1ik7: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,330,058 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,330,058 edits
No edit summary
 
(12 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1ik7.jpg|left|200px]]


{{Structure
==Crystal Structure of the Uncomplexed Pelle Death Domain==
|PDB= 1ik7 |SIZE=350|CAPTION= <scene name='initialview01'>1ik7</scene>, resolution 2.30&Aring;
<StructureSection load='1ik7' size='340' side='right'caption='[[1ik7]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene> and <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>
<table><tr><td colspan='2'>[[1ik7]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IK7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IK7 FirstGlance]. <br>
|ACTIVITY= [http://en.wikipedia.org/wiki/Non-specific_serine/threonine_protein_kinase Non-specific serine/threonine protein kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.11.1 2.7.11.1]  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
|GENE= pelle ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 Drosophila melanogaster])
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></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=1ik7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ik7 OCA], [https://pdbe.org/1ik7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ik7 RCSB], [https://www.ebi.ac.uk/pdbsum/1ik7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ik7 ProSAT]</span></td></tr>
 
</table>
'''Crystal Structure of the Uncomplexed Pelle Death Domain'''
== Function ==
 
[https://www.uniprot.org/uniprot/KPEL_DROME KPEL_DROME] Plays an essential role in the Tl receptor signaling pathway that establishes embryonic dorsoventral polarity; the signal directs import of dl into ventral and ventrolateral nuclei, thereby establishing dorsoventral polarity. Tub recruits pll to the plasma membrane and protein-protein interaction activates pll.<ref>PMID:8440018</ref> <ref>PMID:7527496</ref> <ref>PMID:7635064</ref> <ref>PMID:10330490</ref>
 
== Evolutionary Conservation ==
==Overview==
[[Image:Consurf_key_small.gif|200px|right]]
The death domain (DD) of the protein kinase Pelle adopts a six-helix bundle fold in the crystal structure of the complex with its dimerization partner, Tube-DD. However, in crystals obtained from a solution of 45% 2-methyl-2,4-pentanediol (MPD), the C-terminal half of Pelle-DD folds into a single helix, and the N-terminal half of the molecule is disordered. The helical segment forms an antiparallel dimer with the corresponding helix of a symmetry-related molecule, and together they form extensive lattice interactions similar in number, composition, and buried surface to those in the six-helix bundle of the native fold. Secondary structure analysis by heteronuclear nuclear magnetic resonance spectroscopy (NMR) demonstrates that Pelle-DD adopts a six-helix bundle fold in aqueous solution. The fold is perturbed by MPD, with the largest chemical shift changes in one helix and two loop regions that encompass the Tube-DD binding site. Pelle-DD is stable to urea denaturation with a folding free energy of 7.9 kcal/mol at 25 degrees C but is destabilized, with loss of urea binding sites, in the presence of MPD. The data are consistent with a cosolvent denaturation model in which MPD denatures the N terminus of Pelle-DD but induces the C terminus to form a more compact structure and aggregate. A similar perturbation in vivo might occur at the plasma membrane and could have consequences for Pelle-mediated regulation. Generally, crystallographers should be aware that high concentrations of MPD or related cosolvents can alter the tertiary structure of susceptible proteins.
Check<jmol>
 
  <jmolCheckbox>
==About this Structure==
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ik/1ik7_consurf.spt"</scriptWhenChecked>
1IK7 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IK7 OCA].  
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 
    <text>to colour the structure by Evolutionary Conservation</text>
==Reference==
  </jmolCheckbox>
Cosolvent-induced transformation of a death domain tertiary structure., Xiao T, Gardner KH, Sprang SR, Proc Natl Acad Sci U S A. 2002 Aug 20;99(17):11151-6. Epub 2002 Aug 12. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12177432 12177432]
</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=1ik7 ConSurf].
<div style="clear:both"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Drosophila melanogaster]]
[[Category: Drosophila melanogaster]]
[[Category: Non-specific serine/threonine protein kinase]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Gardner KH]]
[[Category: Gardner, K H.]]
[[Category: Sprang SR]]
[[Category: Sprang, S R.]]
[[Category: Xiao T]]
[[Category: Xiao, T.]]
[[Category: MPD]]
[[Category: TRS]]
[[Category: mpd crystallization]]
[[Category: single helix]]
[[Category: structural transition]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 11:51:26 2008''
Retrieved from "https://proteopedia.org/1ik7"