1d7r
From Proteopedia
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| - | [[Image:1d7r.jpg|left|200px]] | + | [[Image:1d7r.jpg|left|200px]] |
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| - | '''CRYSTAL STRUCTURE OF THE COMPLEX OF 2,2-DIALKYLGLYCINE DECARBOXYLASE WITH 5PA''' | + | {{Structure |
| + | |PDB= 1d7r |SIZE=350|CAPTION= <scene name='initialview01'>1d7r</scene>, resolution 2.00Å | ||
| + | |SITE= | ||
| + | |LIGAND= <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene> and <scene name='pdbligand=5PA:N-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-Y-LMETHYL]-1-AMINO-CYCLOPROPANECARBOXYLIC ACID'>5PA</scene> | ||
| + | |ACTIVITY= [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] | ||
| + | |GENE= | ||
| + | }} | ||
| + | |||
| + | '''CRYSTAL STRUCTURE OF THE COMPLEX OF 2,2-DIALKYLGLYCINE DECARBOXYLASE WITH 5PA''' | ||
| + | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
| - | 1D7R is a [ | + | 1D7R is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Burkholderia_cepacia Burkholderia cepacia]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D7R OCA]. |
==Reference== | ==Reference== | ||
| - | 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:[http:// | + | 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:[http://www.ncbi.nlm.nih.gov/pubmed/10556038 10556038] |
[[Category: 2,2-dialkylglycine decarboxylase (pyruvate)]] | [[Category: 2,2-dialkylglycine decarboxylase (pyruvate)]] | ||
[[Category: Burkholderia cepacia]] | [[Category: Burkholderia cepacia]] | ||
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[[Category: catalytic mechanism]] | [[Category: catalytic mechanism]] | ||
[[Category: decarboxylation inhibitor]] | [[Category: decarboxylation inhibitor]] | ||
| - | [[Category: enzyme | + | [[Category: enzyme complex]] |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 10:34:06 2008'' |
Revision as of 08:34, 20 March 2008
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| , resolution 2.00Å | |||||||
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| Ligands: | , and | ||||||
| Activity: | 2,2-dialkylglycine decarboxylase (pyruvate), with EC number 4.1.1.64 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
CRYSTAL STRUCTURE OF THE COMPLEX OF 2,2-DIALKYLGLYCINE DECARBOXYLASE WITH 5PA
Overview
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.
About this Structure
1D7R is a Single protein structure of sequence from Burkholderia cepacia. Full crystallographic information is available from OCA.
Reference
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
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