5jnb: Difference between revisions

Latest revision as of 18:59, 20 September 2023

structure of GLD-2/RNP-8 complex

Structural highlights

5jnb is a 8 chain structure with sequence from Caenorhabditis elegans. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.486Å
Ligands:	EDO, MG, SO4
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

GLD2_CAEEL Cytoplasmic poly(A) RNA polymerase that adds successive AMP monomers to the 3'-end of specific RNAs, forming a poly(A) tail. Acts as a regulator of mitosis/meiosis required for progression through meiotic prophase during oogenesis and spermatogenesis and for promotion of the entry into meiosis from the mitotic cell cycle. May act by regulating and activating gld-1 mRNA activity in germline.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7]

Publication Abstract from PubMed

Cytoplasmic polyadenylation drives the translational activation of specific mRNAs in early metazoan development and is performed by distinct complexes that share the same catalytic poly(A)-polymerase subunit, GLD-2. The activity and specificity of GLD-2 depend on its binding partners. In Caenorhabditis elegans, GLD-2 promotes spermatogenesis when bound to GLD-3 and oogenesis when bound to RNP-8. GLD-3 and RNP-8 antagonize each other and compete for GLD-2 binding. Following up on our previous mechanistic studies of GLD-2-GLD-3, we report here the 2.5 A resolution structure and biochemical characterization of a GLD-2-RNP-8 core complex. In the structure, RNP-8 embraces the poly(A)-polymerase, docking onto several conserved hydrophobic hotspots present on the GLD-2 surface. RNP-8 stabilizes GLD-2 and indirectly stimulates polyadenylation. RNP-8 has a different amino-acid sequence and structure as compared to GLD-3. Yet, it binds the same surfaces of GLD-2 by forming alternative interactions, rationalizing the remarkable versatility of GLD-2 complexes.

Structural basis for the antagonistic roles of RNP-8 and GLD-3 in GLD-2 poly(A)-polymerase activity.,Nakel K, Bonneau F, Basquin C, Habermann B, Eckmann CR, Conti E RNA. 2016 Jun 10. PMID:27288313^[8]

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

References

↑ Wang L, Eckmann CR, Kadyk LC, Wickens M, Kimble J. A regulatory cytoplasmic poly(A) polymerase in Caenorhabditis elegans. Nature. 2002 Sep 19;419(6904):312-6. PMID:12239571 doi:https://dx.doi.org/10.1038/nature01039
↑ Hansen D, Wilson-Berry L, Dang T, Schedl T. Control of the proliferation versus meiotic development decision in the C. elegans germline through regulation of GLD-1 protein accumulation. Development. 2004 Jan;131(1):93-104. Epub 2003 Dec 3. PMID:14660440 doi:https://dx.doi.org/10.1242/dev.00916
↑ Hansen D, Hubbard EJ, Schedl T. Multi-pathway control of the proliferation versus meiotic development decision in the Caenorhabditis elegans germline. Dev Biol. 2004 Apr 15;268(2):342-57. PMID:15063172 doi:https://dx.doi.org/10.1016/j.ydbio.2003.12.023
↑ Maine EM, Hansen D, Springer D, Vought VE. Caenorhabditis elegans atx-2 promotes germline proliferation and the oocyte fate. Genetics. 2004 Oct;168(2):817-30. PMID:15514056 doi:https://dx.doi.org/10.1534/genetics.104.029355
↑ Vought VE, Ohmachi M, Lee MH, Maine EM. EGO-1, a putative RNA-directed RNA polymerase, promotes germline proliferation in parallel with GLP-1/notch signaling and regulates the spatial organization of nuclear pore complexes and germline P granules in Caenorhabditis elegans. Genetics. 2005 Jul;170(3):1121-32. Epub 2005 May 23. PMID:15911573 doi:https://dx.doi.org/10.1534/genetics.105.042135
↑ Suh N, Jedamzik B, Eckmann CR, Wickens M, Kimble J. The GLD-2 poly(A) polymerase activates gld-1 mRNA in the Caenorhabditis elegans germ line. Proc Natl Acad Sci U S A. 2006 Oct 10;103(41):15108-12. Epub 2006 Sep 29. PMID:17012378 doi:https://dx.doi.org/10.1073/pnas.0607050103
↑ Kadyk LC, Kimble J. Genetic regulation of entry into meiosis in Caenorhabditis elegans. Development. 1998 May;125(10):1803-13. PMID:9550713
↑ Nakel K, Bonneau F, Basquin C, Habermann B, Eckmann CR, Conti E. Structural basis for the antagonistic roles of RNP-8 and GLD-3 in GLD-2 poly(A)-polymerase activity. RNA. 2016 Jun 10. PMID:27288313 doi:https://dx.doi.org/10.1261/rna.056598.116

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OCA

[1] Wang L, Eckmann CR, Kadyk LC, Wickens M, Kimble J. A regulatory cytoplasmic poly(A) polymerase in Caenorhabditis elegans. Nature. 2002 Sep 19;419(6904):312-6. PMID:12239571 doi:https://dx.doi.org/10.1038/nature01039

[2] Hansen D, Wilson-Berry L, Dang T, Schedl T. Control of the proliferation versus meiotic development decision in the C. elegans germline through regulation of GLD-1 protein accumulation. Development. 2004 Jan;131(1):93-104. Epub 2003 Dec 3. PMID:14660440 doi:https://dx.doi.org/10.1242/dev.00916

[3] Hansen D, Hubbard EJ, Schedl T. Multi-pathway control of the proliferation versus meiotic development decision in the Caenorhabditis elegans germline. Dev Biol. 2004 Apr 15;268(2):342-57. PMID:15063172 doi:https://dx.doi.org/10.1016/j.ydbio.2003.12.023

[4] Maine EM, Hansen D, Springer D, Vought VE. Caenorhabditis elegans atx-2 promotes germline proliferation and the oocyte fate. Genetics. 2004 Oct;168(2):817-30. PMID:15514056 doi:https://dx.doi.org/10.1534/genetics.104.029355

[5] Vought VE, Ohmachi M, Lee MH, Maine EM. EGO-1, a putative RNA-directed RNA polymerase, promotes germline proliferation in parallel with GLP-1/notch signaling and regulates the spatial organization of nuclear pore complexes and germline P granules in Caenorhabditis elegans. Genetics. 2005 Jul;170(3):1121-32. Epub 2005 May 23. PMID:15911573 doi:https://dx.doi.org/10.1534/genetics.105.042135

[6] Suh N, Jedamzik B, Eckmann CR, Wickens M, Kimble J. The GLD-2 poly(A) polymerase activates gld-1 mRNA in the Caenorhabditis elegans germ line. Proc Natl Acad Sci U S A. 2006 Oct 10;103(41):15108-12. Epub 2006 Sep 29. PMID:17012378 doi:https://dx.doi.org/10.1073/pnas.0607050103

[7] Kadyk LC, Kimble J. Genetic regulation of entry into meiosis in Caenorhabditis elegans. Development. 1998 May;125(10):1803-13. PMID:9550713

[8] Nakel K, Bonneau F, Basquin C, Habermann B, Eckmann CR, Conti E. Structural basis for the antagonistic roles of RNP-8 and GLD-3 in GLD-2 poly(A)-polymerase activity. RNA. 2016 Jun 10. PMID:27288313 doi:https://dx.doi.org/10.1261/rna.056598.116

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@@ Line 1: / Line 1: @@
 ==structure of GLD-2/RNP-8 complex==
-<StructureSection load='5jnb' size='340' side='right' caption='[[5jnb]], [[Resolution|resolution]] 2.49&Aring;' scene=''>
+<StructureSection load='5jnb' size='340' side='right'caption='[[5jnb]], [[Resolution|resolution]] 2.49&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5jnb]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JNB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JNB FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5jnb]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Caenorhabditis_elegans Caenorhabditis elegans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JNB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JNB FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.486&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Polynucleotide_adenylyltransferase Polynucleotide adenylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.19 2.7.7.19] </span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=5jnb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jnb OCA], [http://pdbe.org/5jnb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jnb RCSB], [http://www.ebi.ac.uk/pdbsum/5jnb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jnb 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=5jnb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jnb OCA], [https://pdbe.org/5jnb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jnb RCSB], [https://www.ebi.ac.uk/pdbsum/5jnb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jnb ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/GLD2_CAEEL GLD2_CAEEL]] Cytoplasmic poly(A) RNA polymerase that adds successive AMP monomers to the 3'-end of specific RNAs, forming a poly(A) tail. Acts as a regulator of mitosis/meiosis required for progression through meiotic prophase during oogenesis and spermatogenesis and for promotion of the entry into meiosis from the mitotic cell cycle. May act by regulating and activating gld-1 mRNA activity in germline.<ref>PMID:12239571</ref> <ref>PMID:14660440</ref> <ref>PMID:15063172</ref> <ref>PMID:15514056</ref> <ref>PMID:15911573</ref> <ref>PMID:17012378</ref> <ref>PMID:9550713</ref>
+[https://www.uniprot.org/uniprot/GLD2_CAEEL GLD2_CAEEL] Cytoplasmic poly(A) RNA polymerase that adds successive AMP monomers to the 3'-end of specific RNAs, forming a poly(A) tail. Acts as a regulator of mitosis/meiosis required for progression through meiotic prophase during oogenesis and spermatogenesis and for promotion of the entry into meiosis from the mitotic cell cycle. May act by regulating and activating gld-1 mRNA activity in germline.<ref>PMID:12239571</ref> <ref>PMID:14660440</ref> <ref>PMID:15063172</ref> <ref>PMID:15514056</ref> <ref>PMID:15911573</ref> <ref>PMID:17012378</ref> <ref>PMID:9550713</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 19: / Line 19: @@
 </div>
 <div class="pdbe-citations 5jnb" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Poly(A) RNA polymerase|Poly(A) RNA polymerase]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Polynucleotide adenylyltransferase]]
+[[Category: Caenorhabditis elegans]]
-[[Category: Basquin, C]]
+[[Category: Large Structures]]
-[[Category: Bonneau, F]]
+[[Category: Basquin C]]
-[[Category: Conti, E]]
+[[Category: Bonneau F]]
-[[Category: Eckmann, C R]]
+[[Category: Conti E]]
-[[Category: Nakel, K]]
+[[Category: Eckmann CR]]
-[[Category: C. elegans germline development]]
+[[Category: Nakel K]]
-[[Category: Polymerase]]
-[[Category: Rna binding]]
-[[Category: Transferase]]
-[[Category: Translational control]]

5jnb: Difference between revisions

Latest revision as of 18:59, 20 September 2023

structure of GLD-2/RNP-8 complex

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

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