4lab: Difference between revisions

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-{{STRUCTURE_4lab|  PDB=4lab  |  SCENE=  }}
-===Crystal structure of the catalytic domain of RluB===
-{{ABSTRACT_PUBMED_24214967}}
-==Function==
+==Crystal structure of the catalytic domain of RluB==
-[[http://www.uniprot.org/uniprot/RLUB_ECOLI RLUB_ECOLI]] Responsible for synthesis of pseudouridine from uracil-2605 in 23S ribosomal RNA.
+<StructureSection load='4lab' size='340' side='right'caption='[[4lab]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[4lab]] is a 1 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=4LAB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4LAB FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5043&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PT:PLATINUM+(II)+ION'>PT</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=4lab FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lab OCA], [https://pdbe.org/4lab PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4lab RCSB], [https://www.ebi.ac.uk/pdbsum/4lab PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4lab ProSAT]</span></td></tr>
+</table>
+== 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;">
+== 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.
-==About this Structure==
+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>
-[[4lab]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LAB OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<ref group="xtra">PMID:024214967</ref><references group="xtra"/><references/>
+</div>
-[[Category: Czudnochowski, N.]]
+<div class="pdbe-citations 4lab" style="background-color:#fffaf0;"></div>
-[[Category: Finer-Moore, J S.]]
-[[Category: Stroud, R M.]]
+==See Also==
-[[Category: Alpha-beta protein]]
+*[[Guide-independent Pseudouridine synthase|Guide-independent Pseudouridine synthase]]
-[[Category: Beta sheet]]
+*[[Pseudouridine synthase 3D structures|Pseudouridine synthase 3D structures]]
-[[Category: E. coli ribosomal rna]]
+== References ==
-[[Category: Pseudouridine synthase]]
+<references/>
-[[Category: Rna binding protein]]
+__TOC__
+</StructureSection>
+[[Category: Escherichia coli K-12]]
+[[Category: Large Structures]]
+[[Category: Czudnochowski N]]
+[[Category: Finer-Moore JS]]
+[[Category: Stroud RM]]