1dfa

From Proteopedia

(Difference between revisions)

Revision as of 08:21, 6 December 2017

CRYSTAL STRUCTURE OF PI-SCEI IN C2 SPACE GROUP

Structural highlights

1dfa is a 1 chain structure with sequence from Atcc 18824. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Related:	1vde
Activity:	H(+)-transporting two-sector ATPase, with EC number 3.6.3.14
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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.^[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 PubMed

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.

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:10644733^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Gimble FS, Thorner J. Homing of a DNA endonuclease gene by meiotic gene conversion in Saccharomyces cerevisiae. Nature. 1992 May 28;357(6376):301-6. PMID:1534148 doi:http://dx.doi.org/10.1038/357301a0
↑ Gimble FS, Thorner J. Homing of a DNA endonuclease gene by meiotic gene conversion in Saccharomyces cerevisiae. Nature. 1992 May 28;357(6376):301-6. PMID:1534148 doi:http://dx.doi.org/10.1038/357301a0
↑ Hu D, Crist M, Duan X, Quiocho FA, Gimble FS. Probing the structure of the PI-SceI-DNA complex by affinity cleavage and affinity photocross-linking. J Biol Chem. 2000 Jan 28;275(4):2705-12. PMID:10644733

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1dfa"

@@ Line 1: / Line 1: @@
 ==CRYSTAL STRUCTURE OF PI-SCEI IN C2 SPACE GROUP==
 <StructureSection load='1dfa' size='340' side='right' caption='[[1dfa]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
@@ Line 5: / Line 6: @@
 </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1vde|1vde]]</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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1dfa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dfa OCA], [http://pdbe.org/1dfa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1dfa RCSB], [http://www.ebi.ac.uk/pdbsum/1dfa PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1dfa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dfa OCA], [http://pdbe.org/1dfa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1dfa RCSB], [http://www.ebi.ac.uk/pdbsum/1dfa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1dfa ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 13: / Line 14: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/df/1dfa_consurf.spt"</scriptWhenChecked>
+    <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>
@@ Line 28: / Line 29: @@
 </div>
 <div class="pdbe-citations 1dfa" style="background-color:#fffaf0;"></div>
-==See Also==
-*[[Endonuclease|Endonuclease]]
 == References ==
 <references/>

1dfa

From Proteopedia

Revision as of 08:21, 6 December 2017

CRYSTAL STRUCTURE OF PI-SCEI IN C2 SPACE GROUP

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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