This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

2zy3

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

dodecameric L-aspartate beta-decarboxylase

Structural highlights

2zy3 is a 6 chain structure with sequence from Alcaligenes faecalis subsp. faecalis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.5Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ASDA_COMTE Bifunctional enzyme that has both L-aspartate decarboxylase and transaminase activity.^[1] [PDB:2ZY3]

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^[2]

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

References

↑ 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

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2zy3"

@@ Line 3: / Line 3: @@
 <StructureSection load='2zy3' size='340' side='right'caption='[[2zy3]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2zy3]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/'alcaligenes_odorans' 'alcaligenes odorans']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZY3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZY3 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2zy3]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Alcaligenes_faecalis_subsp._faecalis Alcaligenes faecalis subsp. faecalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZY3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZY3 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]] 2.5&#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;'>[[2zy2|2zy2]], [[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">asdA-AF ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=32001 'Alcaligenes odorans'])</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=2zy3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zy3 OCA], [https://pdbe.org/2zy3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zy3 RCSB], [https://www.ebi.ac.uk/pdbsum/2zy3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zy3 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/ASDA_COMTE ASDA_COMTE]] Bifunctional enzyme that has both L-aspartate decarboxylase and transaminase activity.<ref>PMID:19368885</ref> [PDB:2ZY3]
+[https://www.uniprot.org/uniprot/ASDA_COMTE ASDA_COMTE] Bifunctional enzyme that has both L-aspartate decarboxylase and transaminase activity.<ref>PMID:19368885</ref> [PDB:2ZY3]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 38: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Alcaligenes odorans]]
+[[Category: Alcaligenes faecalis subsp. faecalis]]
-[[Category: Aspartate 4-decarboxylase]]
 [[Category: Large Structures]]
-[[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]]

2zy3

From Proteopedia

Current revision

dodecameric L-aspartate beta-decarboxylase

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox