4g24

From Proteopedia

(Difference between revisions)

Revision as of 17:24, 5 August 2016

Crystal Structure of proteinaceous RNase P 1 (PRORP1) from A. thaliana with Mn

Structural highlights

4g24 is a 1 chain structure with sequence from Arath. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Related:	4g23, 4g26, 4g25
Gene:	At2g32230, F22D22.2 (ARATH)
Activity:	Ribonuclease P, with EC number 3.1.26.5
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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

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/4g24"

@@ Line 1: / Line 1: @@
 ==Crystal Structure of proteinaceous RNase P 1 (PRORP1) from A. thaliana with Mn==
 <StructureSection load='4g24' size='340' side='right' caption='[[4g24]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4g24]] 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=4G24 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4G24 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4g24]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4G24 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4G24 FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACA:6-AMINOHEXANOIC+ACID'>ACA</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]], [[4g26|4g26]], [[4g25|4g25]]</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='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 ARATH])</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>
-<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=4g24 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4g24 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4g24 RCSB], [http://www.ebi.ac.uk/pdbsum/4g24 PDBsum]</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=4g24 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4g24 OCA], [http://pdbe.org/4g24 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4g24 RCSB], [http://www.ebi.ac.uk/pdbsum/4g24 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4g24 ProSAT]</span></td></tr>
 </table>
 == 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>
+[[http://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;">
 == Publication Abstract from PubMed ==
@@ Line 19: / Line 20: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 4g24" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Arabidopsis thaliana]]
+[[Category: Arath]]
 [[Category: Ribonuclease P]]
 [[Category: Fierke, C A]]

4g24

From Proteopedia

Revision as of 17:24, 5 August 2016

Crystal Structure of proteinaceous RNase P 1 (PRORP1) from A. thaliana with Mn

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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