2fk6

From Proteopedia

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Current revision

Crystal Structure of RNAse Z/tRNA(Thr) complex

Structural highlights

2fk6 is a 2 chain structure with sequence from Bacillus subtilis. The September 2008 RCSB PDB Molecule of the Month feature on Ribonuclease A by David Goodsell is 10.2210/rcsb_pdb/mom_2008_9. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.9Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RNZ_BACSU Zinc phosphodiesterase, which displays some tRNA 3'-processing endonuclease activity. Probably involved in tRNA maturation, by removing a 3'-trailer from precursor tRNA.^[1]

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

The highly conserved ribonuclease RNase Z catalyzes the endonucleolytic removal of the 3' extension of the majority of tRNA precursors. Here we present the structure of the complex between Bacillus subtilis RNase Z and tRNA(Thr), the first structure of a ribonucleolytic processing enzyme bound to tRNA. Binding of tRNA to RNase Z causes conformational changes in both partners to promote reorganization of the catalytic site and tRNA cleavage.

Structure of the ubiquitous 3' processing enzyme RNase Z bound to transfer RNA.,Li de la Sierra-Gallay I, Mathy N, Pellegrini O, Condon C Nat Struct Mol Biol. 2006 Apr;13(4):376-7. Epub 2006 Mar 5. PMID:16518398^[2]

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

References

↑ Pellegrini O, Nezzar J, Marchfelder A, Putzer H, Condon C. Endonucleolytic processing of CCA-less tRNA precursors by RNase Z in Bacillus subtilis. EMBO J. 2003 Sep 1;22(17):4534-43. PMID:12941704 doi:http://dx.doi.org/10.1093/emboj/cdg435
↑ Li de la Sierra-Gallay I, Mathy N, Pellegrini O, Condon C. Structure of the ubiquitous 3' processing enzyme RNase Z bound to transfer RNA. Nat Struct Mol Biol. 2006 Apr;13(4):376-7. Epub 2006 Mar 5. PMID:16518398 doi:10.1038/nsmb1066

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2fk6"

@@ Line 1: / Line 1: @@
-[[Image:2fk6.gif|left|200px]]
- {{Structure
+==Crystal Structure of RNAse Z/tRNA(Thr) complex==
-|PDB= 2fk6 |SIZE=350|CAPTION= <scene name='initialview01'>2fk6</scene>, resolution 2.90&Aring;
+<StructureSection load='2fk6' size='340' side='right'caption='[[2fk6]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=A:ADENOSINE-5&#39;-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5&#39;-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5&#39;-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=U:URIDINE-5&#39;-MONOPHOSPHATE'>U</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>
+<table><tr><td colspan='2'>[[2fk6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. The September 2008 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Ribonuclease A''  by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2008_9 10.2210/rcsb_pdb/mom_2008_9]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FK6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FK6 FirstGlance]. <br>
-|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_Z Ribonuclease Z], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.11 3.1.26.11] </span>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.9&#8491;</td></tr>
-|GENE= RNZ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-|DOMAIN=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2fk6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fk6 OCA], [https://pdbe.org/2fk6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fk6 RCSB], [https://www.ebi.ac.uk/pdbsum/2fk6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fk6 ProSAT]</span></td></tr>
-|RELATEDENTRY=[[1y44|1Y44]], [[1ww1|1WW1]]
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2fk6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fk6 OCA], [http://www.ebi.ac.uk/pdbsum/2fk6 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2fk6 RCSB]</span>
+== Function ==
-}}
+[https://www.uniprot.org/uniprot/RNZ_BACSU RNZ_BACSU] Zinc phosphodiesterase, which displays some tRNA 3'-processing endonuclease activity. Probably involved in tRNA maturation, by removing a 3'-trailer from precursor tRNA.<ref>PMID:12941704</ref>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fk/2fk6_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2fk6 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The highly conserved ribonuclease RNase Z catalyzes the endonucleolytic removal of the 3' extension of the majority of tRNA precursors. Here we present the structure of the complex between Bacillus subtilis RNase Z and tRNA(Thr), the first structure of a ribonucleolytic processing enzyme bound to tRNA. Binding of tRNA to RNase Z causes conformational changes in both partners to promote reorganization of the catalytic site and tRNA cleavage.
-'''Crystal Structure of RNAse Z/tRNA(Thr) complex'''
+Structure of the ubiquitous 3' processing enzyme RNase Z bound to transfer RNA.,Li de la Sierra-Gallay I, Mathy N, Pellegrini O, Condon C Nat Struct Mol Biol. 2006 Apr;13(4):376-7. Epub 2006 Mar 5. PMID:16518398<ref>PMID:16518398</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2fk6" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-The highly conserved ribonuclease RNase Z catalyzes the endonucleolytic removal of the 3' extension of the majority of tRNA precursors. Here we present the structure of the complex between Bacillus subtilis RNase Z and tRNA(Thr), the first structure of a ribonucleolytic processing enzyme bound to tRNA. Binding of tRNA to RNase Z causes conformational changes in both partners to promote reorganization of the catalytic site and tRNA cleavage.
+*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
+*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]]
-==About this Structure==
+== References ==
-FK6 is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FK6 OCA].
+<references/>
+__TOC__
-==Reference==
+</StructureSection>
-Structure of the ubiquitous 3' processing enzyme RNase Z bound to transfer RNA., Li de la Sierra-Gallay I, Mathy N, Pellegrini O, Condon C, Nat Struct Mol Biol. 2006 Apr;13(4):376-7. Epub 2006 Mar 5. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16518398 16518398]
 [[Category: Bacillus subtilis]]
-[[Category: Protein complex]]
+[[Category: Large Structures]]
-[[Category: Ribonuclease Z]]
+[[Category: RCSB PDB Molecule of the Month]]
-[[Category: Condon, C.]]
+[[Category: Ribonuclease A]]
-[[Category: Mathy, N.]]
+[[Category: Condon C]]
-[[Category: Pellegrini, O.]]
+[[Category: Li de la Sierra-Gallay I]]
-[[Category: Sierra-Gallay, I Li de la.]]
+[[Category: Mathy N]]
-[[Category: protein-trna complex]]
+[[Category: Pellegrini O]]
-[[Category: trna maturase]]
-[[Category: zinc-dependent metal hydrolase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 03:03:55 2008''

2fk6

From Proteopedia

Current revision

Crystal Structure of RNAse Z/tRNA(Thr) complex

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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