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1lwt

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Revision as of 08:03, 25 November 2020

Crystal structure of the intein homing endonuclease PI-SceI bound to its substrate DNA (Ca2+ free)

Structural highlights

1lwt is a 3 chain structure with sequence from Atcc 18824. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
NonStd Res:
Related:	1vde, 1lws
Gene:	VMA1 (ATCC 18824)
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 first X-ray structures of an intein-DNA complex, that of the two-domain homing endonuclease PI-SceI bound to its 36-base pair DNA substrate, have been determined in the presence and absence of Ca(2+). The DNA shows an asymmetric bending pattern, with a major 50 degree bend in the endonuclease domain and a minor 22 degree bend in the splicing domain region. Distortions of the DNA bound to the endonuclease domain cause the insertion of the two cleavage sites in the catalytic center. DNA binding induces changes in the protein conformation. The two overlapping non-identical active sites in the endonucleolytic center contain two Ca(+2) ions that coordinate to the catalytic Asp residues. Structure analysis indicates that the top strand may be cleaved first.

Crystal structure of the intein homing endonuclease PI-SceI bound to its recognition sequence.,Moure CM, Gimble FS, Quiocho FA Nat Struct Biol. 2002 Oct;9(10):764-70. PMID:12219083^[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
↑ Moure CM, Gimble FS, Quiocho FA. Crystal structure of the intein homing endonuclease PI-SceI bound to its recognition sequence. Nat Struct Biol. 2002 Oct;9(10):764-70. PMID:12219083 doi:10.1038/nsb840

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

@@ Line 1: / Line 1: @@
 ==Crystal structure of the intein homing endonuclease PI-SceI bound to its substrate DNA (Ca2+ free)==
-<StructureSection load='1lwt' size='340' side='right' caption='[[1lwt]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
+<StructureSection load='1lwt' size='340' side='right'caption='[[1lwt]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1lwt]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LWT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LWT FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1lwt]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LWT OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1LWT FirstGlance]. <br>
 </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1vde|1vde]], [[1lws|1lws]]</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]], [[1lws|1lws]]</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='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=1lwt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lwt OCA], [http://pdbe.org/1lwt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lwt RCSB], [http://www.ebi.ac.uk/pdbsum/1lwt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1lwt ProSAT]</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=1lwt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lwt OCA], [http://pdbe.org/1lwt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lwt RCSB], [http://www.ebi.ac.uk/pdbsum/1lwt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1lwt ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 15: / Line 15: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lw/1lwt_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lw/1lwt_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 30: / Line 30: @@
 </div>
 <div class="pdbe-citations 1lwt" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Endonuclease 3D structures|Endonuclease 3D structures]]
 == References ==
 <references/>
@@ Line 35: / Line 38: @@
 </StructureSection>
 [[Category: Atcc 18824]]
+[[Category: Large Structures]]
 [[Category: Gimble, F S]]
 [[Category: Moure, C M]]

1lwt

From Proteopedia

Revision as of 08:03, 25 November 2020

Crystal structure of the intein homing endonuclease PI-SceI bound to its substrate DNA (Ca2+ free)

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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