View source for 1jva


==CRYSTAL STRUCTURE OF THE VMA1-DERIVED ENDONUCLEASE BEARING THE N AND C EXTEIN PROPEPTIDES==
<StructureSection load='1jva' size='340' side='right'caption='[[1jva]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1jva]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. The November 2010 RCSB PDB [http://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 [http://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=1JVA OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1JVA FirstGlance]. <br>
</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1vde|1vde]], [[1ef0|1ef0]]</div></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">VMA1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1jva FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jva OCA], [http://pdbe.org/1jva PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1jva RCSB], [http://www.ebi.ac.uk/pdbsum/1jva PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1jva ProSAT]</span></td></tr>
</table>
== Function ==
[[http://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/jv/1jva_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=1jva ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Protein splicing excises an internal intein segment from a protein precursor precisely, and concomitantly ligates flanking N and C-extein polypeptides at the respective sides of the precursor. Here, a series of precursor recombinants bearing 11 N-extein and ten C-extein residues is prepared for the intein of the Saccharomyces cerevisiae VMA1-derived homing endonuclease referred to as VDE and as PI-SceI. The recombinant with replacements of C284S, H362N, N737S, and C738S is chosen as a spliceable precursor model and is then subjected to a 2.1A resolution crystallographic analysis. The crystal structure shows that the introduced extein polypeptides are located in the vicinity of the splicing site, and that each of their peptide bonds is in the trans conformation. The S284 O(gamma) atom located at a distance of 3.1A from the G283 C atom in the N-terminal junction suggests that a nucleophilic attack of the C284 S(gamma) atom on the G283 C atom forms a tetrahedral intermediate containing a five-membered thiazolidine ring. The tetrahedral intermediate is supposedly resolved into a thioester acyl group upon the cleavage of the linkage between the G283 C and C284 N atoms, and this thioester acyl formation completes the initial steps of Nright arrowS acyl shift at the junction between the N-extein and intein. The S738 O(gamma) atom in the C-terminal junction is placed in close proximity to the S284 O(gamma) atom at a distance of 3.6A, and is well suited for another nucleophilic attack on the resultant thioester acyl group that is then subjected to the transesterification in the next step. The reaction steps proposed for the acyl shift are driven entirely by protonation and deprotonation, in which proton ingress and egress is balanced within the splicing site.

Protein-splicing reaction via a thiazolidine intermediate: crystal structure of the VMA1-derived endonuclease bearing the N and C-terminal propeptides.,Mizutani R, Nogami S, Kawasaki M, Ohya Y, Anraku Y, Satow Y J Mol Biol. 2002 Mar 1;316(4):919-29. PMID:11884132<ref>PMID:11884132</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1jva" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Atcc 18824]]
[[Category: Inteins]]
[[Category: Large Structures]]
[[Category: RCSB PDB Molecule of the Month]]
[[Category: Mizutani, R]]
[[Category: Satow, Y]]
[[Category: Hydrolase]]
[[Category: Intein]]
[[Category: Protein-splicing]]
[[Category: Thiazolidine intermediate]]
[[Category: Vde]]
[[Category: Vma1-derived endonuclease]]