1s2m: Difference between revisions

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New page: left|200px<br /><applet load="1s2m" size="450" color="white" frame="true" align="right" spinBox="true" caption="1s2m, resolution 2.10Å" /> '''Crystal Structure of...
 
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[[Image:1s2m.gif|left|200px]]<br /><applet load="1s2m" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1s2m, resolution 2.10&Aring;" />
'''Crystal Structure of the DEAD box protein Dhh1p'''<br />


==Overview==
==Crystal Structure of the DEAD box protein Dhh1p==
The control of mRNA translation and degradation are critical for proper, gene expression. A key regulator of both translation and degradation is, Dhh1p, which is a DEAD-box protein, and functions both to repress, translation and enhance decapping. We describe the crystal structure of, the N- and C-terminal truncated Dhh1p (tDhh1p) determined at 2.1 A, resolution. This reveals that, like other DEAD-box proteins, tDhh1p, contains two RecA-like domains, although with a unique arrangement. In, contrast to eIF4A and mjDEAD, in which no motif interactions exist, in, Dhh1p, motif V interacts with motif I and the Q-motif, thereby linking the, two domains together. Electrostatic potential mapping combined with, mutagenesis reveals that motifs I, V, and VI are involved in RNA binding., In addition, trypsin digestion of tDhh1p suggests that ATP binding, enhances an RNA-induced conformational change. Interestingly, some, mutations located in the conserved motifs and at the interface between the, two Dhh1 domains confer dominant negative phenotypes in vivo and disrupt, the conformational switch in vitro. This suggests that this conformational, change is required in Dhh1 function and identifies key residues involved, in that transition.
<StructureSection load='1s2m' size='340' side='right'caption='[[1s2m]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1s2m]] is a 1 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=1S2M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1S2M 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]] 2.1&#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=1s2m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s2m OCA], [https://pdbe.org/1s2m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1s2m RCSB], [https://www.ebi.ac.uk/pdbsum/1s2m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1s2m 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>
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/s2/1s2m_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1s2m ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1S2M is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1S2M OCA].
*[[Helicase 3D structures|Helicase 3D structures]]
 
== References ==
==Reference==
<references/>
Crystal structure and functional analysis of DEAD-box protein Dhh1p., Cheng Z, Coller J, Parker R, Song H, RNA. 2005 Aug;11(8):1258-70. Epub 2005 Jun 29. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15987810 15987810]
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Single protein]]
[[Category: Cheng Z]]
[[Category: Cheng, Z.]]
[[Category: Song H]]
[[Category: Song, H.]]
[[Category: atp-binding]]
[[Category: helicase]]
[[Category: rna-binding]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 02:03:19 2007''

Latest revision as of 16:29, 13 March 2024

Crystal Structure of the DEAD box protein Dhh1pCrystal Structure of the DEAD box protein Dhh1p

Structural highlights

1s2m is a 1 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
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]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

References

  1. ↑ 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
  2. ↑ 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
  3. ↑ 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
  4. ↑ 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
  5. ↑ 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
  6. ↑ 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
  7. ↑ 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
  8. ↑ 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
  9. ↑ 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

1s2m, resolution 2.10Å

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