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3dh3

From Proteopedia

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Crystal Structure of RluF in complex with a 22 nucleotide RNA substrate

Structural highlights

3dh3 is a 8 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 3Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RLUF_ECOLI Responsible for synthesis of pseudouridine from uracil-2604 in 23S ribosomal RNA. Can, to a small extent, also react with uracil-2605.^[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

Escherichia coli pseudouridine synthase RluF is dedicated to modifying U2604 in a stem-loop of 23S RNA, while a homologue, RluB, modifies the adjacent base, U2605. Both uridines are in the same RNA stem, separated by approximately 4 A. The 3.0 A X-ray crystal structure of RluF bound to the isolated stem-loop, in which U2604 is substituted by 5-fluorouridine to prevent catalytic turnover, shows RluF distinguishes closely spaced bases in similar environments by a selectivity mechanism based on a frameshift in base pairing. The RNA stem-loop is bound to a conserved binding groove in the catalytic domain. A base from a bulge in the stem, A2602, has folded into the stem, forcing one strand of the RNA stem to translate by one position and thus positioning U2604 to flip into the active site. RluF does not modify U2604 in mutant stem-loops that lack the A2602 bulge and shows dramatically higher activity for a stem-loop with a mutation designed to facilitate A2602 refolding into the stem with concomitant RNA strand translation. Residues whose side chains contact rearranged bases in the bound stem-loop, while conserved among RluFs, are not conserved between RluFs and RluBs, suggesting that RluB does not bind to the rearranged stem loop.

Crystal structure of an RluF-RNA complex: a base-pair rearrangement is the key to selectivity of RluF for U2604 of the ribosome.,Alian A, DeGiovanni A, Griner SL, Finer-Moore JS, Stroud RM J Mol Biol. 2009 May 15;388(4):785-800. Epub 2009 Mar 17. PMID:19298824^[2]

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

References

↑ Del Campo M, Kaya Y, Ofengand J. Identification and site of action of the remaining four putative pseudouridine synthases in Escherichia coli. RNA. 2001 Nov;7(11):1603-15. PMID:11720289
↑ Alian A, DeGiovanni A, Griner SL, Finer-Moore JS, Stroud RM. Crystal structure of an RluF-RNA complex: a base-pair rearrangement is the key to selectivity of RluF for U2604 of the ribosome. J Mol Biol. 2009 May 15;388(4):785-800. Epub 2009 Mar 17. PMID:19298824 doi:10.1016/j.jmb.2009.03.029

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/3dh3"

@@ Line 3: / Line 3: @@
 <StructureSection load='3dh3' size='340' side='right'caption='[[3dh3]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3dh3]] is a 8 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=3DH3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DH3 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3dh3]] is a 8 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=3DH3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DH3 FirstGlance]. <br>
-</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=FHU:(5S,6R)-5-FLUORO-6-HYDROXY-PSEUDOURIDINE-5-MONOPHOSPHATE'>FHU</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]] 3&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rluF, yjbC, b4022, JW3982 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FHU:(5S,6R)-5-FLUORO-6-HYDROXY-PSEUDOURIDINE-5-MONOPHOSPHATE'>FHU</scene></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=3dh3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dh3 OCA], [https://pdbe.org/3dh3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dh3 RCSB], [https://www.ebi.ac.uk/pdbsum/3dh3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dh3 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/RLUF_ECOLI RLUF_ECOLI]] Responsible for synthesis of pseudouridine from uracil-2604 in 23S ribosomal RNA. Can, to a small extent, also react with uracil-2605.<ref>PMID:11720289</ref>
+[https://www.uniprot.org/uniprot/RLUF_ECOLI RLUF_ECOLI] Responsible for synthesis of pseudouridine from uracil-2604 in 23S ribosomal RNA. Can, to a small extent, also react with uracil-2605.<ref>PMID:11720289</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 37: / Line 37: @@
 __TOC__
 </StructureSection>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
 [[Category: Large Structures]]
-[[Category: Alian, A]]
+[[Category: Alian A]]
-[[Category: DeGiovanni, A]]
+[[Category: DeGiovanni A]]
-[[Category: Finer-Moore, J S]]
+[[Category: Finer-Moore JS]]
-[[Category: Stroud, R M]]
+[[Category: Stroud RM]]
-[[Category: Alpha/beta protein]]
-[[Category: Isomerase]]
-[[Category: Isomerase-rna complex]]
-[[Category: Protein-rna complex]]
-[[Category: Rna-binding]]
-[[Category: Rrna processing]]
-[[Category: S4 domain]]

3dh3

From Proteopedia

Current revision

Crystal Structure of RluF in complex with a 22 nucleotide RNA substrate

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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