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6k0b

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Revision as of 02:18, 11 April 2020

cryo-EM structure of archaeal Ribonuclease P with mature tRNA

6k0b, resolution 4.30Å

Structural highlights

6k0b is a 14 chain structure with sequence from [1] and Metja. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	6k0a
Gene:	rnp2, MJ0494 (METJA), rnp3, MJ1139 (METJA), rnp1, MJ0464 (METJA), rnp4, MJ0962 (METJA), rpl7ae, MJ1203 (METJA)
Activity:	Ribonuclease P, with EC number 3.1.26.5
Experimental data:	Check to display Experimental Data
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[RNP4_METJA] Part of ribonuclease P, a protein complex that generates mature tRNA molecules by cleaving their 5'-ends.[HAMAP-Rule:MF_00757]^[1] ^[2] ^[3] [RNP2_METJA] Part of ribonuclease P, a protein complex that generates mature tRNA molecules by cleaving their 5'-ends.[HAMAP-Rule:MF_00755]^[4] ^[5] ^[6] [RNP1_METJA] Part of ribonuclease P, a protein complex that generates mature tRNA molecules by cleaving their 5'-ends.[HAMAP-Rule:MF_00754]^[7] ^[8] ^[9] [RNP3_METJA] Part of ribonuclease P, a protein complex that generates mature tRNA molecules by cleaving their 5'-ends.[HAMAP-Rule:MF_00756]^[10] ^[11] ^[12] [RL7A_METJA] Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, the RNA component of RNase P, box H/ACA, box C/D and box C'/D' sRNAs.

Publication Abstract from PubMed

Ribonuclease P (RNase P) is an essential ribozyme responsible for tRNA 5' maturation. Here we report the cryo-EM structures of Methanocaldococcus jannaschii (Mja) RNase P holoenzyme alone and in complex with a tRNA substrate at resolutions of 4.6 A and 4.3 A, respectively. The structures reveal that the subunits of MjaRNase P are strung together to organize the holoenzyme in a dimeric conformation required for efficient catalysis. The structures also show that archaeal RNase P is a functional chimera of bacterial and eukaryal RNase Ps that possesses bacterial-like two RNA-based anchors and a eukaryal-like protein-aided stabilization mechanism. The 3'-RCCA sequence of tRNA, which is a key recognition element for bacterial RNase P, is dispensable for tRNA recognition by MjaRNase P. The overall organization of MjaRNase P, particularly within the active site, is similar to those of bacterial and eukaryal RNase Ps, suggesting a universal catalytic mechanism for all RNase Ps.

Cryo-electron microscopy structure of an archaeal ribonuclease P holoenzyme.,Wan F, Wang Q, Tan J, Tan M, Chen J, Shi S, Lan P, Wu J, Lei M Nat Commun. 2019 Jun 13;10(1):2617. doi: 10.1038/s41467-019-10496-3. PMID:31197137^[13]

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

References

↑ Pulukkunat DK, Gopalan V. Studies on Methanocaldococcus jannaschii RNase P reveal insights into the roles of RNA and protein cofactors in RNase P catalysis. Nucleic Acids Res. 2008 Jul;36(12):4172-80. doi: 10.1093/nar/gkn360. Epub 2008, Jun 16. PMID:18558617 doi:http://dx.doi.org/10.1093/nar/gkn360
↑ 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
↑ 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
↑ Pulukkunat DK, Gopalan V. Studies on Methanocaldococcus jannaschii RNase P reveal insights into the roles of RNA and protein cofactors in RNase P catalysis. Nucleic Acids Res. 2008 Jul;36(12):4172-80. doi: 10.1093/nar/gkn360. Epub 2008, Jun 16. PMID:18558617 doi:http://dx.doi.org/10.1093/nar/gkn360
↑ 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
↑ 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
↑ Pulukkunat DK, Gopalan V. Studies on Methanocaldococcus jannaschii RNase P reveal insights into the roles of RNA and protein cofactors in RNase P catalysis. Nucleic Acids Res. 2008 Jul;36(12):4172-80. doi: 10.1093/nar/gkn360. Epub 2008, Jun 16. PMID:18558617 doi:http://dx.doi.org/10.1093/nar/gkn360
↑ 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
↑ 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
↑ Pulukkunat DK, Gopalan V. Studies on Methanocaldococcus jannaschii RNase P reveal insights into the roles of RNA and protein cofactors in RNase P catalysis. Nucleic Acids Res. 2008 Jul;36(12):4172-80. doi: 10.1093/nar/gkn360. Epub 2008, Jun 16. PMID:18558617 doi:http://dx.doi.org/10.1093/nar/gkn360
↑ 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
↑ 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
↑ Wan F, Wang Q, Tan J, Tan M, Chen J, Shi S, Lan P, Wu J, Lei M. Cryo-electron microscopy structure of an archaeal ribonuclease P holoenzyme. Nat Commun. 2019 Jun 13;10(1):2617. doi: 10.1038/s41467-019-10496-3. PMID:31197137 doi:http://dx.doi.org/10.1038/s41467-019-10496-3

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6k0b"

@@ Line 3: / Line 3: @@
 <SX load='6k0b' size='340' side='right' viewer='molstar' caption='[[6k0b]], [[Resolution|resolution]] 4.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6k0b]] is a 14 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Metja Metja]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K0B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6K0B FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6k0b]] is a 14 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Metja Metja]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K0B OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6K0B 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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6k0a|6k0a]]</td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rnp2, MJ0494 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243232 METJA]), rnp3, MJ1139 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243232 METJA]), rnp1, MJ0464 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243232 METJA]), rnp4, MJ0962 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243232 METJA]), rpl7ae, MJ1203 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243232 METJA])</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=6k0b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k0b OCA], [http://pdbe.org/6k0b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k0b RCSB], [http://www.ebi.ac.uk/pdbsum/6k0b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k0b ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6k0b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k0b OCA], [http://pdbe.org/6k0b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k0b RCSB], [http://www.ebi.ac.uk/pdbsum/6k0b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k0b ProSAT]</span></td></tr>
 </table>
 == Function ==

6k0b

From Proteopedia

Revision as of 02:18, 11 April 2020

cryo-EM structure of archaeal Ribonuclease P with mature tRNA

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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