarboxylase

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

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