6k0a: Difference between revisions

Latest revision as of 10:02, 21 December 2022

cryo-EM structure of an archaeal Ribonuclease P

Loading...

Status: waiting for Mol* initialization

Structural highlights

6k0a is a 12 chain structure with sequence from Methanocaldococcus jannaschii and Methanocaldococcus jannaschii DSM 2661. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	ZN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RNP2_METJA Part of ribonuclease P, a protein complex that generates mature tRNA molecules by cleaving their 5'-ends.[HAMAP-Rule:MF_00755]^[1] ^[2] ^[3]

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^[4]

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:https://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:https://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:https://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:https://dx.doi.org/10.1038/s41467-019-10496-3

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] 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:https://dx.doi.org/10.1093/nar/gkn360

[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:https://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:https://dx.doi.org/10.1093/nar/gks013

[4] 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:https://dx.doi.org/10.1038/s41467-019-10496-3

[1]

[2]

[3]

[4]

@@ Line 3: / Line 3: @@
 <SX load='6k0a' size='340' side='right' viewer='molstar' caption='[[6k0a]], [[Resolution|resolution]] 4.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6k0a]] is a 12 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=6K0A OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6K0A FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6k0a]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii] and [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii_DSM_2661 Methanocaldococcus jannaschii DSM 2661]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K0A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6K0A FirstGlance]. <br>
 </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">[[6ahr|6ahr]]</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=6k0a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k0a OCA], [https://pdbe.org/6k0a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6k0a RCSB], [https://www.ebi.ac.uk/pdbsum/6k0a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6k0a ProSAT]</span></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://proteopedia.org/fgij/fg.htm?mol=6k0a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k0a OCA], [http://pdbe.org/6k0a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k0a RCSB], [http://www.ebi.ac.uk/pdbsum/6k0a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k0a ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/RNP4_METJA RNP4_METJA]] Part of ribonuclease P, a protein complex that generates mature tRNA molecules by cleaving their 5'-ends.[HAMAP-Rule:MF_00757]<ref>PMID:18558617</ref> <ref>PMID:21683084</ref> <ref>PMID:22298511</ref>  [[http://www.uniprot.org/uniprot/RNP2_METJA RNP2_METJA]] Part of ribonuclease P, a protein complex that generates mature tRNA molecules by cleaving their 5'-ends.[HAMAP-Rule:MF_00755]<ref>PMID:18558617</ref> <ref>PMID:21683084</ref> <ref>PMID:22298511</ref>  [[http://www.uniprot.org/uniprot/RNP1_METJA RNP1_METJA]] Part of ribonuclease P, a protein complex that generates mature tRNA molecules by cleaving their 5'-ends.[HAMAP-Rule:MF_00754]<ref>PMID:18558617</ref> <ref>PMID:21683084</ref> <ref>PMID:22298511</ref>  [[http://www.uniprot.org/uniprot/RNP3_METJA RNP3_METJA]] Part of ribonuclease P, a protein complex that generates mature tRNA molecules by cleaving their 5'-ends.[HAMAP-Rule:MF_00756]<ref>PMID:18558617</ref> <ref>PMID:21683084</ref> <ref>PMID:22298511</ref>  [[http://www.uniprot.org/uniprot/RL7A_METJA 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.
+[https://www.uniprot.org/uniprot/RNP2_METJA RNP2_METJA] Part of ribonuclease P, a protein complex that generates mature tRNA molecules by cleaving their 5'-ends.[HAMAP-Rule:MF_00755]<ref>PMID:18558617</ref> <ref>PMID:21683084</ref> <ref>PMID:22298511</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 29: / Line 26: @@
 </SX>
 [[Category: Large Structures]]
-[[Category: Metja]]
+[[Category: Methanocaldococcus jannaschii]]
-[[Category: Ribonuclease P]]
+[[Category: Methanocaldococcus jannaschii DSM 2661]]
-[[Category: Lan, P]]
+[[Category: Lan P]]
-[[Category: Lei, M]]
+[[Category: Lei M]]
-[[Category: Wan, F]]
+[[Category: Wan F]]
-[[Category: Wu, J]]
+[[Category: Wu J]]
-[[Category: Ribonuclease p]]
-[[Category: Rna binding protein-rna complex]]
-[[Category: Rna-protein complex]]

6k0a: Difference between revisions

Latest revision as of 10:02, 21 December 2022

cryo-EM structure of an archaeal Ribonuclease P

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools