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| | ==Crystal Structure of proteinaceous RNase P 1 (PRORP1) from A. thaliana, SeMet substituted form with Sr== | | ==Crystal Structure of proteinaceous RNase P 1 (PRORP1) from A. thaliana, SeMet substituted form with Sr== |
| - | <StructureSection load='4g25' size='340' side='right' caption='[[4g25]], [[Resolution|resolution]] 2.00Å' scene=''> | + | <StructureSection load='4g25' size='340' side='right'caption='[[4g25]], [[Resolution|resolution]] 2.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4g25]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4G25 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4G25 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4g25]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4G25 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4G25 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SR:STRONTIUM+ION'>SR</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]] 2Å</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> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4g23|4g23]], [[4g24|4g24]], [[4g26|4g26]]</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=4g25 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4g25 OCA], [https://pdbe.org/4g25 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4g25 RCSB], [https://www.ebi.ac.uk/pdbsum/4g25 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4g25 ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">At2g32230, F22D22.2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 Arabidopsis thaliana])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_P Ribonuclease P], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.5 3.1.26.5] </span></td></tr>
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| - | <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=4g25 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4g25 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4g25 RCSB], [http://www.ebi.ac.uk/pdbsum/4g25 PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/PP179_ARATH PP179_ARATH]] Endonuclease RNase P responsible for the 5' maturation of tRNA precursors. Preferentially cleaves at the unusual cleavage site, but also able to cleave at the classical cleavage site. Also involved in the maturation of mRNAs in mitochondria.<ref>PMID:20473316</ref> <ref>PMID:20660484</ref> <ref>PMID:22549728</ref> | + | [https://www.uniprot.org/uniprot/PRRP1_ARATH PRRP1_ARATH] Endonuclease RNase P responsible for the 5' maturation of tRNA precursors. Preferentially cleaves at the unusual cleavage site, but also able to cleave at the classical cleavage site. Also involved in the maturation of mRNAs in mitochondria.<ref>PMID:20473316</ref> <ref>PMID:20660484</ref> <ref>PMID:22549728</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 4g25" style="background-color:#fffaf0;"></div> |
| | == References == | | == References == |
| | <references/> | | <references/> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Arabidopsis thaliana]] | | [[Category: Arabidopsis thaliana]] |
| - | [[Category: Ribonuclease P]] | + | [[Category: Large Structures]] |
| - | [[Category: Fierke, C A]] | + | [[Category: Fierke CA]] |
| - | [[Category: Howard, M J]] | + | [[Category: Howard MJ]] |
| - | [[Category: Koutmos, M]] | + | [[Category: Koutmos M]] |
| - | [[Category: Chloroplast]]
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| - | [[Category: Metallonuclease]]
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| - | [[Category: Nyn domain]]
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| - | [[Category: Pin]]
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| - | [[Category: Ppr domain]]
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| - | [[Category: Prorp]]
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| - | [[Category: Ribonuclease]]
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| - | [[Category: Rna binding protein]]
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| - | [[Category: Rnase p]]
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| - | [[Category: Trna processing]]
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| Structural highlights
Function
PRRP1_ARATH Endonuclease RNase P responsible for the 5' maturation of tRNA precursors. Preferentially cleaves at the unusual cleavage site, but also able to cleave at the classical cleavage site. Also involved in the maturation of mRNAs in mitochondria.[1] [2] [3]
Publication Abstract from PubMed
Ribonuclease P (RNase P) catalyzes the maturation of the 5' end of tRNA precursors. Typically these enzymes are ribonucleoproteins with a conserved RNA component responsible for catalysis. However, protein-only RNase P (PRORP) enzymes process precursor tRNAs in human mitochondria and in all tRNA-using compartments of Arabidopsis thaliana. PRORP enzymes are nuclear encoded and conserved among many eukaryotes, having evolved recently as yeast mitochondrial genomes encode an RNase P RNA. Here we report the crystal structure of PRORP1 from A. thaliana at 1.75 A resolution, revealing a prototypical metallonuclease domain tethered to a pentatricopeptide repeat (PPR) domain by a structural zinc-binding domain. The metallonuclease domain is a unique high-resolution structure of a Nedd4-BP1, YacP Nucleases (NYN) domain that is a member of the PIN domain-like fold superfamily, including the FLAP nuclease family. The structural similarity between PRORP1 and the FLAP nuclease family suggests that they evolved from a common ancestor. Biochemical data reveal that conserved aspartate residues in PRORP1 are important for catalytic activity and metal binding and that the PPR domain also enhances activity, likely through an interaction with pre-tRNA. These results provide a foundation for understanding tRNA maturation in organelles. Furthermore, these studies allow for a molecular-level comparison of the catalytic strategies used by the only known naturally evolved protein and RNA-based catalysts that perform the same biological function, pre-tRNA maturation, thereby providing insight into the differences between the prebiotic RNA world and the present protein-dominated world.
Mitochondrial ribonuclease P structure provides insight into the evolution of catalytic strategies for precursor-tRNA 5' processing.,Howard MJ, Lim WH, Fierke CA, Koutmos M Proc Natl Acad Sci U S A. 2012 Oct 2;109(40):16149-54. doi:, 10.1073/pnas.1209062109. Epub 2012 Sep 18. PMID:22991464[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Gobert A, Gutmann B, Taschner A, Gossringer M, Holzmann J, Hartmann RK, Rossmanith W, Giege P. A single Arabidopsis organellar protein has RNase P activity. Nat Struct Mol Biol. 2010 Jun;17(6):740-4. doi: 10.1038/nsmb.1812. Epub 2010 May , 16. PMID:20473316 doi:http://dx.doi.org/10.1038/nsmb.1812
- ↑ Placido A, Sieber F, Gobert A, Gallerani R, Giege P, Marechal-Drouard L. Plant mitochondria use two pathways for the biogenesis of tRNAHis. Nucleic Acids Res. 2010 Nov;38(21):7711-7. doi: 10.1093/nar/gkq646. Epub 2010 Jul, 25. PMID:20660484 doi:http://dx.doi.org/10.1093/nar/gkq646
- ↑ Gutmann B, Gobert A, Giege P. PRORP proteins support RNase P activity in both organelles and the nucleus in Arabidopsis. Genes Dev. 2012 May 15;26(10):1022-7. doi: 10.1101/gad.189514.112. Epub 2012 May , 1. PMID:22549728 doi:http://dx.doi.org/10.1101/gad.189514.112
- ↑ Howard MJ, Lim WH, Fierke CA, Koutmos M. Mitochondrial ribonuclease P structure provides insight into the evolution of catalytic strategies for precursor-tRNA 5' processing. Proc Natl Acad Sci U S A. 2012 Oct 2;109(40):16149-54. doi:, 10.1073/pnas.1209062109. Epub 2012 Sep 18. PMID:22991464 doi:http://dx.doi.org/10.1073/pnas.1209062109
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