2pnq: Difference between revisions

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New page: left|200px<br /><applet load="2pnq" size="350" color="white" frame="true" align="right" spinBox="true" caption="2pnq, resolution 1.81Å" /> '''Crystal structure of...
 
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[[Image:2pnq.jpg|left|200px]]<br /><applet load="2pnq" size="350" color="white" frame="true" align="right" spinBox="true"
caption="2pnq, resolution 1.81&Aring;" />
'''Crystal structure of pyruvate dehydrogenase phosphatase 1 (PDP1)'''<br />


==Overview==
==Crystal structure of pyruvate dehydrogenase phosphatase 1 (PDP1)==
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.
<StructureSection load='2pnq' size='340' side='right'caption='[[2pnq]], [[Resolution|resolution]] 1.81&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[2pnq]] is a 2 chain structure with sequence from [https://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]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PNQ FirstGlance]. <br>
2PNQ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus] with <scene name='pdbligand=MG:'>MG</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PNQ OCA].
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.81&#8491;</td></tr>
 
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
==Reference==
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2pnq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pnq OCA], [https://pdbe.org/2pnq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pnq RCSB], [https://www.ebi.ac.uk/pdbsum/2pnq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pnq ProSAT]</span></td></tr>
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://ispc.weizmann.ac.il//pmbin/getpm?pmid=17532339 17532339]
</table>
== Function ==
[https://www.uniprot.org/uniprot/PDP1_RAT PDP1_RAT] Catalyzes the dephosphorylation and concomitant reactivation of the alpha subunit of the E1 component of the pyruvate dehydrogenase complex.
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pn/2pnq_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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=2pnq ConSurf].
<div style="clear:both"></div>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Rattus norvegicus]]
[[Category: Rattus norvegicus]]
[[Category: Single protein]]
[[Category: Symersky J]]
[[Category: [Pyruvate dehydrogenase (lipoamide)]-phosphatase]]
[[Category: Vassylyev DG]]
[[Category: Symersky, J.]]
[[Category: Vassylyev, D.G.]]
[[Category: MG]]
[[Category: catalytic subunit]]
[[Category: crystal structure]]
[[Category: hydrolase]]
[[Category: pdp1c]]
[[Category: pyruvate dehydrogenase phosphatase 1]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 14:03:05 2008''

Latest revision as of 09:10, 21 February 2024

Crystal structure of pyruvate dehydrogenase phosphatase 1 (PDP1)

2pnq, resolution 1.81Å

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