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3g0z

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Structure of S. pombe Pop2p - Zn2+ and Mn2+ bound form

Structural highlights

3g0z is a 1 chain structure with sequence from Schizosaccharomyces pombe. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.004Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CAF1_SCHPO Acts as the catalytic component of the CCR4-NOT core complex, which in the nucleus seems to be a general transcription factor, and in the cytoplasm the major mRNA deadenylase involved in mRNA turnover. In vivo and in vitro, caf1 has 3'-exoribonuclease activity with a preference for poly(A) RNAs.^[1] ^[2]

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

In eukaryotic organisms, initiation of mRNA turnover is controlled by progressive shortening of the poly-A tail, a process involving the mega-Dalton Ccr4-Not complex and its two associated 3'-5' exonucleases, Ccr4p and Pop2p (Caf1p). RNA degradation by the 3'-5' DEDDh exonuclease, Pop2p, is governed by the classical two metal ion mechanism traditionally assumed to be dependent on Mg(2+) ions bound in the active site. Here, we show biochemically and structurally that fission yeast (Schizosaccharomyces pombe) Pop2p prefers Mn(2+) and Zn(2+) over Mg(2+) at the concentrations of the ions found inside cells and that the identity of the ions in the active site affects the activity of the enzyme. Ion replacement experiments further suggest that mRNA deadenylation could be subtly regulated by local Zn(2+) levels in the cell. Finally, we use site-directed mutagenesis to propose a mechanistic model for the basis of the preference for poly-A sequences exhibited by the Pop2p-type deadenylases as well as their distributive enzymatic behavior.

The activity and selectivity of fission yeast Pop2p are affected by a high affinity for Zn2+ and Mn2+ in the active site.,Andersen KR, Jonstrup AT, Van LB, Brodersen DE RNA. 2009 May;15(5):850-61. Epub 2009 Mar 23. PMID:19307292^[3]

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

References

↑ Jonstrup AT, Andersen KR, Van LB, Brodersen DE. The 1.4-A crystal structure of the S. pombe Pop2p deadenylase subunit unveils the configuration of an active enzyme. Nucleic Acids Res. 2007;35(9):3153-64. Epub 2007 Apr 22. PMID:17452359 doi:http://dx.doi.org/10.1093/nar/gkm178
↑ Andersen KR, Jonstrup AT, Van LB, Brodersen DE. The activity and selectivity of fission yeast Pop2p are affected by a high affinity for Zn2+ and Mn2+ in the active site. RNA. 2009 May;15(5):850-61. Epub 2009 Mar 23. PMID:19307292 doi:10.1261/rna.1489409
↑ Andersen KR, Jonstrup AT, Van LB, Brodersen DE. The activity and selectivity of fission yeast Pop2p are affected by a high affinity for Zn2+ and Mn2+ in the active site. RNA. 2009 May;15(5):850-61. Epub 2009 Mar 23. PMID:19307292 doi:10.1261/rna.1489409

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/3g0z"

@@ Line 3: / Line 3: @@
 <StructureSection load='3g0z' size='340' side='right'caption='[[3g0z]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3g0z]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Cbs_356 Cbs 356]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G0Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3G0Z FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3g0z]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Schizosaccharomyces_pombe Schizosaccharomyces pombe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G0Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3G0Z FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.004&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3g10|3g10]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">caf1, SPCC18.06c ([https://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'>[https://proteopedia.org/fgij/fg.htm?mol=3g0z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g0z OCA], [https://pdbe.org/3g0z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3g0z RCSB], [https://www.ebi.ac.uk/pdbsum/3g0z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3g0z ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/CAF1_SCHPO CAF1_SCHPO]] Acts as the catalytic component of the CCR4-NOT core complex, which in the nucleus seems to be a general transcription factor, and in the cytoplasm the major mRNA deadenylase involved in mRNA turnover. In vivo and in vitro, caf1 has 3'-exoribonuclease activity with a preference for poly(A) RNAs.<ref>PMID:17452359</ref> <ref>PMID:19307292</ref>
+[https://www.uniprot.org/uniprot/CAF1_SCHPO CAF1_SCHPO] Acts as the catalytic component of the CCR4-NOT core complex, which in the nucleus seems to be a general transcription factor, and in the cytoplasm the major mRNA deadenylase involved in mRNA turnover. In vivo and in vitro, caf1 has 3'-exoribonuclease activity with a preference for poly(A) RNAs.<ref>PMID:17452359</ref> <ref>PMID:19307292</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 34: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Cbs 356]]
 [[Category: Large Structures]]
-[[Category: Andersen, K R]]
+[[Category: Schizosaccharomyces pombe]]
-[[Category: Brodersen, D E]]
+[[Category: Andersen KR]]
-[[Category: Jonstrup, A T]]
+[[Category: Brodersen DE]]
-[[Category: Van, L B]]
+[[Category: Jonstrup AT]]
-[[Category: Caf1p]]
+[[Category: Van LB]]
-[[Category: Ccr4-not]]
-[[Category: Deadenylation]]
-[[Category: Dedd exonuclease]]
-[[Category: Gene regulation]]
-[[Category: Hydrolase]]
-[[Category: Mrna turnover]]
-[[Category: Pop2p]]

3g0z

From Proteopedia

Current revision

Structure of S. pombe Pop2p - Zn2+ and Mn2+ bound form

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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