1dgd

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[[Image:1dgd.jpg|left|200px]]
[[Image:1dgd.jpg|left|200px]]
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{{Structure
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<!--
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|PDB= 1dgd |SIZE=350|CAPTION= <scene name='initialview01'>1dgd</scene>, resolution 2.8&Aring;
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The line below this paragraph, containing "STRUCTURE_1dgd", creates the "Structure Box" on the page.
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|SITE=
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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|LIGAND= <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&#39;-PHOSPHATE'>PLP</scene>
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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|ACTIVITY= <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>
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or leave the SCENE parameter empty for the default display.
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|GENE=
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|DOMAIN=
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{{STRUCTURE_1dgd| PDB=1dgd | SCENE= }}
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|RELATEDENTRY=
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1dgd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dgd OCA], [http://www.ebi.ac.uk/pdbsum/1dgd PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1dgd RCSB]</span>
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}}
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'''AN ALKALI METAL ION SIZE-DEPENDENT SWITCH IN THE ACTIVE SITE STRUCTURE OF DIALKYLGLYCINE DECARBOXYLASE'''
'''AN ALKALI METAL ION SIZE-DEPENDENT SWITCH IN THE ACTIVE SITE STRUCTURE OF DIALKYLGLYCINE DECARBOXYLASE'''
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==Reference==
==Reference==
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:[http://www.ncbi.nlm.nih.gov/pubmed/7947767 7947767]
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:[http://www.ncbi.nlm.nih.gov/pubmed/7947767 7947767]
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[[Category: 2,2-dialkylglycine decarboxylase (pyruvate)]]
 
[[Category: Burkholderia cepacia]]
[[Category: Burkholderia cepacia]]
[[Category: Single protein]]
[[Category: Single protein]]
[[Category: Hohenester, E.]]
[[Category: Hohenester, E.]]
[[Category: Jansonius, J N.]]
[[Category: Jansonius, J N.]]
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[[Category: lyase]]
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[[Category: Lyase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 13:49:51 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:41:20 2008''
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Revision as of 10:49, 2 May 2008

Image:1dgd.jpg

Template:STRUCTURE 1dgd

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


Overview

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., & 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.

About this Structure

1DGD is a Single protein structure of sequence from Burkholderia cepacia. Full crystallographic information is available from OCA.

Reference

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 Page seeded by OCA on Fri May 2 13:49:51 2008

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