4oe1

From Proteopedia

(Difference between revisions)

Revision as of 07:19, 25 January 2023

Crystal structure of the pentatricopeptide repeat protein PPR10 (C256S/C430S/C449S) in complex with an 18-nt PSAJ rna element

Structural highlights

4oe1 is a 4 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, particularly abundant in plastids and mitochrondria of angiosperms, include a large number of sequence-specific RNA binding proteins which are involved indiverse aspects of organelle RNA metabolisms. PPR proteins contain multiple tandom repeats and each repeat can specifically recognize a RNA base through residues 2, 5, and 35 in a modular fashion. The crystal structure of PPR10 from maize chloroplast exhibits dimeric existence both in the absence and presence of the 18-nucleotide (nt) psaJ RNA element. However, previous biochemical analysis suggested a monomeric shift of PPR10 upon RNA binding. In this report, we show that the amino-ternimal segments of PPR10 determine the dimerization state of PPR10. A single amino acid alteration of cysteine to serine within repeat 10 of PPR10 further drives dimerization of PPR10. The biochemical elucidation of the determinants for PPR10 dimerization may provide an important foundation to understand the working mechanisms of PPR proteins underlying their diverse physiological functions.

Examination of the Dimerization States of the Single-stranded RNA-recognition Protein PPR10.,Li Q, Yan C, Xu H, Wang Z, Long J, Li W, Wu J, Yin P, Yan N J Biol Chem. 2014 Sep 17. pii: jbc.M114.575472. PMID:25231995^[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
↑ Li Q, Yan C, Xu H, Wang Z, Long J, Li W, Wu J, Yin P, Yan N. Examination of the Dimerization States of the Single-stranded RNA-recognition Protein PPR10. J Biol Chem. 2014 Sep 17. pii: jbc.M114.575472. PMID:25231995 doi:http://dx.doi.org/10.1074/jbc.M114.575472

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/4oe1"

@@ Line 3: / Line 3: @@
 <StructureSection load='4oe1' size='340' side='right'caption='[[4oe1]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4oe1]] is a 4 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=4OE1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OE1 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4oe1]] is a 4 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=4OE1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OE1 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=4oe1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oe1 OCA], [https://pdbe.org/4oe1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4oe1 RCSB], [https://www.ebi.ac.uk/pdbsum/4oe1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4oe1 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=4oe1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oe1 OCA], [http://pdbe.org/4oe1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4oe1 RCSB], [http://www.ebi.ac.uk/pdbsum/4oe1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4oe1 ProSAT]</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 23: / Line 23: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Maize]]
+[[Category: Zea mays]]
-[[Category: Li, Q]]
+[[Category: Li Q]]
-[[Category: Wu, J]]
+[[Category: Wu J]]
-[[Category: Yan, C]]
+[[Category: Yan C]]
-[[Category: Yan, N]]
+[[Category: Yan N]]
-[[Category: Yin, P]]
+[[Category: Yin P]]
-[[Category: Pentatricopeptide repeat]]
-[[Category: Rna]]
-[[Category: Rna binding protein]]
-[[Category: Rna binding protein-rna complex]]
-[[Category: Superhelical]]

4oe1

From Proteopedia

Revision as of 07:19, 25 January 2023

Crystal structure of the pentatricopeptide repeat protein PPR10 (C256S/C430S/C449S) in complex with an 18-nt PSAJ rna element

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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