1udq

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of the tRNA processing enzyme RNase PH T125A mutant from Aquifex aeolicus

Structural highlights

1udq is a 1 chain structure with sequence from Aquifex aeolicus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.3Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

RNPH_AQUAE 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 (By similarity).

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 one of the exoribonucleases that catalyze the 3' end processing of tRNA in bacteria. RNase PH removes nucleotides following the CCA sequence of tRNA precursors by phosphorolysis and generates mature tRNAs with amino acid acceptor activity. In this study, we determined the crystal structure of Aquifex aeolicus RNase PH bound with a phosphate, a co-substrate, in the active site at 2.3-A resolution. RNase PH has the typical alpha/beta fold, which forms a hexameric ring structure as a trimer of dimers. This ring structure resembles that of the polynucleotide phosphorylase core domain homotrimer, another phosphorolytic exoribonuclease. Four amino acid residues, Arg-86, Gly-124, Thr-125, and Arg-126, of RNase PH are involved in the phosphate-binding site. Mutational analyses of these residues showed their importance in the phosphorolysis reaction. A docking model with the tRNA acceptor stem suggests how RNase PH accommodates substrate RNAs.

Crystal structure of the tRNA processing enzyme RNase PH from Aquifex aeolicus.,Ishii R, Nureki O, Yokoyama S J Biol Chem. 2003 Aug 22;278(34):32397-404. Epub 2003 May 12. PMID:12746447^[1]

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

References

↑ Ishii R, Nureki O, Yokoyama S. Crystal structure of the tRNA processing enzyme RNase PH from Aquifex aeolicus. J Biol Chem. 2003 Aug 22;278(34):32397-404. Epub 2003 May 12. PMID:12746447 doi:http://dx.doi.org/10.1074/jbc.M300639200

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/1udq"

Categories: Aquifex aeolicus | Large Structures | Ishii R | Nureki O | Yokoyama S

@@ Line 3: / Line 3: @@
 <StructureSection load='1udq' size='340' side='right'caption='[[1udq]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1udq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"aquifex_aeolicus"_huber_and_stetter_2001 "aquifex aeolicus" huber and stetter 2001]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UDQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UDQ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1udq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UDQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UDQ FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1udn|1udn]], [[1udo|1udo]], [[1uds|1uds]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=1udq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1udq OCA], [https://pdbe.org/1udq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1udq RCSB], [https://www.ebi.ac.uk/pdbsum/1udq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1udq ProSAT], [https://www.topsan.org/Proteins/RSGI/1udq TOPSAN]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/RNPH_AQUAE RNPH_AQUAE]] 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 (By similarity).
+[https://www.uniprot.org/uniprot/RNPH_AQUAE RNPH_AQUAE] 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 (By similarity).
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 37: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Aquifex aeolicus huber and stetter 2001]]
+[[Category: Aquifex aeolicus]]
 [[Category: Large Structures]]
-[[Category: TRNA nucleotidyltransferase]]
+[[Category: Ishii R]]
-[[Category: Ishii, R]]
+[[Category: Nureki O]]
-[[Category: Nureki, O]]
+[[Category: Yokoyama S]]
-[[Category: Structural genomic]]
-[[Category: Yokoyama, S]]
-[[Category: Rsgi]]
-[[Category: Transferase]]

1udq

From Proteopedia

Current revision

Crystal structure of the tRNA processing enzyme RNase PH T125A mutant from Aquifex aeolicus

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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