This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

2euv

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 05:23, 10 September 2015

Principles of protein-DNA recognition revealed in the structural analysis of Ndt80-MSE DNA complexes

Structural highlights

2euv 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.
Related:	1mnn, 1mn4, 1m6u, 1m7u, 2etw, 2euw, 2eux, 2euz, 2evf, 2evg, 2evh, 2ehi, 2ehj
Gene:	ndt80 (ATCC 18824)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum

Function

[NDT80_YEAST] Transcription factor required for successful completion of meiosis and spore formation. Gets activated after completion of meiotic recombination at the end of prophase I. Recognizes and binds to the middle sporulation element (MSE) 5'-C[AG]CAAA[AT]-3' in the promoter region of stage-specific genes that are required for progression through meiosis and sporulation. Competes for binding to MSE with the transcriptional repressor SUM1, which represses middle sporulation-specific genes during mitosis and early sporulation.^[1] ^[2] ^[3] ^[4]

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 Saccharomyces cerevisiae transcription factor Ndt80 selectively binds a DNA consensus sequence (the middle sporulation element [MSE]) to activate gene expression after the successful completion of meiotic recombination. Here we report the X-ray crystal structures of Ndt80 bound to ten distinct MSE variants. Comparison of these structures with the structure of Ndt80 bound to a consensus MSE reveals structural principles that determine the DNA binding specificity of this transcription factor. The 5' GC-rich end of the MSE contains distinct 5'-YpG-3' steps that are recognized by arginine side chains through a combination of hydrogen bonding and cation-pi interactions. The 3' AT-rich region is recognized via minor groove contacts that sterically exclude the N2 atom of GC base pairs. The conformation of the AT-rich region is fixed by interactions with the protein that favor recognition of poly(A)-poly(T) versus mixed AT sequences through an avoidance of major groove steric clashes at 5'-ApT-3' steps.

Principles of protein-DNA recognition revealed in the structural analysis of Ndt80-MSE DNA complexes.,Lamoureux JS, Glover JN Structure. 2006 Mar;14(3):555-65. PMID:16531239^[5]

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

References

↑ Xu L, Ajimura M, Padmore R, Klein C, Kleckner N. NDT80, a meiosis-specific gene required for exit from pachytene in Saccharomyces cerevisiae. Mol Cell Biol. 1995 Dec;15(12):6572-81. PMID:8524222
↑ Chu S, Herskowitz I. Gametogenesis in yeast is regulated by a transcriptional cascade dependent on Ndt80. Mol Cell. 1998 Apr;1(5):685-96. PMID:9660952
↑ Hepworth SR, Friesen H, Segall J. NDT80 and the meiotic recombination checkpoint regulate expression of middle sporulation-specific genes in Saccharomyces cerevisiae. Mol Cell Biol. 1998 Oct;18(10):5750-61. PMID:9742092
↑ Pierce M, Benjamin KR, Montano SP, Georgiadis MM, Winter E, Vershon AK. Sum1 and Ndt80 proteins compete for binding to middle sporulation element sequences that control meiotic gene expression. Mol Cell Biol. 2003 Jul;23(14):4814-25. PMID:12832469
↑ Lamoureux JS, Glover JN. Principles of protein-DNA recognition revealed in the structural analysis of Ndt80-MSE DNA complexes. Structure. 2006 Mar;14(3):555-65. PMID:16531239 doi:10.1016/j.str.2005.11.017

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/2euv"

@@ Line 2: / Line 2: @@
 <StructureSection load='2euv' size='340' side='right' caption='[[2euv]], [[Resolution|resolution]] 1.94&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2euv]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EUV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EUV FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2euv]] 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=2EUV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EUV FirstGlance]. <br>
 </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1mnn|1mnn]], [[1mn4|1mn4]], [[1m6u|1m6u]], [[1m7u|1m7u]], [[2etw|2etw]], [[2euw|2euw]], [[2eux|2eux]], [[2euz|2euz]], [[2evf|2evf]], [[2evg|2evg]], [[2evh|2evh]], [[2ehi|2ehi]], [[2ehj|2ehj]]</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ndt80 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ndt80 ([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=2euv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2euv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2euv RCSB], [http://www.ebi.ac.uk/pdbsum/2euv 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=2euv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2euv OCA], [http://pdbe.org/2euv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2euv RCSB], [http://www.ebi.ac.uk/pdbsum/2euv PDBsum]</span></td></tr>
 </table>
 == Function ==
@@ Line 27: / Line 27: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2euv" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Saccharomyces cerevisiae]]
+[[Category: Atcc 18824]]
 [[Category: Glover, J N]]
 [[Category: Lamoureux, J S]]

2euv

From Proteopedia

Revision as of 05:23, 10 September 2015

Principles of protein-DNA recognition revealed in the structural analysis of Ndt80-MSE DNA complexes

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox