4bru

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of the yeast Dhh1-Edc3 complex

Structural highlights

4bru is a 2 chain structure with sequence from 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 3.245Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DHH1_YEAST ATP-dependent RNA helicase involved in mRNA turnover, and more specifically in mRNA decapping by activating the decapping enzyme DCP1. Is involved in G1/S DNA-damage checkpoint recovery, probably through the regulation of the translational status of a subset of mRNAs. May also have a role in translation and mRNA nuclear export. Required for sporulation.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9]

Publication Abstract from PubMed

Translational repression and deadenylation of eukaryotic mRNAs result either in the sequestration of the transcripts in a nontranslatable pool or in their degradation. Removal of the 5' cap structure is a crucial step that commits deadenylated mRNAs to 5'-to-3' degradation. Pat1, Edc3 and the DEAD-box protein Dhh1 are evolutionary conserved factors known to participate in both translational repression and decapping, but their interplay is currently unclear. We report the 2.8 A resolution structure of yeast Dhh1 bound to the N-terminal domain of Pat1. The structure shows how Pat1 wraps around the C-terminal RecA domain of Dhh1, docking onto the Phe-Asp-Phe (FDF) binding site. The FDF-binding site of Dhh1 also recognizes Edc3, revealing why the binding of Pat1 and Edc3 on Dhh1 are mutually exclusive events. Using co-immunoprecipitation assays and structure-based mutants, we demonstrate that the mode of Dhh1-Pat1 recognition is conserved in humans. Pat1 and Edc3 also interfere and compete with the RNA-binding properties of Dhh1. Mapping the RNA-binding sites on Dhh1 with a crosslinking-mass spectrometry approach shows a large RNA-binding surface around the C-terminal RecA domain, including the FDF-binding pocket. The results suggest a model for how Dhh1-containing messenger ribonucleoprotein particles might be remodeled upon Pat1 and Edc3 binding.

Structural analysis of the yeast Dhh1-Pat1 complex reveals how Dhh1 engages Pat1, Edc3 and RNA in mutually exclusive interactions.,Sharif H, Ozgur S, Sharma K, Basquin C, Urlaub H, Conti E Nucleic Acids Res. 2013 Jul 12. PMID:23851565^[10]

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

References

↑ Hata H, Mitsui H, Liu H, Bai Y, Denis CL, Shimizu Y, Sakai A. Dhh1p, a putative RNA helicase, associates with the general transcription factors Pop2p and Ccr4p from Saccharomyces cerevisiae. Genetics. 1998 Feb;148(2):571-9. PMID:9504907
↑ Coller JM, Tucker M, Sheth U, Valencia-Sanchez MA, Parker R. The DEAD box helicase, Dhh1p, functions in mRNA decapping and interacts with both the decapping and deadenylase complexes. RNA. 2001 Dec;7(12):1717-27. PMID:11780629
↑ Fischer N, Weis K. The DEAD box protein Dhh1 stimulates the decapping enzyme Dcp1. EMBO J. 2002 Jun 3;21(11):2788-97. PMID:12032091 doi:10.1093/emboj/21.11.2788
↑ Maillet L, Collart MA. Interaction between Not1p, a component of the Ccr4-not complex, a global regulator of transcription, and Dhh1p, a putative RNA helicase. J Biol Chem. 2002 Jan 25;277(4):2835-42. Epub 2001 Nov 5. PMID:11696541 doi:10.1074/jbc.M107979200
↑ Tseng-Rogenski SS, Chong JL, Thomas CB, Enomoto S, Berman J, Chang TH. Functional conservation of Dhh1p, a cytoplasmic DExD/H-box protein present in large complexes. Nucleic Acids Res. 2003 Sep 1;31(17):4995-5002. PMID:12930949
↑ Sheth U, Parker R. Decapping and decay of messenger RNA occur in cytoplasmic processing bodies. Science. 2003 May 2;300(5620):805-8. PMID:12730603 doi:10.1126/science.1082320
↑ Bergkessel M, Reese JC. An essential role for the Saccharomyces cerevisiae DEAD-box helicase DHH1 in G1/S DNA-damage checkpoint recovery. Genetics. 2004 May;167(1):21-33. PMID:15166134
↑ Teixeira D, Sheth U, Valencia-Sanchez MA, Brengues M, Parker R. Processing bodies require RNA for assembly and contain nontranslating mRNAs. RNA. 2005 Apr;11(4):371-82. Epub 2005 Feb 9. PMID:15703442 doi:10.1261/rna.7258505
↑ Muhlrad D, Parker R. The yeast EDC1 mRNA undergoes deadenylation-independent decapping stimulated by Not2p, Not4p, and Not5p. EMBO J. 2005 Mar 9;24(5):1033-45. Epub 2005 Feb 10. PMID:15706350 doi:10.1038/sj.emboj.7600560
↑ Sharif H, Ozgur S, Sharma K, Basquin C, Urlaub H, Conti E. Structural analysis of the yeast Dhh1-Pat1 complex reveals how Dhh1 engages Pat1, Edc3 and RNA in mutually exclusive interactions. Nucleic Acids Res. 2013 Jul 12. PMID:23851565 doi:10.1093/nar/gkt600

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4bru"

@@ Line 1: / Line 1: @@
-{{STRUCTURE_4bru|  PDB=4bru  |  SCENE=  }}
-===Crystal structure of the yeast Dhh1-Edc3 complex===
-{{ABSTRACT_PUBMED_23851565}}
-==Function==
+==Crystal structure of the yeast Dhh1-Edc3 complex==
-[[http://www.uniprot.org/uniprot/DHH1_YEAST DHH1_YEAST]] ATP-dependent RNA helicase involved in mRNA turnover, and more specifically in mRNA decapping by activating the decapping enzyme DCP1. Is involved in G1/S DNA-damage checkpoint recovery, probably through the regulation of the translational status of a subset of mRNAs. May also have a role in translation and mRNA nuclear export. Required for sporulation.<ref>PMID:9504907</ref> <ref>PMID:11780629</ref> <ref>PMID:12032091</ref> <ref>PMID:11696541</ref> <ref>PMID:12930949</ref> <ref>PMID:12730603</ref> <ref>PMID:15166134</ref> <ref>PMID:15703442</ref> <ref>PMID:15706350</ref>  [[http://www.uniprot.org/uniprot/EDC3_YEAST EDC3_YEAST]] Stimulates decapping of both stable and unstable mRNA during mRNA decay. Does not affect nonsense-mediated mRNA decay. Required for normal P-body assembly.<ref>PMID:18678652</ref> <ref>PMID:15020463</ref>
+<StructureSection load='4bru' size='340' side='right'caption='[[4bru]], [[Resolution|resolution]] 3.25&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[4bru]] is a 2 chain structure with sequence from [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=4BRU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4BRU 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]] 3.245&#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=4bru FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4bru OCA], [https://pdbe.org/4bru PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4bru RCSB], [https://www.ebi.ac.uk/pdbsum/4bru PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4bru ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DHH1_YEAST DHH1_YEAST] ATP-dependent RNA helicase involved in mRNA turnover, and more specifically in mRNA decapping by activating the decapping enzyme DCP1. Is involved in G1/S DNA-damage checkpoint recovery, probably through the regulation of the translational status of a subset of mRNAs. May also have a role in translation and mRNA nuclear export. Required for sporulation.<ref>PMID:9504907</ref> <ref>PMID:11780629</ref> <ref>PMID:12032091</ref> <ref>PMID:11696541</ref> <ref>PMID:12930949</ref> <ref>PMID:12730603</ref> <ref>PMID:15166134</ref> <ref>PMID:15703442</ref> <ref>PMID:15706350</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Translational repression and deadenylation of eukaryotic mRNAs result either in the sequestration of the transcripts in a nontranslatable pool or in their degradation. Removal of the 5' cap structure is a crucial step that commits deadenylated mRNAs to 5'-to-3' degradation. Pat1, Edc3 and the DEAD-box protein Dhh1 are evolutionary conserved factors known to participate in both translational repression and decapping, but their interplay is currently unclear. We report the 2.8 A resolution structure of yeast Dhh1 bound to the N-terminal domain of Pat1. The structure shows how Pat1 wraps around the C-terminal RecA domain of Dhh1, docking onto the Phe-Asp-Phe (FDF) binding site. The FDF-binding site of Dhh1 also recognizes Edc3, revealing why the binding of Pat1 and Edc3 on Dhh1 are mutually exclusive events. Using co-immunoprecipitation assays and structure-based mutants, we demonstrate that the mode of Dhh1-Pat1 recognition is conserved in humans. Pat1 and Edc3 also interfere and compete with the RNA-binding properties of Dhh1. Mapping the RNA-binding sites on Dhh1 with a crosslinking-mass spectrometry approach shows a large RNA-binding surface around the C-terminal RecA domain, including the FDF-binding pocket. The results suggest a model for how Dhh1-containing messenger ribonucleoprotein particles might be remodeled upon Pat1 and Edc3 binding.
-==About this Structure==
+Structural analysis of the yeast Dhh1-Pat1 complex reveals how Dhh1 engages Pat1, Edc3 and RNA in mutually exclusive interactions.,Sharif H, Ozgur S, Sharma K, Basquin C, Urlaub H, Conti E Nucleic Acids Res. 2013 Jul 12. PMID:23851565<ref>PMID:23851565</ref>
-[[4bru]] is a 2 chain structure with sequence from [http://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=4BRU OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<ref group="xtra">PMID:023851565</ref><references group="xtra"/><references/>
+</div>
-[[Category: RNA helicase]]
+<div class="pdbe-citations 4bru" style="background-color:#fffaf0;"></div>
-[[Category: Saccharomyces cerevisiae s288c]]
-[[Category: Basquin, C.]]
+==See Also==
-[[Category: Conti, E.]]
+*[[Helicase 3D structures|Helicase 3D structures]]
-[[Category: Ozgur, S.]]
+== References ==
-[[Category: Sharif, H.]]
+<references/>
-[[Category: Sharma, K.]]
+__TOC__
-[[Category: Urlaub, H.]]
+</StructureSection>
-[[Category: Dead-box]]
+[[Category: Large Structures]]
-[[Category: Decapping]]
+[[Category: Saccharomyces cerevisiae S288C]]
-[[Category: Hydrolase]]
+[[Category: Basquin C]]
-[[Category: Mrnp remodel p-body]]
+[[Category: Conti E]]
-[[Category: Translational repression]]
+[[Category: Ozgur S]]
+[[Category: Sharif H]]
+[[Category: Sharma K]]
+[[Category: Urlaub H]]

4bru

From Proteopedia

Current revision

Crystal structure of the yeast Dhh1-Edc3 complex

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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