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| | ==Crystal structure of the catalytic domain of RluB in complex with a 21-nucleotide RNA substrate== | | ==Crystal structure of the catalytic domain of RluB in complex with a 21-nucleotide RNA substrate== |
| - | <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 [http://en.wikipedia.org/wiki/Ecoli Ecoli]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4LGT FirstGlance]. <br> | + | <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='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>, <scene name='pdbligand=OCS:CYSTEINESULFONIC+ACID'>OCS</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]] 1.3Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4lab|4lab]]</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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rluB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/23S_rRNA_pseudouridine(2605)_synthase 23S rRNA pseudouridine(2605) synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.99.22 5.4.99.22] </span></td></tr>
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| - | <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=4lgt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lgt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4lgt RCSB], [http://www.ebi.ac.uk/pdbsum/4lgt PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/RLUB_ECOLI RLUB_ECOLI]] Responsible for synthesis of pseudouridine from uracil-2605 in 23S ribosomal RNA. | + | [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 == |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 4lgt" 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 == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Ecoli]] | + | [[Category: Escherichia coli K-12]] |
| - | [[Category: Czudnochowski, N]]
| + | [[Category: Large Structures]] |
| - | [[Category: Finer-Moore, J S]]
| + | [[Category: Czudnochowski N]] |
| - | [[Category: Stroud, R M]] | + | [[Category: Finer-Moore JS]] |
| - | [[Category: Beta sheet alpha-beta protein]] | + | [[Category: Stroud RM]] |
| - | [[Category: E. coli ribosomal rna]] | + | |
| - | [[Category: Isomerase-rna complex]]
| + | |
| - | [[Category: Rrna modification peudouridine synthase]] | + | |
| Structural highlights
Function
RLUB_ECOLI Responsible for synthesis of pseudouridine from uracil-2605 in 23S ribosomal RNA.
Publication Abstract from PubMed
RluB 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 Also
References
- ↑ Czudnochowski N, Ashley GW, Santi DV, Alian A, Finer-Moore J, Stroud RM. The mechanism of pseudouridine synthases from a covalent complex with RNA, and alternate specificity for U2605 versus U2604 between close homologs. Nucleic Acids Res. 2013 Nov 7. PMID:24214967 doi:http://dx.doi.org/10.1093/nar/gkt1050
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