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| | ==Crystal structure of the complex of 2,2-dialkylglycine decarboxylase with LCS== | | ==Crystal structure of the complex of 2,2-dialkylglycine decarboxylase with LCS== |
| - | <StructureSection load='1d7u' size='340' side='right' caption='[[1d7u]], [[Resolution|resolution]] 1.95Å' scene=''> | + | <StructureSection load='1d7u' size='340' side='right'caption='[[1d7u]], [[Resolution|resolution]] 1.95Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1d7u]] is a 1 chain structure with sequence from [http://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=1D7U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D7U FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1d7u]] 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=1D7U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D7U FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=LCS:[5-HYDROXY-6-METHYL-4-({[(4E)-3-OXO-1,2-OXAZOLIDIN-4-YLIDENE]AMINO}METHYL)PYRIDIN-3-YL]METHYL+DIHYDROGEN+PHOSPHATE'>LCS</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.95Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1d7v|1d7v]], [[1d7r|1d7r]], [[1d7s|1d7s]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=LCS:[5-HYDROXY-6-METHYL-4-({[(4E)-3-OXO-1,2-OXAZOLIDIN-4-YLIDENE]AMINO}METHYL)PYRIDIN-3-YL]METHYL+DIHYDROGEN+PHOSPHATE'>LCS</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2,2-dialkylglycine_decarboxylase_(pyruvate) 2,2-dialkylglycine decarboxylase (pyruvate)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.64 4.1.1.64] </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=1d7u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d7u OCA], [https://pdbe.org/1d7u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d7u RCSB], [https://www.ebi.ac.uk/pdbsum/1d7u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d7u ProSAT]</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=1d7u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d7u OCA], [http://pdbe.org/1d7u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1d7u RCSB], [http://www.ebi.ac.uk/pdbsum/1d7u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1d7u ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://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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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Pseudomonas cepacia burkholder 1950]] | + | [[Category: Burkholderia cepacia]] |
| - | [[Category: Jansonius, J N]] | + | [[Category: Large Structures]] |
| - | [[Category: Keller, J]] | + | [[Category: Jansonius JN]] |
| - | [[Category: Malashkevich, V N]] | + | [[Category: Keller J]] |
| - | [[Category: Strop, P]] | + | [[Category: Malashkevich VN]] |
| - | [[Category: Toney, M D]] | + | [[Category: Strop P]] |
| - | [[Category: Catalytic mechanism]]
| + | [[Category: Toney MD]] |
| - | [[Category: Decarboxylation inhibitor]]
| + | |
| - | [[Category: Enzyme complex]]
| + | |
| - | [[Category: Lyase]]
| + | |
| Structural highlights
Function
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
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 crystal structures of four inhibitor complexes of dialkylglycine decarboxylase are reported. The enzyme does not undergo a domain closure, as does aspartate aminotransferase, upon inhibitor binding. Two active-site conformations have been observed in previous structures that differ in alkali metal ion content, and two active-site conformations have been shown to coexist in solution when a single type of metal ion is present. There is no indication of coexisting conformers in the structures reported here or in the previously reported structures, and the observed conformation is that expected based on the presence of potassium in the enzyme. Thus, although two active-site conformations coexist in solution, a single conformation, corresponding to the more active enzyme, predominates in the crystal. The structure of 1-aminocyclopropane-1-carboxylate bound in the active site shows the aldimine double bond to the pyridoxal phosphate cofactor to be fully out of the plane of the coenzyme ring, whereas the Calpha-CO2(-) bond lies close to it. This provides an explanation for the observed lack of decarboxylation reactivity with this amino acid. The carboxylate groups of both 1-aminocyclopropane-1-carboxylate and 5'-phosphopyridoxyl-2-methylalanine interact with Ser215 and Arg406 as previously proposed. This demonstrates structurally that alternative binding modes, which constitute substrate inhibition, occur in the decarboxylation half-reaction. The structures of d and l-cycloserine bound to the active-site show that the l-isomer is deprotonated at C(alpha), presumably by Lys272, while the d-isomer is not. This difference explains the approximately 3000-fold greater potency of the l versus the d-isomer as a competitive inhibitor of dialkylglycine decarboxylase.
Crystal structures of dialkylglycine decarboxylase inhibitor complexes.,Malashkevich VN, Strop P, Keller JW, Jansonius JN, Toney MD J Mol Biol. 1999 Nov 19;294(1):193-200. PMID:10556038[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Malashkevich VN, Strop P, Keller JW, Jansonius JN, Toney MD. Crystal structures of dialkylglycine decarboxylase inhibitor complexes. J Mol Biol. 1999 Nov 19;294(1):193-200. PMID:10556038 doi:http://dx.doi.org/10.1006/jmbi.1999.3254
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