4b8c

From Proteopedia

(Difference between revisions)

Revision as of 07:03, 31 August 2022

nuclease module of the yeast Ccr4-Not complex

Structural highlights

4b8c is a 12 chain structure with sequence from Baker's yeast. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Related:	1uoc, 4b89, 4b8a, 4b8b
Activity:	Poly(A)-specific ribonuclease, with EC number 3.1.13.4
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[POP2_YEAST] Acts as probably 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 vitro, POP2 has 3'-exoribonuclease activity with a preference for poly(A) RNAs, but also degrades poly(U) and poly(C) RNAs. Is part of a glucose-sensing system involved in growth control in response to glucose availability.^[1] ^[2] ^[3] ^[4] [CCR4_YEAST] Acts as 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. CCR4 has 3'-5' RNase activity with a strong preference for polyadenylated substrates and also low exonuclease activity towards single-stranded DNA. Discovered because of its role in the control of ADH2 gene expression. It is required for the expression of genes involved in non-fermentative growth and it mediates or is required for the action of the SPT6 and SPT10 genes.^[5] ^[6] ^[7] ^[8] [NOT1_YEAST] Acts as 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. The NOT protein subcomplex negatively regulates the basal and activated transcription of many genes. Preferentially affects TC-type TATA element-dependent transcription. Could directly or indirectly inhibit component(s) of the general transcription machinery.^[9]

Publication Abstract from PubMed

Shortening eukaryotic poly(A) tails represses mRNA translation and induces mRNA turnover. The major cytoplasmic deadenylase, the Ccr4-Not complex, is a conserved multisubunit assembly. Ccr4-Not is organized around Not1, a large scaffold protein that recruits two 3'-5' exoribonucleases, Caf1 and Ccr4. We report structural studies showing that the N-terminal arm of yeast Not1 has a HEAT-repeat structure with domains related to the MIF4G fold. A MIF4G domain positioned centrally within the Not1 protein recognizes Caf1, which in turn binds the LRR domain of Ccr4 and tethers the Ccr4 nuclease domain. The interactions that form the nuclease core of the Ccr4-Not complex are evolutionarily conserved. Their specific disruption affects cell growth and mRNA deadenylation and decay in vivo in yeast. Thus, the N-terminal arm of Not1 forms an extended platform reminiscent of scaffolding proteins like eIF4G and CBP80, and places the two nucleases in a pivotal position within the Ccr4-Not complex.

Architecture of the nuclease module of the yeast ccr4-not complex: the not1-caf1-ccr4 interaction.,Basquin J, Roudko VV, Rode M, Basquin C, Seraphin B, Conti E Mol Cell. 2012 Oct 26;48(2):207-18. doi: 10.1016/j.molcel.2012.08.014. Epub 2012 , Sep 6. PMID:22959269^[10]

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

References

↑ Liu HY, Badarinarayana V, Audino DC, Rappsilber J, Mann M, Denis CL. The NOT proteins are part of the CCR4 transcriptional complex and affect gene expression both positively and negatively. EMBO J. 1998 Feb 16;17(4):1096-106. PMID:9463387 doi:http://dx.doi.org/10.1093/emboj/17.4.1096
↑ Tucker M, Valencia-Sanchez MA, Staples RR, Chen J, Denis CL, Parker R. The transcription factor associated Ccr4 and Caf1 proteins are components of the major cytoplasmic mRNA deadenylase in Saccharomyces cerevisiae. Cell. 2001 Feb 9;104(3):377-86. PMID:11239395
↑ Daugeron MC, Mauxion F, Seraphin B. The yeast POP2 gene encodes a nuclease involved in mRNA deadenylation. Nucleic Acids Res. 2001 Jun 15;29(12):2448-55. PMID:11410650
↑ Thore S, Mauxion F, Seraphin B, Suck D. X-ray structure and activity of the yeast Pop2 protein: a nuclease subunit of the mRNA deadenylase complex. EMBO Rep. 2003 Dec;4(12):1150-5. Epub 2003 Nov 14. PMID:14618157 doi:http://dx.doi.org/10.1038/sj.embor.7400020
↑ Tucker M, Valencia-Sanchez MA, Staples RR, Chen J, Denis CL, Parker R. The transcription factor associated Ccr4 and Caf1 proteins are components of the major cytoplasmic mRNA deadenylase in Saccharomyces cerevisiae. Cell. 2001 Feb 9;104(3):377-86. PMID:11239395
↑ Chen J, Chiang YC, Denis CL. CCR4, a 3'-5' poly(A) RNA and ssDNA exonuclease, is the catalytic component of the cytoplasmic deadenylase. EMBO J. 2002 Mar 15;21(6):1414-26. PMID:11889047 doi:http://dx.doi.org/10.1093/emboj/21.6.1414
↑ Tucker M, Staples RR, Valencia-Sanchez MA, Muhlrad D, Parker R. Ccr4p is the catalytic subunit of a Ccr4p/Pop2p/Notp mRNA deadenylase complex in Saccharomyces cerevisiae. EMBO J. 2002 Mar 15;21(6):1427-36. PMID:11889048 doi:http://dx.doi.org/10.1093/emboj/21.6.1427
↑ Liu HY, Badarinarayana V, Audino DC, Rappsilber J, Mann M, Denis CL. The NOT proteins are part of the CCR4 transcriptional complex and affect gene expression both positively and negatively. EMBO J. 1998 Feb 16;17(4):1096-106. PMID:9463387 doi:http://dx.doi.org/10.1093/emboj/17.4.1096
↑ Liu HY, Badarinarayana V, Audino DC, Rappsilber J, Mann M, Denis CL. The NOT proteins are part of the CCR4 transcriptional complex and affect gene expression both positively and negatively. EMBO J. 1998 Feb 16;17(4):1096-106. PMID:9463387 doi:http://dx.doi.org/10.1093/emboj/17.4.1096
↑ Basquin J, Roudko VV, Rode M, Basquin C, Seraphin B, Conti E. Architecture of the nuclease module of the yeast ccr4-not complex: the not1-caf1-ccr4 interaction. Mol Cell. 2012 Oct 26;48(2):207-18. doi: 10.1016/j.molcel.2012.08.014. Epub 2012 , Sep 6. PMID:22959269 doi:http://dx.doi.org/10.1016/j.molcel.2012.08.014

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/4b8c"

Categories: Baker's yeast | Large Structures | Basquin, J | Conti, E | Hydrolase-cell cycle complex

@@ Line 3: / Line 3: @@
 <StructureSection load='4b8c' size='340' side='right'caption='[[4b8c]], [[Resolution|resolution]] 3.41&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4b8c]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4B8C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4B8C FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4b8c]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4B8C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4B8C FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1uoc|1uoc]], [[4b89|4b89]], [[4b8a|4b8a]], [[4b8b|4b8b]]</td></tr>
+</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1uoc|1uoc]], [[4b89|4b89]], [[4b8a|4b8a]], [[4b8b|4b8b]]</div></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Poly(A)-specific_ribonuclease Poly(A)-specific ribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.13.4 3.1.13.4] </span></td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Poly(A)-specific_ribonuclease Poly(A)-specific ribonuclease], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.13.4 3.1.13.4] </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=4b8c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4b8c OCA], [http://pdbe.org/4b8c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4b8c RCSB], [http://www.ebi.ac.uk/pdbsum/4b8c PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4b8c ProSAT]</span></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=4b8c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4b8c OCA], [https://pdbe.org/4b8c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4b8c RCSB], [https://www.ebi.ac.uk/pdbsum/4b8c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4b8c ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/POP2_YEAST POP2_YEAST]] Acts as probably 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 vitro, POP2 has 3'-exoribonuclease activity with a preference for poly(A) RNAs, but also degrades poly(U) and poly(C) RNAs. Is part of a glucose-sensing system involved in growth control in response to glucose availability.<ref>PMID:9463387</ref> <ref>PMID:11239395</ref> <ref>PMID:11410650</ref> <ref>PMID:14618157</ref>  [[http://www.uniprot.org/uniprot/CCR4_YEAST CCR4_YEAST]] Acts as 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. CCR4 has 3'-5' RNase activity with a strong preference for polyadenylated substrates and also low exonuclease activity towards single-stranded DNA. Discovered because of its role in the control of ADH2 gene expression. It is required for the expression of genes involved in non-fermentative growth and it mediates or is required for the action of the SPT6 and SPT10 genes.<ref>PMID:11239395</ref> <ref>PMID:11889047</ref> <ref>PMID:11889048</ref> <ref>PMID:9463387</ref>  [[http://www.uniprot.org/uniprot/NOT1_YEAST NOT1_YEAST]] Acts as 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. The NOT protein subcomplex negatively regulates the basal and activated transcription of many genes. Preferentially affects TC-type TATA element-dependent transcription. Could directly or indirectly inhibit component(s) of the general transcription machinery.<ref>PMID:9463387</ref>
+[[https://www.uniprot.org/uniprot/POP2_YEAST POP2_YEAST]] Acts as probably 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 vitro, POP2 has 3'-exoribonuclease activity with a preference for poly(A) RNAs, but also degrades poly(U) and poly(C) RNAs. Is part of a glucose-sensing system involved in growth control in response to glucose availability.<ref>PMID:9463387</ref> <ref>PMID:11239395</ref> <ref>PMID:11410650</ref> <ref>PMID:14618157</ref>  [[https://www.uniprot.org/uniprot/CCR4_YEAST CCR4_YEAST]] Acts as 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. CCR4 has 3'-5' RNase activity with a strong preference for polyadenylated substrates and also low exonuclease activity towards single-stranded DNA. Discovered because of its role in the control of ADH2 gene expression. It is required for the expression of genes involved in non-fermentative growth and it mediates or is required for the action of the SPT6 and SPT10 genes.<ref>PMID:11239395</ref> <ref>PMID:11889047</ref> <ref>PMID:11889048</ref> <ref>PMID:9463387</ref>  [[https://www.uniprot.org/uniprot/NOT1_YEAST NOT1_YEAST]] Acts as 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. The NOT protein subcomplex negatively regulates the basal and activated transcription of many genes. Preferentially affects TC-type TATA element-dependent transcription. Could directly or indirectly inhibit component(s) of the general transcription machinery.<ref>PMID:9463387</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 22: @@
 ==See Also==
 *[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
-*[[Temp|Temp]]
 == References ==
 <references/>

4b8c

From Proteopedia

Revision as of 07:03, 31 August 2022

nuclease module of the yeast Ccr4-Not complex

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox