3ngz

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of RNase T in complex with a non-preferred ssDNA (GC) with one Mg in the active site

Structural highlights

3ngz is a 4 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.1Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RNT_ECOLI Responsible for the end-turnover of tRNA: specifically removes the terminal AMP residue from uncharged tRNA (tRNA-C-C-A). Also appears to be involved in tRNA biosynthesis, especially in strains lacking other exoribonucleases.[HAMAP-Rule:MF_00157]

Publication Abstract from PubMed

RNA maturation relies on various exonucleases to remove nucleotides successively from the 5' or 3' end of nucleic acids. However, little is known regarding the molecular basis for substrate and cleavage preference of exonucleases. Our biochemical and structural analyses on RNase T-DNA complexes show that the RNase T dimer has an ideal architecture for binding a duplex with a short 3' overhang to produce a digestion product of a duplex with a 2-nucleotide (nt) or 1-nt 3' overhang, depending on the composition of the last base pair in the duplex. A 'C-filter' in RNase T screens out the nucleic acids with 3'-terminal cytosines for hydrolysis by inducing a disruptive conformational change at the active site. Our results reveal the general principles and the working mechanism for the final trimming step made by RNase T in the maturation of stable RNA and pave the way for the understanding of other DEDD family exonucleases.

Structural basis for RNA trimming by RNase T in stable RNA 3'-end maturation.,Hsiao YY, Yang CC, Lin CL, Lin JL, Duh Y, Yuan HS Nat Chem Biol. 2011 Feb 13. PMID:21317904^[1]

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

References

↑ Hsiao YY, Yang CC, Lin CL, Lin JL, Duh Y, Yuan HS. Structural basis for RNA trimming by RNase T in stable RNA 3'-end maturation. Nat Chem Biol. 2011 Feb 13. PMID:21317904 doi:10.1038/nchembio.524

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3ngz"

Categories: Escherichia coli | Large Structures | Hsiao Y-Y | Yuan HS

@@ Line 3: / Line 3: @@
 <StructureSection load='3ngz' size='340' side='right'caption='[[3ngz]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3ngz]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NGZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NGZ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3ngz]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NGZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NGZ FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.1&#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;'>[[3ngy|3ngy]], [[3nh0|3nh0]], [[3nh1|3nh1]], [[3nh2|3nh2]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rnt ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=3ngz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ngz OCA], [https://pdbe.org/3ngz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ngz RCSB], [https://www.ebi.ac.uk/pdbsum/3ngz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ngz ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/RNT_ECOLI RNT_ECOLI]] Responsible for the end-turnover of tRNA: specifically removes the terminal AMP residue from uncharged tRNA (tRNA-C-C-A). Also appears to be involved in tRNA biosynthesis, especially in strains lacking other exoribonucleases.[HAMAP-Rule:MF_00157]
+[https://www.uniprot.org/uniprot/RNT_ECOLI RNT_ECOLI] Responsible for the end-turnover of tRNA: specifically removes the terminal AMP residue from uncharged tRNA (tRNA-C-C-A). Also appears to be involved in tRNA biosynthesis, especially in strains lacking other exoribonucleases.[HAMAP-Rule:MF_00157]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 27: / Line 26: @@
 __TOC__
 </StructureSection>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
 [[Category: Large Structures]]
-[[Category: Hsiao, Y Y]]
+[[Category: Hsiao Y-Y]]
-[[Category: Yuan, H S]]
+[[Category: Yuan HS]]
-[[Category: Exo-nuclease]]
-[[Category: Exoribonuclease]]
-[[Category: Hydrolase-dna complex]]
-[[Category: Protein-dna complex]]
-[[Category: Protein-dna interaction]]
-[[Category: Rna maturation]]
-[[Category: Rna processing]]

3ngz

From Proteopedia

Current revision

Crystal structure of RNase T in complex with a non-preferred ssDNA (GC) with one Mg in the active site

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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