5hod

From Proteopedia

(Difference between revisions)

Current revision

Structure of LHX4 transcription factor complexed with DNA

Structural highlights

5hod is a 4 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.682Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

LHX4_HUMAN Hypothyroidism due to deficient transcription factors involved in pituitary development or function;Pituitary stalk interruption syndrome;Short stature - pituitary and cerebellar defects - small sella turcica. The disease is caused by mutations affecting the gene represented in this entry. A chromosomal aberration involving LHX4 may be a cause of acute lymphoblastic leukemia. Translocation t(1;14)(q25;q32) with IGHG1.^[1]

Function

LHX4_HUMAN May play a critical role in the development of respiratory control mechanisms and in the normal growth and maturation of the lung.

Publication Abstract from PubMed

The majority of CpG dinucleotides in the human genome are methylated at cytosine bases. However, active gene regulatory elements are generally hypomethylated relative to their flanking regions, and the binding of some transcription factors (TFs) is diminished by methylation of their target sequences. By analysis of 542 human TFs with methylation-sensitive SELEX (systematic evolution of ligands by exponential enrichment), we found that there are also many TFs that prefer CpG-methylated sequences. Most of these are in the extended homeodomain family. Structural analysis showed that homeodomain specificity for methylcytosine depends on direct hydrophobic interactions with the methylcytosine 5-methyl group. This study provides a systematic examination of the effect of an epigenetic DNA modification on human TF binding specificity and reveals that many developmentally important proteins display preference for mCpG-containing sequences.

Impact of cytosine methylation on DNA binding specificities of human transcription factors.,Yin Y, Morgunova E, Jolma A, Kaasinen E, Sahu B, Khund-Sayeed S, Das PK, Kivioja T, Dave K, Zhong F, Nitta KR, Taipale M, Popov A, Ginno PA, Domcke S, Yan J, Schubeler D, Vinson C, Taipale J Science. 2017 May 5;356(6337). pii: eaaj2239. doi: 10.1126/science.aaj2239. PMID:28473536^[2]

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

References

↑ Machinis K, Pantel J, Netchine I, Leger J, Camand OJ, Sobrier ML, Dastot-Le Moal F, Duquesnoy P, Abitbol M, Czernichow P, Amselem S. Syndromic short stature in patients with a germline mutation in the LIM homeobox LHX4. Am J Hum Genet. 2001 Nov;69(5):961-8. Epub 2001 Sep 20. PMID:11567216
↑ Yin Y, Morgunova E, Jolma A, Kaasinen E, Sahu B, Khund-Sayeed S, Das PK, Kivioja T, Dave K, Zhong F, Nitta KR, Taipale M, Popov A, Ginno PA, Domcke S, Yan J, Schubeler D, Vinson C, Taipale J. Impact of cytosine methylation on DNA binding specificities of human transcription factors. Science. 2017 May 5;356(6337). pii: eaaj2239. doi: 10.1126/science.aaj2239. PMID:28473536 doi:http://dx.doi.org/10.1126/science.aaj2239

1 Structural highlights
2 Disease
3 Function
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/5hod"

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 5hod is ON HOLD
+==Structure of LHX4 transcription factor complexed with DNA==
+<StructureSection load='5hod' size='340' side='right'caption='[[5hod]], [[Resolution|resolution]] 2.68&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5hod]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HOD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5HOD FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.682&#8491;</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=5hod FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hod OCA], [https://pdbe.org/5hod PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5hod RCSB], [https://www.ebi.ac.uk/pdbsum/5hod PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5hod ProSAT]</span></td></tr>
+</table>
+== Disease ==
+[https://www.uniprot.org/uniprot/LHX4_HUMAN LHX4_HUMAN] Hypothyroidism due to deficient transcription factors involved in pituitary development or function;Pituitary stalk interruption syndrome;Short stature - pituitary and cerebellar defects - small sella turcica. The disease is caused by mutations affecting the gene represented in this entry.  A chromosomal aberration involving LHX4 may be a cause of acute lymphoblastic leukemia. Translocation t(1;14)(q25;q32) with IGHG1.<ref>PMID:11567216</ref>
+== Function ==
+[https://www.uniprot.org/uniprot/LHX4_HUMAN LHX4_HUMAN] May play a critical role in the development of respiratory control mechanisms and in the normal growth and maturation of the lung.
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The majority of CpG dinucleotides in the human genome are methylated at cytosine bases. However, active gene regulatory elements are generally hypomethylated relative to their flanking regions, and the binding of some transcription factors (TFs) is diminished by methylation of their target sequences. By analysis of 542 human TFs with methylation-sensitive SELEX (systematic evolution of ligands by exponential enrichment), we found that there are also many TFs that prefer CpG-methylated sequences. Most of these are in the extended homeodomain family. Structural analysis showed that homeodomain specificity for methylcytosine depends on direct hydrophobic interactions with the methylcytosine 5-methyl group. This study provides a systematic examination of the effect of an epigenetic DNA modification on human TF binding specificity and reveals that many developmentally important proteins display preference for mCpG-containing sequences.
-Authors: Morgunova, E., Yin, Y., Popov, A., Taipale, J.
+Impact of cytosine methylation on DNA binding specificities of human transcription factors.,Yin Y, Morgunova E, Jolma A, Kaasinen E, Sahu B, Khund-Sayeed S, Das PK, Kivioja T, Dave K, Zhong F, Nitta KR, Taipale M, Popov A, Ginno PA, Domcke S, Yan J, Schubeler D, Vinson C, Taipale J Science. 2017 May 5;356(6337). pii: eaaj2239. doi: 10.1126/science.aaj2239. PMID:28473536<ref>PMID:28473536</ref>
-Description: Structure of LHX4 transcription factor complexed with DNA
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Popov, A]]
+<div class="pdbe-citations 5hod" style="background-color:#fffaf0;"></div>
-[[Category: Yin, Y]]
+== References ==
-[[Category: Taipale, J]]
+<references/>
-[[Category: Morgunova, E]]
+__TOC__
+</StructureSection>
+[[Category: Homo sapiens]]
+[[Category: Large Structures]]
+[[Category: Morgunova E]]
+[[Category: Popov A]]
+[[Category: Taipale J]]
+[[Category: Yin Y]]

5hod

From Proteopedia

Current revision

Structure of LHX4 transcription factor complexed with DNA

Structural highlights

Disease

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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