3fqg

From Proteopedia

(Difference between revisions)

Revision as of 23:46, 4 August 2016

Crystal Structure of the S. pombe Rai1

Structural highlights

3fqg is a 1 chain structure with sequence from Cbs 356. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	3fqd, 3fqi, 3fqj
Gene:	din1, Rai1, SPAC19D5.06c (CBS 356)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[DXO_SCHPO] Ribonuclease that specifically degrades pre-mRNAs with a defective 5' end cap and is part of a pre-mRNA capping quality control. Has decapping and pyrophosphohydrolase activities. Has decapping activity toward incomplete 5' end cap mRNAs such as unmethylated 5' end-capped RNA to release GpppN and 5' end monophosphate RNA (By similarity). Also possesses RNA 5'-pyrophosphohydrolase activity by hydrolyzing the 5' end triphosphate to release pyrophosphates. Stimulates exoribonuclease activity of rat1, allowing it to degrade RNAs with stable secondary structure more effectively.^[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

The 5'-->3' exoribonucleases (XRNs) comprise a large family of conserved enzymes in eukaryotes with crucial functions in RNA metabolism and RNA interference. XRN2, or Rat1 in yeast, functions primarily in the nucleus and also has an important role in transcription termination by RNA polymerase II (refs 7-14). Rat1 exoribonuclease activity is stimulated by the protein Rai1 (refs 15, 16). Here we report the crystal structure at 2.2 A resolution of Schizosaccharomyces pombe Rat1 in complex with Rai1, as well as the structures of Rai1 and its murine homologue Dom3Z alone at 2.0 A resolution. The structures reveal the molecular mechanism for the activation of Rat1 by Rai1 and for the exclusive exoribonuclease activity of Rat1. Biochemical studies confirm these observations, and show that Rai1 allows Rat1 to degrade RNAs with stable secondary structure more effectively. There are large differences in the active site landscape of Rat1 compared to related and PIN (PilT N terminus) domain-containing nucleases. Unexpectedly, we identified a large pocket in Rai1 and Dom3Z that contains highly conserved residues, including three acidic side chains that coordinate a divalent cation. Mutagenesis and biochemical studies demonstrate that Rai1 possesses pyrophosphohydrolase activity towards 5' triphosphorylated RNA. Such an activity is important for messenger RNA degradation in bacteria, but this is, to our knowledge, the first demonstration of this activity in eukaryotes and suggests that Rai1/Dom3Z may have additional important functions in RNA metabolism.

Structure and function of the 5'-->3' exoribonuclease Rat1 and its activating partner Rai1.,Xiang S, Cooper-Morgan A, Jiao X, Kiledjian M, Manley JL, Tong L Nature. 2009 Apr 9;458(7239):784-8. Epub 2009 Feb 4. PMID:19194460^[2]

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

References

↑ Xiang S, Cooper-Morgan A, Jiao X, Kiledjian M, Manley JL, Tong L. Structure and function of the 5'-->3' exoribonuclease Rat1 and its activating partner Rai1. Nature. 2009 Apr 9;458(7239):784-8. Epub 2009 Feb 4. PMID:19194460 doi:http://dx.doi.org/10.1038/nature07731
↑ Xiang S, Cooper-Morgan A, Jiao X, Kiledjian M, Manley JL, Tong L. Structure and function of the 5'-->3' exoribonuclease Rat1 and its activating partner Rai1. Nature. 2009 Apr 9;458(7239):784-8. Epub 2009 Feb 4. PMID:19194460 doi:http://dx.doi.org/10.1038/nature07731

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/3fqg"

@@ Line 1: / Line 1: @@
 ==Crystal Structure of the S. pombe Rai1==
 <StructureSection load='3fqg' size='340' side='right' caption='[[3fqg]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3fqg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Schizosaccharomyces_pombe Schizosaccharomyces pombe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FQG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FQG FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3fqg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cbs_356 Cbs 356]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FQG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FQG FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3fqd|3fqd]], [[3fqi|3fqi]], [[3fqj|3fqj]]</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">din1, Rai1, SPAC19D5.06c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4896 Schizosaccharomyces pombe])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">din1, Rai1, SPAC19D5.06c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4896 CBS 356])</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3fqg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fqg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3fqg RCSB], [http://www.ebi.ac.uk/pdbsum/3fqg PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3fqg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fqg OCA], [http://pdbe.org/3fqg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3fqg RCSB], [http://www.ebi.ac.uk/pdbsum/3fqg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3fqg ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/DOM3Z_SCHPO DOM3Z_SCHPO]] Ribonuclease that specifically degrades pre-mRNAs with a defective 5' end cap and is part of a pre-mRNA capping quality control. Has decapping and pyrophosphohydrolase activities. Has decapping activity toward incomplete 5' end cap mRNAs such as unmethylated 5' end-capped RNA to release GpppN and 5' end monophosphate RNA (By similarity). Also possesses RNA 5'-pyrophosphohydrolase activity by hydrolyzing the 5' end triphosphate to release pyrophosphates. Stimulates exoribonuclease activity of rat1, allowing it to degrade RNAs with stable secondary structure more effectively.<ref>PMID:19194460</ref>
+[[http://www.uniprot.org/uniprot/DXO_SCHPO DXO_SCHPO]] Ribonuclease that specifically degrades pre-mRNAs with a defective 5' end cap and is part of a pre-mRNA capping quality control. Has decapping and pyrophosphohydrolase activities. Has decapping activity toward incomplete 5' end cap mRNAs such as unmethylated 5' end-capped RNA to release GpppN and 5' end monophosphate RNA (By similarity). Also possesses RNA 5'-pyrophosphohydrolase activity by hydrolyzing the 5' end triphosphate to release pyrophosphates. Stimulates exoribonuclease activity of rat1, allowing it to degrade RNAs with stable secondary structure more effectively.<ref>PMID:19194460</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 18: / Line 19: @@
     <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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=3fqg ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 28: / Line 29: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3fqg" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Schizosaccharomyces pombe]]
+[[Category: Cbs 356]]
 [[Category: Tong, L]]
 [[Category: Xiang, S]]

3fqg

From Proteopedia

Revision as of 23:46, 4 August 2016

Crystal Structure of the S. pombe Rai1

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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