4lgt: Difference between revisions
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<StructureSection load='4lgt' size='340' side='right'caption='[[4lgt]], [[Resolution|resolution]] 1.30Å' scene=''> | <StructureSection load='4lgt' size='340' side='right'caption='[[4lgt]], [[Resolution|resolution]] 1.30Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4lgt]] is a 4 chain structure with sequence from [ | <table><tr><td colspan='2'>[[4lgt]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LGT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4LGT FirstGlance]. <br> | ||
</td></tr><tr id=' | </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>, <scene name='pdbligand=OCS:CYSTEINESULFONIC+ACID'>OCS</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=4lgt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lgt OCA], [https://pdbe.org/4lgt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4lgt RCSB], [https://www.ebi.ac.uk/pdbsum/4lgt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4lgt ProSAT]</span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | == Function == | ||
[ | [https://www.uniprot.org/uniprot/RLUB_ECOLI RLUB_ECOLI] Responsible for synthesis of pseudouridine from uracil-2605 in 23S ribosomal RNA. | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
| Line 24: | Line 21: | ||
==See Also== | ==See Also== | ||
*[[Guide-independent Pseudouridine synthase|Guide-independent Pseudouridine synthase]] | *[[Guide-independent Pseudouridine synthase|Guide-independent Pseudouridine synthase]] | ||
*[[Pseudouridine synthase 3D structures|Pseudouridine synthase 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Escherichia coli K-12]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Czudnochowski | [[Category: Czudnochowski N]] | ||
[[Category: Finer-Moore | [[Category: Finer-Moore JS]] | ||
[[Category: Stroud | [[Category: Stroud RM]] | ||
Revision as of 14:00, 14 December 2022
Crystal structure of the catalytic domain of RluB in complex with a 21-nucleotide RNA substrateCrystal structure of the catalytic domain of RluB in complex with a 21-nucleotide RNA substrate
Structural highlights
FunctionRLUB_ECOLI Responsible for synthesis of pseudouridine from uracil-2605 in 23S ribosomal RNA. Publication Abstract from PubMedRluB catalyses the modification of U2605 to pseudouridine (Psi) in a stem-loop at the peptidyl transferase center of Escherichia coli 23S rRNA. The homolog RluF is specific to the adjacent nucleotide in the stem, U2604. The 1.3 A resolution crystal structure of the complex between the catalytic domain of RluB and the isolated substrate stem-loop, in which the target uridine is substituted by 5-fluorouridine (5-FU), reveals a covalent bond between the isomerized target base and tyrosine 140. The structure is compared with the catalytic domain alone determined at 2.5 A resolution. The RluB-bound stem-loop has essentially the same secondary structure as in the ribosome, with a bulge at A2602, but with 5-FU2605 flipped into the active site. We showed earlier that RluF induced a frame-shift of the RNA, moving A2602 into the stem and translating its target, U2604, into the active site. A hydrogen-bonding network stabilizes the bulge in the RluB-RNA but is not conserved in RluF and so RluF cannot stabilize the bulge. On the basis of the covalent bond between enzyme and isomerized 5-FU we propose a Michael addition mechanism for pseudouridine formation that is consistent with all experimental data. The mechanism of pseudouridine synthases from a covalent complex with RNA, and alternate specificity for U2605 versus U2604 between close homologs.,Czudnochowski N, Ashley GW, Santi DV, Alian A, Finer-Moore J, Stroud RM Nucleic Acids Res. 2013 Nov 7. PMID:24214967[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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