2lcq: Difference between revisions

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==Solution structure of the endonuclease Nob1 from P.horikoshii==
==Solution structure of the endonuclease Nob1 from P.horikoshii==
<StructureSection load='2lcq' size='340' side='right' caption='[[2lcq]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
<StructureSection load='2lcq' size='340' side='right'caption='[[2lcq]]' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2lcq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermomicrobium_roseum Thermomicrobium roseum]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LCQ OCA]. <br>
<table><tr><td colspan='2'>[[2lcq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LCQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LCQ FirstGlance]. <br>
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">vapC6, PH0709 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=500 Thermomicrobium roseum])</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><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </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=2lcq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lcq OCA], [https://pdbe.org/2lcq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lcq RCSB], [https://www.ebi.ac.uk/pdbsum/2lcq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lcq ProSAT]</span></td></tr>
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2lcq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lcq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2lcq RCSB], [http://www.ebi.ac.uk/pdbsum/2lcq PDBsum]</span></td></tr>
</table>
<table>
== Function ==
<div style="background-color:#fffaf0;">
[https://www.uniprot.org/uniprot/NOB1_PYRHO NOB1_PYRHO] Toxic component of a toxin-antitoxin (TA) module (Potential). Processes pre-16S-rRNA at its 3' end (the D-site) to yield the mature 3' end.<ref>PMID:22156373</ref>  
== Publication Abstract from PubMed ==
Eukaryotic ribosome biogenesis requires the concerted action of numerous ribosome assembly factors, for most of which structural and functional information is currently lacking. Nob1, which can be identified in eukaryotes and archaea, is required for the final maturation of the small subunit ribosomal RNA in yeast by catalyzing cleavage at site D after export of the preribosomal subunit into the cytoplasm. Here, we show that this also holds true for Nob1 from the archaeon Pyrococcus horikoshii, which efficiently cleaves RNA-substrates containing the D-site of the preribosomal RNA in a manganese-dependent manner. The structure of PhNob1 solved by nuclear magnetic resonance spectroscopy revealed a PIN domain common with many nucleases and a zinc ribbon domain, which are structurally connected by a flexible linker. We show that amino acid residues required for substrate binding reside in the PIN domain whereas the zinc ribbon domain alone is sufficient to bind helix 40 of the small subunit rRNA. This suggests that the zinc ribbon domain acts as an anchor point for the protein on the nascent subunit positioning it in the proximity of the cleavage site.
 
Structural and functional analysis of the archaeal endonuclease Nob1.,Veith T, Martin R, Wurm JP, Weis BL, Duchardt-Ferner E, Safferthal C, Hennig R, Mirus O, Bohnsack MT, Wohnert J, Schleiff E Nucleic Acids Res. 2012 Apr 1;40(7):3259-74. Epub 2011 Dec 10. PMID:22156373<ref>PMID:22156373</ref>
 
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
</div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Thermomicrobium roseum]]
[[Category: Large Structures]]
[[Category: Bohnsack, M T.]]
[[Category: Pyrococcus horikoshii OT3]]
[[Category: Duchardt-Ferner, E.]]
[[Category: Bohnsack MT]]
[[Category: Hennig, R.]]
[[Category: Duchardt-Ferner E]]
[[Category: Martin, R.]]
[[Category: Hennig R]]
[[Category: Mirus, O.]]
[[Category: Martin R]]
[[Category: Safferthal, C.]]
[[Category: Mirus O]]
[[Category: Schleiff, E.]]
[[Category: Safferthal C]]
[[Category: Veith, T.]]
[[Category: Schleiff E]]
[[Category: Weis, B.]]
[[Category: Veith T]]
[[Category: Woehnert, J.]]
[[Category: Weis B]]
[[Category: Wurm, J P.]]
[[Category: Woehnert J]]
[[Category: Metal binding protein]]
[[Category: Wurm JP]]
[[Category: Pin domain]]
[[Category: Ribosome biogenesis]]
[[Category: Zn ribbon domain]]

Latest revision as of 09:55, 1 May 2024

Solution structure of the endonuclease Nob1 from P.horikoshiiSolution structure of the endonuclease Nob1 from P.horikoshii

Structural highlights

2lcq is a 1 chain structure with sequence from Pyrococcus horikoshii OT3. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:Solution NMR
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NOB1_PYRHO Toxic component of a toxin-antitoxin (TA) module (Potential). Processes pre-16S-rRNA at its 3' end (the D-site) to yield the mature 3' end.[1]

References

  1. ↑ Veith T, Martin R, Wurm JP, Weis BL, Duchardt-Ferner E, Safferthal C, Hennig R, Mirus O, Bohnsack MT, Wohnert J, Schleiff E. Structural and functional analysis of the archaeal endonuclease Nob1. Nucleic Acids Res. 2012 Apr 1;40(7):3259-74. Epub 2011 Dec 10. PMID:22156373 doi:10.1093/nar/gkr1186
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