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4m57

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Crystal structure of the pentatricopeptide repeat protein PPR10 from maize

Structural highlights

4m57 is a 1 chain structure with sequence from Zea mays. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PPR10_MAIZE Involved in chloroplast mRNA stability (PubMed:19424177, PubMed:21173259, PubMed:22156165). Binds specifically to two intergenic RNA regions of similar sequence located in the chloroplast atpH 5'-UTR and psaJ 3'-UTR, and serves as a barrier to RNA decay (PubMed:19424177). Binding to a specific site in the intergenic region of the chloroplast atpH is sufficient to block 5'-3' and 3'-5' exonucleases (PubMed:21173259). Acts as protein barrier to block mRNA degradation by exonucleases, and defines processed mRNA termini in chloroplasts (PubMed:22156165). Remodels the structure of the atpH ribosome-binding site in a manner that can account for its ability to enhance translation (PubMed:21173259). Stabilizes a RNA 3'-end downstream from psaI (PubMed:30125002). Binds atpH RNA as a monomer (PubMed:25609698).^[1] ^[2] ^[3] ^[4] ^[5]

Publication Abstract from PubMed

Pentatricopeptide repeat (PPR) proteins represent a large family of sequence-specific RNA-binding proteins that are involved in multiple aspects of RNA metabolism. PPR proteins, which are found in exceptionally large numbers in the mitochondria and chloroplasts of terrestrial plants, recognize single-stranded RNA (ssRNA) in a modular fashion. The maize chloroplast protein PPR10 binds to two similar RNA sequences from the ATPI-ATPH and PSAJ-RPL33 intergenic regions, referred to as ATPH and PSAJ, respectively. By protecting the target RNA elements from 5' or 3' exonucleases, PPR10 defines the corresponding 5' and 3' messenger RNA termini. Despite rigorous functional characterizations, the structural basis of sequence-specific ssRNA recognition by PPR proteins remains to be elucidated. Here we report the crystal structures of PPR10 in RNA-free and RNA-bound states at resolutions of 2.85 and 2.45 A, respectively. In the absence of RNA binding, the nineteen repeats of PPR10 are assembled into a right-handed superhelical spiral. PPR10 forms an antiparallel, intertwined homodimer and exhibits considerable conformational changes upon binding to its target ssRNA, an 18-nucleotide PSAJ element. Six nucleotides of PSAJ are specifically recognized by six corresponding PPR10 repeats following the predicted code. The molecular basis for the specific and modular recognition of RNA bases A, G and U is revealed. The structural elucidation of RNA recognition by PPR proteins provides an important framework for potential biotechnological applications of PPR proteins in RNA-related research areas.

Structural basis for the modular recognition of single-stranded RNA by PPR proteins.,Yin P, Li Q, Yan C, Liu Y, Liu J, Yu F, Wang Z, Long J, He J, Wang HW, Wang J, Zhu JK, Shi Y, Yan N Nature. 2013 Oct 27. doi: 10.1038/nature12651. PMID:24162847^[6]

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

References

↑ Pfalz J, Bayraktar OA, Prikryl J, Barkan A. Site-specific binding of a PPR protein defines and stabilizes 5' and 3' mRNA termini in chloroplasts. EMBO J. 2009 Jul 22;28(14):2042-52. doi: 10.1038/emboj.2009.121. Epub 2009 May 7. PMID:19424177 doi:http://dx.doi.org/10.1038/emboj.2009.121
↑ Prikryl J, Rojas M, Schuster G, Barkan A. Mechanism of RNA stabilization and translational activation by a pentatricopeptide repeat protein. Proc Natl Acad Sci U S A. 2011 Jan 4;108(1):415-20. doi: 10.1073/pnas.1012076108., Epub 2010 Dec 20. PMID:21173259 doi:http://dx.doi.org/10.1073/pnas.1012076108
↑ Zhelyazkova P, Hammani K, Rojas M, Voelker R, Vargas-Suarez M, Borner T, Barkan A. Protein-mediated protection as the predominant mechanism for defining processed mRNA termini in land plant chloroplasts. Nucleic Acids Res. 2012 Apr;40(7):3092-105. doi: 10.1093/nar/gkr1137. Epub 2011 , Dec 8. PMID:22156165 doi:http://dx.doi.org/10.1093/nar/gkr1137
↑ Gully BS, Cowieson N, Stanley WA, Shearston K, Small ID, Barkan A, Bond CS. The solution structure of the pentatricopeptide repeat protein PPR10 upon binding atpH RNA. Nucleic Acids Res. 2015 Feb 18;43(3):1918-26. doi: 10.1093/nar/gkv027. Epub 2015 , Jan 21. PMID:25609698 doi:http://dx.doi.org/10.1093/nar/gkv027
↑ Rojas M, Ruwe H, Miranda RG, Zoschke R, Hase N, Schmitz-Linneweber C, Barkan A. Unexpected functional versatility of the pentatricopeptide repeat proteins PGR3, PPR5 and PPR10. Nucleic Acids Res. 2018 Nov 2;46(19):10448-10459. doi: 10.1093/nar/gky737. PMID:30125002 doi:http://dx.doi.org/10.1093/nar/gky737
↑ Yin P, Li Q, Yan C, Liu Y, Liu J, Yu F, Wang Z, Long J, He J, Wang HW, Wang J, Zhu JK, Shi Y, Yan N. Structural basis for the modular recognition of single-stranded RNA by PPR proteins. Nature. 2013 Oct 27. doi: 10.1038/nature12651. PMID:24162847 doi:http://dx.doi.org/10.1038/nature12651

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4m57"

@@ Line 1: / Line 1: @@
 ==Crystal structure of the pentatricopeptide repeat protein PPR10 from maize==
-<StructureSection load='4m57' size='340' side='right' caption='[[4m57]], [[Resolution|resolution]] 2.86&Aring;' scene=''>
+<StructureSection load='4m57' size='340' side='right'caption='[[4m57]], [[Resolution|resolution]] 2.86&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4m57]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Maize Maize]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4M57 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4M57 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4m57]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Zea_mays Zea mays]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4M57 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4M57 FirstGlance]. <br>
-</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4m59|4m59]]</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=4m57 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4m57 OCA], [https://pdbe.org/4m57 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4m57 RCSB], [https://www.ebi.ac.uk/pdbsum/4m57 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4m57 ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ppr10, ZEAMMB73_867042 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4577 MAIZE])</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=4m57 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4m57 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4m57 RCSB], [http://www.ebi.ac.uk/pdbsum/4m57 PDBsum]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/PPR10_MAIZE PPR10_MAIZE] Involved in chloroplast mRNA stability (PubMed:19424177, PubMed:21173259, PubMed:22156165). Binds specifically to two intergenic RNA regions of similar sequence located in the chloroplast atpH 5'-UTR and psaJ 3'-UTR, and serves as a barrier to RNA decay (PubMed:19424177). Binding to a specific site in the intergenic region of the chloroplast atpH is sufficient to block 5'-3' and 3'-5' exonucleases (PubMed:21173259). Acts as protein barrier to block mRNA degradation by exonucleases, and defines processed mRNA termini in chloroplasts (PubMed:22156165). Remodels the structure of the atpH ribosome-binding site in a manner that can account for its ability to enhance translation (PubMed:21173259). Stabilizes a RNA 3'-end downstream from psaI (PubMed:30125002). Binds atpH RNA as a monomer (PubMed:25609698).<ref>PMID:19424177</ref> <ref>PMID:21173259</ref> <ref>PMID:22156165</ref> <ref>PMID:25609698</ref> <ref>PMID:30125002</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 16: / Line 17: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 4m57" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Maize]]
+[[Category: Large Structures]]
-[[Category: Li, Q]]
+[[Category: Zea mays]]
-[[Category: Liu, Y]]
+[[Category: Li Q]]
-[[Category: Yan, C]]
+[[Category: Liu Y]]
-[[Category: Yan, N]]
+[[Category: Yan C]]
-[[Category: Yin, P]]
+[[Category: Yan N]]
-[[Category: Pentatricopeptide repeat]]
+[[Category: Yin P]]
-[[Category: Rna]]
-[[Category: Rna binding protein]]
-[[Category: Superhelical]]

4m57

From Proteopedia

Current revision

Crystal structure of the pentatricopeptide repeat protein PPR10 from maize

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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