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1oyp

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Revision as of 09:22, 8 September 2021

Crystal Structure of the phosphorolytic exoribonuclease RNase PH from Bacillus subtilis

Structural highlights

1oyp is a 6 chain structure with sequence from Bacillus subtilis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	1oyr, 1oys
Activity:	tRNA nucleotidyltransferase, with EC number 2.7.7.56
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[RNPH_BACSU] Phosphorolytic exoribonuclease that removes nucleotide residues following the -CCA terminus of tRNA and adds nucleotides to the ends of RNA molecules by using nucleoside diphosphates as substrates. Plays a role in the secondary pathway of 23S rRNA 3' end maturation.^[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

RNase PH is a member of the family of phosphorolytic 3' --> 5' exoribonucleases that also includes polynucleotide phosphorylase (PNPase). RNase PH is involved in the maturation of tRNA precursors and especially important for removal of nucleotide residues near the CCA acceptor end of the mature tRNAs. Wild-type and triple mutant R68Q-R73Q-R76Q RNase PH from Bacillus subtilis have been crystallized and the structures determined by X-ray diffraction to medium resolution. Wild-type and triple mutant RNase PH crystallize as a hexamer and dimer, respectively. The structures contain a rare left-handed beta alpha beta-motif in the N-terminal portion of the protein. This motif has also been identified in other enzymes involved in RNA metabolism. The RNase PH structure and active site can, despite low sequence similarity, be overlayed with the N-terminal core of the structure and active site of Streptomyces antibioticus PNPase. The surface of the RNase PH dimer fit the shape of a tRNA molecule.

Crystal structure of the phosphorolytic exoribonuclease RNase PH from Bacillus subtilis and implications for its quaternary structure and tRNA binding.,Harlow LS, Kadziola A, Jensen KF, Larsen S Protein Sci. 2004 Mar;13(3):668-77. Epub 2004 Feb 6. PMID:14767080^[2]

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

References

↑ Redko Y, Condon C. Maturation of 23S rRNA in Bacillus subtilis in the absence of Mini-III. J Bacteriol. 2010 Jan;192(1):356-9. doi: 10.1128/JB.01096-09. Epub . PMID:19880604 doi:http://dx.doi.org/10.1128/JB.01096-09
↑ Harlow LS, Kadziola A, Jensen KF, Larsen S. Crystal structure of the phosphorolytic exoribonuclease RNase PH from Bacillus subtilis and implications for its quaternary structure and tRNA binding. Protein Sci. 2004 Mar;13(3):668-77. Epub 2004 Feb 6. PMID:14767080 doi:10.1110/ps.03477004

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/1oyp"

@@ Line 3: / Line 3: @@
 <StructureSection load='1oyp' size='340' side='right'caption='[[1oyp]], [[Resolution|resolution]] 2.76&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1oyp]] is a 6 chain structure with sequence 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=1OYP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1OYP FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1oyp]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OYP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OYP FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1oyr|1oyr]], [[1oys|1oys]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1oyr|1oyr]], [[1oys|1oys]]</div></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/tRNA_nucleotidyltransferase tRNA nucleotidyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.56 2.7.7.56] </span></td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/tRNA_nucleotidyltransferase tRNA nucleotidyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.56 2.7.7.56] </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=1oyp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oyp OCA], [http://pdbe.org/1oyp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1oyp RCSB], [http://www.ebi.ac.uk/pdbsum/1oyp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1oyp 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=1oyp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oyp OCA], [https://pdbe.org/1oyp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1oyp RCSB], [https://www.ebi.ac.uk/pdbsum/1oyp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1oyp ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/RNPH_BACSU RNPH_BACSU]] Phosphorolytic exoribonuclease that removes nucleotide residues following the -CCA terminus of tRNA and adds nucleotides to the ends of RNA molecules by using nucleoside diphosphates as substrates. Plays a role in the secondary pathway of 23S rRNA 3' end maturation.<ref>PMID:19880604</ref>
+[[https://www.uniprot.org/uniprot/RNPH_BACSU RNPH_BACSU]] Phosphorolytic exoribonuclease that removes nucleotide residues following the -CCA terminus of tRNA and adds nucleotides to the ends of RNA molecules by using nucleoside diphosphates as substrates. Plays a role in the secondary pathway of 23S rRNA 3' end maturation.<ref>PMID:19880604</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 32: / Line 32: @@
 ==See Also==
-*[[Ribonuclease|Ribonuclease]]
+*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
-*[[Temp|Temp]]
 == References ==
 <references/>

1oyp

From Proteopedia

Revision as of 09:22, 8 September 2021

Crystal Structure of the phosphorolytic exoribonuclease RNase PH from Bacillus subtilis

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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