2bh2

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{{Seed}}
 
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[[Image:2bh2.png|left|200px]]
 
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==Crystal Structure of E. coli 5-methyluridine methyltransferase RumA in complex with ribosomal RNA substrate and S-adenosylhomocysteine.==
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The line below this paragraph, containing "STRUCTURE_2bh2", creates the "Structure Box" on the page.
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<StructureSection load='2bh2' size='340' side='right'caption='[[2bh2]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<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>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.15&#8491;</td></tr>
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<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>
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{{STRUCTURE_2bh2| PDB=2bh2 | SCENE= }}
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<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>
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</table>
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== Function ==
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[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>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bh/2bh2_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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===CRYSTAL STRUCTURE OF E. COLI 5-METHYLURIDINE METHYLTRANSFERASE RUMA IN COMPLEX WITH RIBOSOMAL RNA SUBSTRATE AND S-ADENOSYLHOMOCYSTEINE.===
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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>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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The line below this paragraph, {{ABSTRACT_PUBMED_15766524}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 2bh2" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 15766524 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_15766524}}
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__TOC__
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</StructureSection>
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==About this Structure==
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2BH2 is a 4 chains structure of sequences from [http://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].
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==Reference==
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<ref group="xtra">PMID:15766524</ref><references group="xtra"/>
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[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Agarwalla, S.]]
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[[Category: Large Structures]]
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[[Category: Lee, T T.]]
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[[Category: Agarwalla S]]
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[[Category: Stroud, R M.]]
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[[Category: Lee TT]]
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[[Category: 4fe-4]]
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[[Category: Stroud RM]]
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[[Category: Base flipping]]
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[[Category: Base stacking]]
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[[Category: Direct protein sequencing]]
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[[Category: General base]]
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[[Category: Iron-sulfur cluster]]
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[[Category: Metal-binding]]
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[[Category: Methyltransferase]]
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[[Category: Ob-fold]]
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[[Category: Product release]]
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[[Category: Protein-rna complex]]
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[[Category: Rna modification]]
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[[Category: Rna processing]]
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[[Category: Ruma]]
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[[Category: Sam]]
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[[Category: Substrate selectivity]]
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[[Category: Transferase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 20:41:02 2009''
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Current revision

Crystal Structure of E. coli 5-methyluridine methyltransferase RumA in complex with ribosomal RNA substrate and S-adenosylhomocysteine.

PDB ID 2bh2

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