7e29

From Proteopedia

(Difference between revisions)

Current revision

Crystal Structure of Saccharomyces cerevisiae Ioc4 PWWP domain fused with MBP

Structural highlights

7e29 is a 1 chain structure with sequence from Escherichia coli K-12 and Saccharomyces cerevisiae S288C. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.303Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

MALE_ECOLI Involved in the high-affinity maltose membrane transport system MalEFGK. Initial receptor for the active transport of and chemotaxis toward maltooligosaccharides.IOC4_YEAST Functions as component of the ISW1B complex, which acts in remodeling the chromatin by catalyzing an ATP-dependent alteration in the structure of nucleosomal DNA. The ISW1B complex acts within coding regions to control the amount of RNA polymerase II released into productive elongation and to coordinate elongation with termination and pre-mRNA processing.^[1] ^[2]

Publication Abstract from PubMed

The Isw1b chromatin-remodeling complex is specifically recruited to gene bodies to help retain pre-existing histones during transcription by RNA polymerase II. Recruitment is dependent on H3K36 methylation and the Isw1b subunit Ioc4, which contains an N-terminal PWWP domain. Here, we present the crystal structure of the Ioc4-PWWP domain, including a detailed functional characterization of the domain on its own as well as in the context of full-length Ioc4 and the Isw1b remodeler. The Ioc4-PWWP domain preferentially binds H3K36me3-containing nucleosomes. Its ability to bind DNA is required for nucleosome binding. It is also furthered by the unique insertion motif present in Ioc4-PWWP. The ability to bind H3K36me3 and DNA promotes the interaction of full-length Ioc4 with nucleosomes in vitro and they are necessary for its recruitment to gene bodies in vivo. Furthermore, a fully functional Ioc4-PWWP domain promotes efficient remodeling by Isw1b and the maintenance of ordered chromatin in vivo, thereby preventing the production of non-coding RNAs.

H3K36 methylation and DNA-binding both promote Ioc4 recruitment and Isw1b remodeler function.,Li J, Bergmann L, Rafael de Almeida A, Webb KM, Gogol MM, Voigt P, Liu Y, Liang H, Smolle MM Nucleic Acids Res. 2022 Mar 21;50(5):2549-2565. doi: 10.1093/nar/gkac077. PMID:35188579^[3]

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

References

↑ Vary JC Jr, Gangaraju VK, Qin J, Landel CC, Kooperberg C, Bartholomew B, Tsukiyama T. Yeast Isw1p forms two separable complexes in vivo. Mol Cell Biol. 2003 Jan;23(1):80-91. PMID:12482963
↑ Morillon A, Karabetsou N, O'Sullivan J, Kent N, Proudfoot N, Mellor J. Isw1 chromatin remodeling ATPase coordinates transcription elongation and termination by RNA polymerase II. Cell. 2003 Nov 14;115(4):425-35. PMID:14622597
↑ Li J, Bergmann L, Rafael de Almeida A, Webb KM, Gogol MM, Voigt P, Liu Y, Liang H, Smolle MM. H3K36 methylation and DNA-binding both promote Ioc4 recruitment and Isw1b remodeler function. Nucleic Acids Res. 2022 Mar 21;50(5):2549-2565. doi: 10.1093/nar/gkac077. PMID:35188579 doi:http://dx.doi.org/10.1093/nar/gkac077

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/7e29"

@@ Line 3: / Line 3: @@
 <StructureSection load='7e29' size='340' side='right'caption='[[7e29]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[7e29]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7E29 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7E29 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[7e29]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12] and [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7E29 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7E29 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</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]] 2.303&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=PRD_900001:alpha-maltose'>PRD_900001</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=7e29 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7e29 OCA], [https://pdbe.org/7e29 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7e29 RCSB], [https://www.ebi.ac.uk/pdbsum/7e29 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7e29 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/MALE_ECOLI MALE_ECOLI]] Involved in the high-affinity maltose membrane transport system MalEFGK. Initial receptor for the active transport of and chemotaxis toward maltooligosaccharides.
+[https://www.uniprot.org/uniprot/MALE_ECOLI MALE_ECOLI] Involved in the high-affinity maltose membrane transport system MalEFGK. Initial receptor for the active transport of and chemotaxis toward maltooligosaccharides.[https://www.uniprot.org/uniprot/IOC4_YEAST IOC4_YEAST] Functions as component of the ISW1B complex, which acts in remodeling the chromatin by catalyzing an ATP-dependent alteration in the structure of nucleosomal DNA. The ISW1B complex acts within coding regions to control the amount of RNA polymerase II released into productive elongation and to coordinate elongation with termination and pre-mRNA processing.<ref>PMID:12482963</ref> <ref>PMID:14622597</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 23: @@
 __TOC__
 </StructureSection>
+[[Category: Escherichia coli K-12]]
 [[Category: Large Structures]]
-[[Category: Li, J]]
+[[Category: Saccharomyces cerevisiae S288C]]
-[[Category: Liang, H]]
+[[Category: Li J]]
-[[Category: Liu, Y]]
+[[Category: Liang H]]
-[[Category: Smolle, M]]
+[[Category: Liu Y]]
-[[Category: Gene regulation]]
+[[Category: Smolle M]]
-[[Category: Pwwp]]
-[[Category: Transcription]]

7e29

From Proteopedia

Current revision

Crystal Structure of Saccharomyces cerevisiae Ioc4 PWWP domain fused with MBP

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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