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== | ==Crystal Structure of E. coli 5-methyluridine methyltransferase RumA in complex with ribosomal RNA substrate and S-adenosylhomocysteine.== | ||
A single base (U1939) within E. coli 23S ribosomal RNA is methylated by | <StructureSection load='2bh2' size='340' side='right'caption='[[2bh2]], [[Resolution|resolution]] 2.15Å' scene=''> | ||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[2bh2]] is a 4 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=2BH2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BH2 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]] 2.15Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMU:5-FLUORO-5-METHYLURIDINE-5-MONOPHOSPHATE'>FMU</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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=2bh2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bh2 OCA], [https://pdbe.org/2bh2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bh2 RCSB], [https://www.ebi.ac.uk/pdbsum/2bh2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bh2 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/RLMD_ECOLI RLMD_ECOLI] Catalyzes the formation of 5-methyl-uridine at position 1939 (m5U1939) in 23S rRNA.[HAMAP-Rule:MF_01010]<ref>PMID:11779873</ref> <ref>PMID:12907714</ref> | |||
== 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/bh/2bh2_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | |||
<text>to colour the structure by Evolutionary Conservation</text> | |||
</jmolCheckbox> | |||
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2bh2 ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
A single base (U1939) within E. coli 23S ribosomal RNA is methylated by its dedicated enzyme, RumA. The structure of RumA/RNA/S-adenosylhomocysteine uncovers the mechanism for achieving unique selectivity. The single-stranded substrate is "refolded" on the enzyme into a compact conformation with six key intra-RNA interactions. The RNA substrate contributes directly to catalysis. In addition to the target base, a second base is "flipped out" from the core loop to stack against the adenine of the cofactor S-adenosylhomocysteine. Nucleotides in permuted sequence order are stacked into the site vacated by the everted target U1939 and compensate for the energetic penalty of base eversion. The 3' hairpin segment of the RNA binds distal to the active site and provides binding energy that contributes to enhanced catalytic efficiency. Active collaboration of RNA in catalysis leads us to conclude that RumA and its substrate RNA may reflect features from the earliest RNA-protein era. | |||
A unique RNA Fold in the RumA-RNA-cofactor ternary complex contributes to substrate selectivity and enzymatic function.,Lee TT, Agarwalla S, Stroud RM Cell. 2005 Mar 11;120(5):599-611. PMID:15766524<ref>PMID:15766524</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2bh2" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Escherichia coli]] | [[Category: Escherichia coli]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Agarwalla | [[Category: Agarwalla S]] | ||
[[Category: Lee | [[Category: Lee TT]] | ||
[[Category: Stroud | [[Category: Stroud RM]] | ||
Latest revision as of 16:36, 13 December 2023
Crystal Structure of E. coli 5-methyluridine methyltransferase RumA in complex with ribosomal RNA substrate and S-adenosylhomocysteine.Crystal Structure of E. coli 5-methyluridine methyltransferase RumA in complex with ribosomal RNA substrate and S-adenosylhomocysteine.
Structural highlights
FunctionRLMD_ECOLI Catalyzes the formation of 5-methyl-uridine at position 1939 (m5U1939) in 23S rRNA.[HAMAP-Rule:MF_01010][1] [2] 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 PubMedA single base (U1939) within E. coli 23S ribosomal RNA is methylated by its dedicated enzyme, RumA. The structure of RumA/RNA/S-adenosylhomocysteine uncovers the mechanism for achieving unique selectivity. The single-stranded substrate is "refolded" on the enzyme into a compact conformation with six key intra-RNA interactions. The RNA substrate contributes directly to catalysis. In addition to the target base, a second base is "flipped out" from the core loop to stack against the adenine of the cofactor S-adenosylhomocysteine. Nucleotides in permuted sequence order are stacked into the site vacated by the everted target U1939 and compensate for the energetic penalty of base eversion. The 3' hairpin segment of the RNA binds distal to the active site and provides binding energy that contributes to enhanced catalytic efficiency. Active collaboration of RNA in catalysis leads us to conclude that RumA and its substrate RNA may reflect features from the earliest RNA-protein era. A unique RNA Fold in the RumA-RNA-cofactor ternary complex contributes to substrate selectivity and enzymatic function.,Lee TT, Agarwalla S, Stroud RM Cell. 2005 Mar 11;120(5):599-611. PMID:15766524[3] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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