1um2: Difference between revisions
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< | ==Crystal Structure of the Vma1-Derived Endonuclease with the Ligated Extein Segment== | ||
<StructureSection load='1um2' size='340' side='right'caption='[[1um2]], [[Resolution|resolution]] 2.90Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1um2]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. The November 2010 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Inteins'' by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2010_11 10.2210/rcsb_pdb/mom_2010_11]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UM2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UM2 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]] 2.9Å</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=1um2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1um2 OCA], [https://pdbe.org/1um2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1um2 RCSB], [https://www.ebi.ac.uk/pdbsum/1um2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1um2 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/um/1um2_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=1um2 ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Protein splicing precisely excises out an internal intein segment from a protein precursor, and concomitantly ligates the N- and C-terminal extein polypeptides flanking the intein. A recombinant X10SNS bearing N- and C-extein polypeptides has been prepared for the intein endonuclease derived from the Saccharomyces cerevisiae VMA1 gene. X10SNS has replacements of C284S, H362N and C738S, and forms the intein and extein segments in the crystal lattice. The crystal structure of X10SNS revealed a linkage between the N- and C-extein segments, and showed that the C284 amino group of the resultant intein segment is in interaction with the G283 O atom of the N-extein segment. A mechanism for the final S --> N acyl shift step proposes that a tetrahedral intermediate involves a five-membered thiazolidine ring at G283-C738 junction. An oxyanion of the thiazolidine intermediate is to be stabilized by the C284 N atom. | |||
Protein splicing of yeast VMA1-derived endonuclease via thiazolidine intermediates.,Mizutani R, Anraku Y, Satow Y J Synchrotron Radiat. 2004 Jan 1;11(Pt 1):109-12. Epub 2003 Nov 28. PMID:14646148<ref>PMID:14646148</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1um2" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
= | |||
== | |||
< | |||
[[Category: Inteins]] | [[Category: Inteins]] | ||
[[Category: Large Structures]] | |||
[[Category: RCSB PDB Molecule of the Month]] | [[Category: RCSB PDB Molecule of the Month]] | ||
[[Category: Saccharomyces cerevisiae]] | [[Category: Saccharomyces cerevisiae]] | ||
[[Category: Anraku | [[Category: Anraku Y]] | ||
[[Category: Mizutani | [[Category: Mizutani R]] | ||
[[Category: Satow | [[Category: Satow Y]] | ||
Latest revision as of 10:42, 25 October 2023
Crystal Structure of the Vma1-Derived Endonuclease with the Ligated Extein SegmentCrystal Structure of the Vma1-Derived Endonuclease with the Ligated Extein Segment
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 PubMedProtein splicing precisely excises out an internal intein segment from a protein precursor, and concomitantly ligates the N- and C-terminal extein polypeptides flanking the intein. A recombinant X10SNS bearing N- and C-extein polypeptides has been prepared for the intein endonuclease derived from the Saccharomyces cerevisiae VMA1 gene. X10SNS has replacements of C284S, H362N and C738S, and forms the intein and extein segments in the crystal lattice. The crystal structure of X10SNS revealed a linkage between the N- and C-extein segments, and showed that the C284 amino group of the resultant intein segment is in interaction with the G283 O atom of the N-extein segment. A mechanism for the final S --> N acyl shift step proposes that a tetrahedral intermediate involves a five-membered thiazolidine ring at G283-C738 junction. An oxyanion of the thiazolidine intermediate is to be stabilized by the C284 N atom. Protein splicing of yeast VMA1-derived endonuclease via thiazolidine intermediates.,Mizutani R, Anraku Y, Satow Y J Synchrotron Radiat. 2004 Jan 1;11(Pt 1):109-12. Epub 2003 Nov 28. PMID:14646148[3] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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