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==The solution structure of RPP29-RPP21 complex from Pyrococcus furiosus==
==The solution structure of RPP29-RPP21 complex from Pyrococcus furiosus==
<StructureSection load='2ki7' size='340' side='right' caption='[[2ki7]], [[NMR_Ensembles_of_Models | 10 NMR models]]' scene=''>
<StructureSection load='2ki7' size='340' side='right'caption='[[2ki7]], [[NMR_Ensembles_of_Models | 10 NMR models]]' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2ki7]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrfu Pyrfu]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KI7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2KI7 FirstGlance]. <br>
<table><tr><td colspan='2'>[[2ki7]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrfu Pyrfu]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KI7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KI7 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rnp1, PF1816 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU]), rnp4, PF1613 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU])</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rnp1, PF1816 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU]), rnp4, PF1613 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU])</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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Ribonuclease_P Ribonuclease P], with EC number [https://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=2ki7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ki7 OCA], [http://pdbe.org/2ki7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ki7 RCSB], [http://www.ebi.ac.uk/pdbsum/2ki7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2ki7 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=2ki7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ki7 OCA], [https://pdbe.org/2ki7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ki7 RCSB], [https://www.ebi.ac.uk/pdbsum/2ki7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ki7 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/RNP1_PYRFU RNP1_PYRFU]] Part of ribonuclease P, a protein complex that generates mature tRNA molecules by cleaving their 5'-ends. The RNA is catalytic, but its KM for pre-tRNA is 170-fold decreased in the presence of the 4 known protein subunits (Rnp1-4). The protein subunits also decrease the amount of Mg(2+) needed for activity.<ref>PMID:17053064</ref> <ref>PMID:21683084</ref> <ref>PMID:22298511</ref>  [[http://www.uniprot.org/uniprot/RNP4_PYRFU RNP4_PYRFU]] Part of ribonuclease P, a protein complex that generates mature tRNA molecules by cleaving their 5'-ends. The RNA is catalytic, but its KM for pre-tRNA is 170-fold decreased in the presence of the 4 known protein subunits (Rnp1-4). The protein subunits also decrease the amount of Mg(2+) needed for activity.<ref>PMID:17053064</ref> <ref>PMID:21683084</ref> <ref>PMID:22298511</ref>   
[[https://www.uniprot.org/uniprot/RNP1_PYRFU RNP1_PYRFU]] Part of ribonuclease P, a protein complex that generates mature tRNA molecules by cleaving their 5'-ends. The RNA is catalytic, but its KM for pre-tRNA is 170-fold decreased in the presence of the 4 known protein subunits (Rnp1-4). The protein subunits also decrease the amount of Mg(2+) needed for activity.<ref>PMID:17053064</ref> <ref>PMID:21683084</ref> <ref>PMID:22298511</ref>  [[https://www.uniprot.org/uniprot/RNP4_PYRFU RNP4_PYRFU]] Part of ribonuclease P, a protein complex that generates mature tRNA molecules by cleaving their 5'-ends. The RNA is catalytic, but its KM for pre-tRNA is 170-fold decreased in the presence of the 4 known protein subunits (Rnp1-4). The protein subunits also decrease the amount of Mg(2+) needed for activity.<ref>PMID:17053064</ref> <ref>PMID:21683084</ref> <ref>PMID:22298511</ref>   
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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==See Also==
==See Also==
*[[Ribonuclease|Ribonuclease]]
*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
*[[Temp|Temp]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Pyrfu]]
[[Category: Pyrfu]]
[[Category: Ribonuclease P]]
[[Category: Ribonuclease P]]

Revision as of 10:26, 14 April 2021

The solution structure of RPP29-RPP21 complex from Pyrococcus furiosusThe solution structure of RPP29-RPP21 complex from Pyrococcus furiosus

