2oml

From Proteopedia

(Difference between revisions)

Current revision

crystal structure of E. coli pseudouridine synthase RluE

Structural highlights

2oml is a 1 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 1.2Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RLUE_ECOLI Responsible for synthesis of pseudouridine from uracil-2457 in 23S ribosomal RNA.

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

Pseudouridine synthase RluE modifies U2457 in a stem of 23 S RNA in Escherichia coli. This modification is located in the peptidyl transferase center of the ribosome. We determined the crystal structures of the C-terminal, catalytic domain of E. coli RluE at 1.2 A resolution and of full-length RluE at 1.6 A resolution. The crystals of the full-length enzyme contain two molecules in the asymmetric unit and in both molecules the N-terminal domain is disordered. The protein has an active site cleft, conserved in all other pseudouridine synthases, that contains invariant Asp and Tyr residues implicated in catalysis. An electropositive surface patch that covers the active site cleft is just wide enough to accommodate an RNA stem. The RNA substrate stem can be docked to this surface such that the catalytic Asp is adjacent to the target base, and a conserved Arg is positioned to help flip the target base out of the stem into the enzyme active site. A flexible RluE specific loop lies close to the conserved region of the stem in the model, and may contribute to substrate specificity. The stem alone is not a good RluE substrate, suggesting RluE makes additional interactions with other regions in the ribosome.

The crystal structure of E. coli rRNA pseudouridine synthase RluE.,Pan H, Ho JD, Stroud RM, Finer-Moore J J Mol Biol. 2007 Apr 13;367(5):1459-70. Epub 2007 Feb 7. PMID:17320904^[1]

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

References

↑ Pan H, Ho JD, Stroud RM, Finer-Moore J. The crystal structure of E. coli rRNA pseudouridine synthase RluE. J Mol Biol. 2007 Apr 13;367(5):1459-70. Epub 2007 Feb 7. PMID:17320904 doi:10.1016/j.jmb.2007.01.084

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/2oml"

@@ Line 1: / Line 1: @@
 ==crystal structure of E. coli pseudouridine synthase RluE==
-<StructureSection load='2oml' size='340' side='right' caption='[[2oml]], [[Resolution|resolution]] 1.20&Aring;' scene=''>
+<StructureSection load='2oml' size='340' side='right'caption='[[2oml]], [[Resolution|resolution]] 1.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2oml]] is a 1 chain structure with sequence from [http://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=2OML OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OML FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2oml]] is a 1 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=2OML OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OML 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='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.2&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2olw|2olw]]</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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rluE ([http://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=2oml FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oml OCA], [https://pdbe.org/2oml PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2oml RCSB], [https://www.ebi.ac.uk/pdbsum/2oml PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2oml ProSAT]</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=2oml FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oml OCA], [http://pdbe.org/2oml PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2oml RCSB], [http://www.ebi.ac.uk/pdbsum/2oml PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2oml ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/RLUE_ECOLI RLUE_ECOLI]] Responsible for synthesis of pseudouridine from uracil-2457 in 23S ribosomal RNA.
+[https://www.uniprot.org/uniprot/RLUE_ECOLI RLUE_ECOLI] Responsible for synthesis of pseudouridine from uracil-2457 in 23S ribosomal RNA.
 == 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/om/2oml_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/om/2oml_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 30: / Line 29: @@
 </div>
 <div class="pdbe-citations 2oml" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Guide-independent Pseudouridine synthase|Guide-independent Pseudouridine synthase]]
+*[[Pseudouridine synthase 3D structures|Pseudouridine synthase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
-[[Category: Finer-Moore, J]]
+[[Category: Large Structures]]
-[[Category: Ho, J D]]
+[[Category: Finer-Moore J]]
-[[Category: Pan, H]]
+[[Category: Ho JD]]
-[[Category: Stroud, R M]]
+[[Category: Pan H]]
-[[Category: Bifurcated beta sheet]]
+[[Category: Stroud RM]]
-[[Category: Isomerase]]
-[[Category: Thrombin-cleaved]]

2oml

From Proteopedia

Current revision

crystal structure of E. coli pseudouridine synthase RluE

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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