4lab: Difference between revisions
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==Crystal structure of the catalytic domain of RluB== | |||
=== | <StructureSection load='4lab' size='340' side='right' caption='[[4lab]], [[Resolution|resolution]] 2.50Å' scene=''> | ||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4lab]] is a 1 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=4LAB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4LAB FirstGlance]. <br> | |||
==Function== | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PT:PLATINUM+(II)+ION'>PT</scene></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">b1269, JW1261, rluB, yciL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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> | |||
<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=4lab FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lab OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4lab RCSB], [http://www.ebi.ac.uk/pdbsum/4lab PDBsum]</span></td></tr> | |||
</table> | |||
== Function == | |||
[[http://www.uniprot.org/uniprot/RLUB_ECOLI RLUB_ECOLI]] Responsible for synthesis of pseudouridine from uracil-2605 in 23S ribosomal RNA. | [[http://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;"> | |||
== 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<ref>PMID:24214967</ref> | |||
== | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Ecoli]] | [[Category: Ecoli]] | ||
[[Category: Czudnochowski, N | [[Category: Czudnochowski, N]] | ||
[[Category: Finer-Moore, J S | [[Category: Finer-Moore, J S]] | ||
[[Category: Stroud, R M | [[Category: Stroud, R M]] | ||
[[Category: Alpha-beta protein]] | [[Category: Alpha-beta protein]] | ||
[[Category: Beta sheet]] | [[Category: Beta sheet]] | ||
Revision as of 11:09, 25 December 2014
Crystal structure of the catalytic domain of RluB
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