Structural highlights

2ki7 is a 2 chain structure with sequence from Pyrfu. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Gene:rnp1, PF1816 (PYRFU), rnp4, PF1613 (PYRFU)
Activity:Ribonuclease P, with EC number 3.1.26.5
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[RNP1_PYRFU] Part of ribonuclease P, a protein complex that generates mature tRNA molecules by cleaving their 5'-ends. The RNA is catalytic, but its KM for pre-tRNA is 170-fold decreased in the presence of the 4 known protein subunits (Rnp1-4). The protein subunits also decrease the amount of Mg(2+) needed for activity.[1] [2] [3] [RNP4_PYRFU] Part of ribonuclease P, a protein complex that generates mature tRNA molecules by cleaving their 5'-ends. The RNA is catalytic, but its KM for pre-tRNA is 170-fold decreased in the presence of the 4 known protein subunits (Rnp1-4). The protein subunits also decrease the amount of Mg(2+) needed for activity.[4] [5] [6]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Ribonuclease P (RNase P) is a ribonucleoprotein (RNP) enzyme that catalyzes the Mg(2+)-dependent 5' maturation of precursor tRNAs. In all domains of life, it is a ribozyme: the RNase P RNA (RPR) component has been demonstrated to be responsible for catalysis. However, the number of RNase P protein subunits (RPPs) varies from 1 in bacteria to 9 or 10 in eukarya. The archaeal RPR is associated with at least 4 RPPs, which function in pairs (RPP21-RPP29 and RPP30-POP5). We used solution NMR spectroscopy to determine the three-dimensional structure of the protein-protein complex comprising Pyrococcus furiosus RPP21 and RPP29. We found that the protein-protein interaction is characterized by coupled folding of secondary structural elements that participate in interface formation. In addition to detailing the intermolecular contacts that stabilize this 30-kDa binary complex, the structure identifies surfaces rich in conserved basic residues likely vital for recognition of the RPR and/or precursor tRNA. Furthermore, enzymatic footprinting experiments allowed us to localize the RPP21-RPP29 complex to the specificity domain of the RPR. These findings provide valuable new insights into mechanisms of RNP assembly and serve as important steps towards a three-dimensional model of this ancient RNP enzyme.

Solution structure of an archaeal RNase P binary protein complex: formation of the 30-kDa complex between Pyrococcus furiosus RPP21 and RPP29 is accompanied by coupled protein folding and highlights critical features for protein-protein and protein-RNA interactions.,Xu Y, Amero CD, Pulukkunat DK, Gopalan V, Foster MP J Mol Biol. 2009 Nov 13;393(5):1043-55. Epub 2009 Sep 3. PMID:19733182[7]

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

See Also

References

  1. ↑ Tsai HY, Pulukkunat DK, Woznick WK, Gopalan V. Functional reconstitution and characterization of Pyrococcus furiosus RNase P. Proc Natl Acad Sci U S A. 2006 Oct 31;103(44):16147-52. Epub 2006 Oct 19. PMID:17053064 doi:http://dx.doi.org/10.1073/pnas.0608000103
  2. ↑ Chen WY, Xu Y, Cho IM, Oruganti SV, Foster MP, Gopalan V. Cooperative RNP assembly: complementary rescue of structural defects by protein and RNA subunits of archaeal RNase P. J Mol Biol. 2011 Aug 12;411(2):368-83. doi: 10.1016/j.jmb.2011.05.012. Epub 2011 , Jun 12. PMID:21683084 doi:http://dx.doi.org/10.1016/j.jmb.2011.05.012
  3. ↑ Chen WY, Singh D, Lai LB, Stiffler MA, Lai HD, Foster MP, Gopalan V. Fidelity of tRNA 5'-maturation: a possible basis for the functional dependence of archaeal and eukaryal RNase P on multiple protein cofactors. Nucleic Acids Res. 2012 May;40(10):4666-80. doi: 10.1093/nar/gks013. Epub 2012, Jan 31. PMID:22298511 doi:http://dx.doi.org/10.1093/nar/gks013
  4. ↑ Tsai HY, Pulukkunat DK, Woznick WK, Gopalan V. Functional reconstitution and characterization of Pyrococcus furiosus RNase P. Proc Natl Acad Sci U S A. 2006 Oct 31;103(44):16147-52. Epub 2006 Oct 19. PMID:17053064 doi:http://dx.doi.org/10.1073/pnas.0608000103
  5. ↑ Chen WY, Xu Y, Cho IM, Oruganti SV, Foster MP, Gopalan V. Cooperative RNP assembly: complementary rescue of structural defects by protein and RNA subunits of archaeal RNase P. J Mol Biol. 2011 Aug 12;411(2):368-83. doi: 10.1016/j.jmb.2011.05.012. Epub 2011 , Jun 12. PMID:21683084 doi:http://dx.doi.org/10.1016/j.jmb.2011.05.012
  6. ↑ Chen WY, Singh D, Lai LB, Stiffler MA, Lai HD, Foster MP, Gopalan V. Fidelity of tRNA 5'-maturation: a possible basis for the functional dependence of archaeal and eukaryal RNase P on multiple protein cofactors. Nucleic Acids Res. 2012 May;40(10):4666-80. doi: 10.1093/nar/gks013. Epub 2012, Jan 31. PMID:22298511 doi:http://dx.doi.org/10.1093/nar/gks013
  7. ↑ Xu Y, Amero CD, Pulukkunat DK, Gopalan V, Foster MP. Solution structure of an archaeal RNase P binary protein complex: formation of the 30-kDa complex between Pyrococcus furiosus RPP21 and RPP29 is accompanied by coupled protein folding and highlights critical features for protein-protein and protein-RNA interactions. J Mol Biol. 2009 Nov 13;393(5):1043-55. Epub 2009 Sep 3. PMID:19733182 doi:10.1016/j.jmb.2009.08.068
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