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New page: left|200px<br /><applet load="1dfa" size="450" color="white" frame="true" align="right" spinBox="true" caption="1dfa, resolution 2.0Å" /> '''CRYSTAL STRUCTURE OF ...
 
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[[Image:1dfa.gif|left|200px]]<br /><applet load="1dfa" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1dfa, resolution 2.0&Aring;" />
'''CRYSTAL STRUCTURE OF PI-SCEI IN C2 SPACE GROUP'''<br />


==Overview==
==CRYSTAL STRUCTURE OF PI-SCEI IN C2 SPACE GROUP==
The PI-SceI protein is an intein-encoded homing endonuclease that, initiates the mobility of its gene by making a double strand break at a, single site in the yeast genome. The PI-SceI protein splicing and, endonucleolytic active sites are separately located in each of two domains, in the PI-SceI structure. To determine the spatial relationship between, bases in the PI-SceI recognition sequence and selected PI-SceI amino, acids, the PI-SceI-DNA complex was probed by photocross-linking and, affinity cleavage methods. Unique solvent-accessible cysteine residues, were introduced into the two PI-SceI domains at positions 91, 97, 170, 230, 376, and 378, and the mutant proteins were modified with either, 4-azidophenacyl bromide or iron, (S)-1-(p-bromoacetamidobenzyl)-ethylenediaminetetraacetate (FeBABE). The, phenyl azide-coupled proteins cross-linked to the PI-SceI target sequence, and the FeBABE-modified proteins cleaved the DNA proximal to the, derivatized amino acid. The results suggest that an extended beta-hairpin, loop in the endonuclease domain that contains residues 376 and 378, contacts the major groove near the PI-SceI cleavage site. Conversely, residues 91, 97, and 170 in the protein splicing domain are in close, proximity to a distant region of the substrate. To interpret our results, we used a new PI-SceI structure that is ordered in regions of the protein, that bind DNA. The data strongly support a model of the PI-SceI-DNA, complex derived from this structure.
<StructureSection load='1dfa' size='340' side='right'caption='[[1dfa]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1dfa]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DFA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DFA FirstGlance]. <br>
</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&#8491;</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=1dfa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dfa OCA], [https://pdbe.org/1dfa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dfa RCSB], [https://www.ebi.ac.uk/pdbsum/1dfa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dfa ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/VATA_YEAST VATA_YEAST] Catalytic subunit of the peripheral V1 complex of vacuolar ATPase. V-ATPase (vacuolar ATPase) is responsible for acidifying a variety of intracellular compartments in eukaryotic cells. It is an electrogenic proton pump that generates a proton motive force of 180 mV, inside positive and acidic, in the vacuolar membrane vesicles. It may participate in maintenance of cytoplasmic Ca(2+) homeostasis. This is a catalytic subunit.<ref>PMID:1534148</ref>  PI-SceI is an endonuclease that can cleave at a site present in a VMA1 allele that lacks the derived endonuclease segment of the open reading frame; cleavage at this site only occurs during meiosis and initiates "homing", a genetic event that converts a VMA1 allele lacking VDE into one that contains it.<ref>PMID:1534148</ref>
== 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/df/1dfa_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=1dfa ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1DFA is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Active as [http://en.wikipedia.org/wiki/H(+)-transporting_two-sector_ATPase H(+)-transporting two-sector ATPase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.3.14 3.6.3.14] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1DFA OCA].
*[[Endonuclease 3D structures|Endonuclease 3D structures]]
 
== References ==
==Reference==
<references/>
Probing the structure of the PI-SceI-DNA complex by affinity cleavage and affinity photocross-linking., Hu D, Crist M, Duan X, Quiocho FA, Gimble FS, J Biol Chem. 2000 Jan 28;275(4):2705-12. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10644733 10644733]
__TOC__
[[Category: H(+)-transporting two-sector ATPase]]
</StructureSection>
[[Category: Large Structures]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Single protein]]
[[Category: Crist M]]
[[Category: Crist, M.]]
[[Category: Duan X]]
[[Category: Duan, X.]]
[[Category: Gimble FS]]
[[Category: Gimble, F.S.]]
[[Category: Hu D]]
[[Category: Hu, D.]]
[[Category: Quiocho FA]]
[[Category: Quiocho, F.A.]]
[[Category: homing endonuclease]]
[[Category: hydrolase]]
[[Category: intein]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 13:14:17 2007''

Latest revision as of 06:53, 7 February 2024

CRYSTAL STRUCTURE OF PI-SCEI IN C2 SPACE GROUP

1dfa, resolution 2.00Å

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