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<StructureSection load='1dgd' size='340' side='right'caption='[[1dgd]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
<StructureSection load='1dgd' size='340' side='right'caption='[[1dgd]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1dgd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"pseudomonas_cepacia"_burkholder_1950 "pseudomonas cepacia" burkholder 1950]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DGD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DGD FirstGlance]. <br>
<table><tr><td colspan='2'>[[1dgd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Burkholderia_cepacia Burkholderia cepacia]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DGD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DGD FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LI:LITHIUM+ION'>LI</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <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]] 2.8&#8491;</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/2,2-dialkylglycine_decarboxylase_(pyruvate) 2,2-dialkylglycine decarboxylase (pyruvate)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.64 4.1.1.64] </span></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LI:LITHIUM+ION'>LI</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></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=1dgd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dgd OCA], [https://pdbe.org/1dgd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dgd RCSB], [https://www.ebi.ac.uk/pdbsum/1dgd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dgd ProSAT]</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=1dgd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dgd OCA], [https://pdbe.org/1dgd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dgd RCSB], [https://www.ebi.ac.uk/pdbsum/1dgd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dgd ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/DGDA_BURCE DGDA_BURCE]] The dialkylglycine decarboxylase is of interest because it normally catalyzes both decarboxylation and amino transfer. It may be more properly described as a decarboxylating aminotransferase rather than an aminotransferring decarboxylase.  
[https://www.uniprot.org/uniprot/DGDA_BURCE DGDA_BURCE] The dialkylglycine decarboxylase is of interest because it normally catalyzes both decarboxylation and amino transfer. It may be more properly described as a decarboxylating aminotransferase rather than an aminotransferring decarboxylase.
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=1dgd ConSurf].
</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=1dgd ConSurf].
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<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The pyridoxal 5'-phosphate-dependent enzyme dialkylglycine decarboxylase (DGD) is activated by K+ and Rb+ ions, whereas Li+ and Na+ ions are inhibitory. A binding site for alkali metal ions close to the active site (site 1) was discovered in the crystal structure of DGD, and an exchange of K+ for Na+ at this site was shown to affect the conformation of two active site residues [Toney, M. D., Hohenester, E., Cowan, S. W., &amp; Jansonius, J. N. (1993) Science 261, 756-759]. We have investigated the effects of alkali metal ions on DGD activity and have determined the crystal structures at 2.8 A resolution of DGD with Li+ and Rb+ bound at site 1. Due to the weak scattering of the Li+ ion, its position had to be modeled using information from small molecule structures. A comparison of the DGD structures with Li+, Na+, K+, and Rb+ bound at site 1 reveals a striking correlation between active site structure and enzymatic activity. The small, inhibitory ions Li+ and Na+ are accommodated by replacing two protein-derived ligands of the larger, activating ions K+ and Rb+ by a single water molecule. This actuates a two-state structural switch between active and inactive enzyme that involves a concerted reorientation of the active site residues Ser80 and Tyr301 and a small change in the quaternary structure of the DGD tetramer. An important role of the essential K+ ion in both cofactor binding and the organization of a catalytically competent active site structure is proposed. In the structure of DGD with Rb+ bound at site 1, a second Rb+ ion has partially replaced the structural Na+ ion at metal binding site 2 on the surface of the DGD molecule, without significantly altering the protein structure. In contrast to Na+, the Rb+ ion is bound with unfavorable geometry, and it is proposed that the rigid site 2 structure results in a pronounced selectivity for Na+ ions.
An alkali metal ion size-dependent switch in the active site structure of dialkylglycine decarboxylase.,Hohenester E, Keller JW, Jansonius JN Biochemistry. 1994 Nov 22;33(46):13561-70. PMID:7947767<ref>PMID:7947767</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1dgd" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Pseudomonas cepacia burkholder 1950]]
[[Category: Burkholderia cepacia]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Hohenester, E]]
[[Category: Hohenester E]]
[[Category: Jansonius, J N]]
[[Category: Jansonius JN]]
[[Category: Lyase]]

Revision as of 09:50, 20 March 2024

AN ALKALI METAL ION SIZE-DEPENDENT SWITCH IN THE ACTIVE SITE STRUCTURE OF DIALKYLGLYCINE DECARBOXYLASE

1dgd, resolution 2.80Å

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