1gpp: Difference between revisions
m Protected "1gpp" [edit=sysop:move=sysop] |
No edit summary |
||
| (8 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
==Crystal structure of the S.cerevisiae Homing Endonuclease PI-SceI Domain I== | |||
<StructureSection load='1gpp' size='340' side='right'caption='[[1gpp]], [[Resolution|resolution]] 1.35Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1gpp]] 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=1GPP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GPP 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]] 1.35Å</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=1gpp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gpp OCA], [https://pdbe.org/1gpp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gpp RCSB], [https://www.ebi.ac.uk/pdbsum/1gpp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gpp 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/gp/1gpp_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=1gpp ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The homing endonuclease PI-SceI from Saccharo myces cerevisiae consists of two domains. The protein splicing domain I catalyzes the excision of the mature endonuclease (intein) from a precursor protein and the religation of the flanking amino acid sequences (exteins) to a functional protein. Furthermore, domain I is involved in binding and recognition of the specific DNA substrate. Domain II of PI-SceI, the endonuclease domain, which is structurally homologous to other homing endonucleases from the LAGLIDADG family, harbors the endonucleolytic center of PI-SceI, which in vivo initiates the homing process by introducing a double-strand cut in the approximately 35 bp recognition sequence. At 1.35 A resolution, the crystal structure of PI-SceI domain I provides a detailed view of the part of the protein that is responsible for tight and specific DNA binding. A geometry-based docking of the 75 degrees bent recognition sequence to the full-length protein implies a conformational change or hinge movement of a subdomain of domain I, the tongs part, that is predicted to reach into the major groove near base pairs +16 to +18. | |||
High resolution crystal structure of domain I of the Saccharomyces cerevisiae homing endonuclease PI-SceI.,Werner E, Wende W, Pingoud A, Heinemann U Nucleic Acids Res. 2002 Sep 15;30(18):3962-71. PMID:12235380<ref>PMID:12235380</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1gpp" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
*[[Endonuclease|Endonuclease]] | *[[Endonuclease 3D structures|Endonuclease 3D structures]] | ||
== References == | |||
== | <references/> | ||
< | __TOC__ | ||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Saccharomyces cerevisiae]] | [[Category: Saccharomyces cerevisiae]] | ||
[[Category: Heinemann | [[Category: Heinemann U]] | ||
[[Category: Pingoud | [[Category: Pingoud A]] | ||
[[Category: Wende | [[Category: Wende W]] | ||
[[Category: Werner | [[Category: Werner E]] | ||
Latest revision as of 15:03, 13 December 2023
Crystal structure of the S.cerevisiae Homing Endonuclease PI-SceI Domain ICrystal structure of the S.cerevisiae Homing Endonuclease PI-SceI Domain I
Structural highlights
FunctionVATA_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.[1] 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.[2] Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe homing endonuclease PI-SceI from Saccharo myces cerevisiae consists of two domains. The protein splicing domain I catalyzes the excision of the mature endonuclease (intein) from a precursor protein and the religation of the flanking amino acid sequences (exteins) to a functional protein. Furthermore, domain I is involved in binding and recognition of the specific DNA substrate. Domain II of PI-SceI, the endonuclease domain, which is structurally homologous to other homing endonucleases from the LAGLIDADG family, harbors the endonucleolytic center of PI-SceI, which in vivo initiates the homing process by introducing a double-strand cut in the approximately 35 bp recognition sequence. At 1.35 A resolution, the crystal structure of PI-SceI domain I provides a detailed view of the part of the protein that is responsible for tight and specific DNA binding. A geometry-based docking of the 75 degrees bent recognition sequence to the full-length protein implies a conformational change or hinge movement of a subdomain of domain I, the tongs part, that is predicted to reach into the major groove near base pairs +16 to +18. High resolution crystal structure of domain I of the Saccharomyces cerevisiae homing endonuclease PI-SceI.,Werner E, Wende W, Pingoud A, Heinemann U Nucleic Acids Res. 2002 Sep 15;30(18):3962-71. PMID:12235380[3] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
|
| ||||||||||||||||