1k61

From Proteopedia

(Difference between revisions)

Current revision

MATALPHA2 HOMEODOMAIN BOUND TO DNA

Structural highlights

1k61 is a 6 chain structure with sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.1Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

MTAL2_YEAST Mating type proteins are sequence specific DNA-binding proteins that act as master switches in yeast differentiation by controlling gene expression in a cell type-specific fashion. Transcriptional corepressor that binds cooperatively with MCM1 to a 31-basepair DNA sequence termed the a-specific gene (asg) operator, to repress the transcription of a-cell-specific genes. Additionally, in a/alpha diploid cells, binds cooperatively with the A1 protein to a 21-basepair DNA sequence termed the haploid-specific gene (hsg) operator, to repress transcription of haploid-specific genes and of MATALPHA1.^[1]

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

Hoogsteen base pairs within duplex DNA typically are only observed in regions containing significant distortion or near sites of drug intercalation. We report here the observation of a Hoogsteen base pair embedded within undistorted, unmodified B-DNA. The Hoogsteen base pair, consisting of a syn adenine base paired with an anti thymine base, is found in the 2.1 A resolution structure of the MATalpha2 homeodomain bound to DNA in a region where a specifically and a non-specifically bound homeodomain contact overlapping sites. NMR studies of the free DNA show no evidence of Hoogsteen base pair formation, suggesting that protein binding favors the transition from a Watson-Crick to a Hoogsteen base pair. Molecular dynamics simulations of the homeodomain-DNA complex support a role for the non-specifically bound protein in favoring Hoogsteen base pair formation. The presence of a Hoogsteen base pair in the crystal structure of a protein-DNA complex raises the possibility that Hoogsteen base pairs could occur within duplex DNA and play a hitherto unrecognized role in transcription, replication and other cellular processes.

A Hoogsteen base pair embedded in undistorted B-DNA.,Aishima J, Gitti RK, Noah JE, Gan HH, Schlick T, Wolberger C Nucleic Acids Res. 2002 Dec 1;30(23):5244-52. PMID:12466549^[2]

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

References

↑ Johnson AD. Molecular mechanisms of cell-type determination in budding yeast. Curr Opin Genet Dev. 1995 Oct;5(5):552-8. PMID:8664541
↑ Aishima J, Gitti RK, Noah JE, Gan HH, Schlick T, Wolberger C. A Hoogsteen base pair embedded in undistorted B-DNA. Nucleic Acids Res. 2002 Dec 1;30(23):5244-52. PMID:12466549

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/1k61"

@@ Line 3: / Line 3: @@
 <StructureSection load='1k61' size='340' side='right'caption='[[1k61]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1k61]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K61 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K61 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1k61]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K61 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K61 FirstGlance]. <br>
-</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5IU:5-IODO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>5IU</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1apl|1apl]], [[1yrn|1yrn]], [[1mnm|1mnm]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5IU:5-IODO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>5IU</scene></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=1k61 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k61 OCA], [https://pdbe.org/1k61 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k61 RCSB], [https://www.ebi.ac.uk/pdbsum/1k61 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k61 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/MTAL2_YEAST MTAL2_YEAST] Mating type proteins are sequence specific DNA-binding proteins that act as master switches in yeast differentiation by controlling gene expression in a cell type-specific fashion. Transcriptional corepressor that binds cooperatively with MCM1 to a 31-basepair DNA sequence termed the a-specific gene (asg) operator, to repress the transcription of a-cell-specific genes. Additionally, in a/alpha diploid cells, binds cooperatively with the A1 protein to a 21-basepair DNA sequence termed the haploid-specific gene (hsg) operator, to repress transcription of haploid-specific genes and of MATALPHA1.<ref>PMID:8664541</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 32: / Line 34: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Aishima, J]]
+[[Category: Saccharomyces cerevisiae]]
-[[Category: Gan, H H]]
+[[Category: Aishima J]]
-[[Category: Gitti, R K]]
+[[Category: Gan HH]]
-[[Category: Noah, J E]]
+[[Category: Gitti RK]]
-[[Category: Schlick, T]]
+[[Category: Noah JE]]
-[[Category: Wolberger, C]]
+[[Category: Schlick T]]
-[[Category: Homeodomain]]
+[[Category: Wolberger C]]
-[[Category: Hoogsteen base pair]]
-[[Category: Protein-dna complex]]
-[[Category: Transcription-dna complex]]

1k61

From Proteopedia

Current revision

MATALPHA2 HOMEODOMAIN BOUND TO DNA

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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