2pnq
From Proteopedia
| Line 1: | Line 1: | ||
| - | [[Image:2pnq.jpg|left|200px]] | + | [[Image:2pnq.jpg|left|200px]] |
| - | + | ||
| - | '''Crystal structure of pyruvate dehydrogenase phosphatase 1 (PDP1)''' | + | {{Structure |
| + | |PDB= 2pnq |SIZE=350|CAPTION= <scene name='initialview01'>2pnq</scene>, resolution 1.81Å | ||
| + | |SITE= | ||
| + | |LIGAND= <scene name='pdbligand=MG:MAGNESIUM ION'>MG</scene> | ||
| + | |ACTIVITY= [http://en.wikipedia.org/wiki/[Pyruvate_dehydrogenase_(lipoamide)]-phosphatase [Pyruvate dehydrogenase (lipoamide)]-phosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.43 3.1.3.43] | ||
| + | |GENE= Pdp1, Ppm2c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Rattus norvegicus]) | ||
| + | }} | ||
| + | |||
| + | '''Crystal structure of pyruvate dehydrogenase phosphatase 1 (PDP1)''' | ||
| + | |||
==Overview== | ==Overview== | ||
| Line 7: | Line 16: | ||
==About this Structure== | ==About this Structure== | ||
| - | 2PNQ is a [ | + | 2PNQ is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PNQ OCA]. |
==Reference== | ==Reference== | ||
| - | Crystal structure of pyruvate dehydrogenase phosphatase 1 and its functional implications., Vassylyev DG, Symersky J, J Mol Biol. 2007 Jul 13;370(3):417-26. Epub 2007 May 10. PMID:[http:// | + | Crystal structure of pyruvate dehydrogenase phosphatase 1 and its functional implications., Vassylyev DG, Symersky J, J Mol Biol. 2007 Jul 13;370(3):417-26. Epub 2007 May 10. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17532339 17532339] |
[[Category: Rattus norvegicus]] | [[Category: Rattus norvegicus]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| Line 23: | Line 32: | ||
[[Category: pyruvate dehydrogenase phosphatase 1]] | [[Category: pyruvate dehydrogenase phosphatase 1]] | ||
| - | ''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 18:15:20 2008'' |
Revision as of 16:15, 20 March 2008
| |||||||
| , resolution 1.81Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | |||||||
| Gene: | Pdp1, Ppm2c (Rattus norvegicus) | ||||||
| Activity: | [Pyruvate_dehydrogenase_(lipoamide)-phosphatase [Pyruvate dehydrogenase (lipoamide)]-phosphatase], with EC number 3.1.3.43 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of pyruvate dehydrogenase phosphatase 1 (PDP1)
Overview
Pyruvate dehydrogenase phosphatase 1 (PDP1) catalyzes dephosphorylation of pyruvate dehydrogenase (E1) in the mammalian pyruvate dehydrogenase complex (PDC), whose activity is regulated by the phosphorylation-dephosphorylation cycle by the corresponding protein kinases (PDHKs) and phosphatases. The activity of PDP1 is greatly enhanced through Ca2+ -dependent binding of the catalytic subunit (PDP1c) to the L2 (inner lipoyl) domain of dihydrolipoyl acetyltransferase (E2), which is also integrated in PDC. Here, we report the crystal structure of the rat PDP1c at 1.8 A resolution. The structure reveals that PDP1 belongs to the PPM family of protein serine/threonine phosphatases, which, in spite of a low level of sequence identity, share the structural core consisting of the central beta-sandwich flanked on both sides by loops and alpha-helices. Consistent with the previous studies, two well-fixed magnesium ions are coordinated by five active site residues and five water molecules in the PDP1c catalytic center. Structural analysis indicates that, while the central portion of the PDP1c molecule is highly conserved among the members of the PPM protein family, a number of structural insertions and deletions located at the periphery of PDP1c likely define its functional specificity towards the PDC. One notable feature of PDP1c is a long insertion (residues 98-151) forming a unique hydrophobic pocket on the surface that likely accommodates the lipoyl moiety of the E2 domain in a fashion similar to that of PDHKs. The cavity, however, appears more open than in PDHK, suggesting that its closure may be required to achieve tight, specific binding of the lipoic acid. We propose a mechanism in which the closure of the lipoic acid binding site is triggered by the formation of the intermolecular (PDP1c/L2) Ca2+ binding site in a manner reminiscent of the Ca2+ -induced closure of the regulatory domain of troponin C.
About this Structure
2PNQ is a Single protein structure of sequence from Rattus norvegicus. Full crystallographic information is available from OCA.
Reference
Crystal structure of pyruvate dehydrogenase phosphatase 1 and its functional implications., Vassylyev DG, Symersky J, J Mol Biol. 2007 Jul 13;370(3):417-26. Epub 2007 May 10. PMID:17532339[[Category: [Pyruvate dehydrogenase (lipoamide)]-phosphatase]]
Page seeded by OCA on Thu Mar 20 18:15:20 2008
