3ps9: Difference between revisions
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==Crystal structure of MnmC from E. coli== | ==Crystal structure of MnmC from E. coli== | ||
<StructureSection load='3ps9' size='340' side='right' caption='[[3ps9]], [[Resolution|resolution]] 2.54Å' scene=''> | <StructureSection load='3ps9' size='340' side='right'caption='[[3ps9]], [[Resolution|resolution]] 2.54Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3ps9]] is a 1 chain structure with sequence from [ | <table><tr><td colspan='2'>[[3ps9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecobb Ecobb]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PS9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PS9 FirstGlance]. <br> | ||
</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=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene></td></tr> | </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=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">B21_02209, mnmC, yfcK ([ | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">B21_02209, mnmC, yfcK ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=511693 ECOBB])</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.61 2.1.1.61] </span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ps9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ps9 OCA], [https://pdbe.org/3ps9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ps9 RCSB], [https://www.ebi.ac.uk/pdbsum/3ps9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ps9 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[[ | [[https://www.uniprot.org/uniprot/C6ELC9_ECOBD C6ELC9_ECOBD]] Catalyzes the last two steps in the biosynthesis of 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at the wobble position (U34) in tRNA. Catalyzes the FAD-dependent demodification of cmnm(5)s(2)U34 to nm(5)s(2)U34, followed by the transfer of a methyl group from S-adenosyl-L-methionine to nm(5)s(2)U34, to form mnm(5)s(2)U34 (By similarity).[SAAS:SAAS006076_004_060760][HAMAP-Rule:MF_01102] | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Ecobb]] | [[Category: Ecobb]] | ||
[[Category: Large Structures]] | |||
[[Category: Almo, S C]] | [[Category: Almo, S C]] | ||
[[Category: Kim, J]] | [[Category: Kim, J]] | ||
Revision as of 11:52, 25 May 2022
Crystal structure of MnmC from E. coliCrystal structure of MnmC from E. coli
Structural highlights
Function[C6ELC9_ECOBD] Catalyzes the last two steps in the biosynthesis of 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at the wobble position (U34) in tRNA. Catalyzes the FAD-dependent demodification of cmnm(5)s(2)U34 to nm(5)s(2)U34, followed by the transfer of a methyl group from S-adenosyl-L-methionine to nm(5)s(2)U34, to form mnm(5)s(2)U34 (By similarity).[SAAS:SAAS006076_004_060760][HAMAP-Rule:MF_01102] Publication Abstract from PubMedBACKGROUND: Methylaminomethyl modification of uridine or 2-thiouridine (mnm5U34 or mnm5s2U34) at the wobble position of tRNAs specific for glutamate, lysine and arginine are observed in Escherichia coli and allow for specific recognition of codons ending in A or G. In the biosynthetic pathway responsible for this post-transcriptional modification, the bifunctional enzyme MnmC catalyzes the conversion of its hypermodified substrate carboxymethylaminomethyl uridine (cmnm5U34) to mnm5U34. MnmC catalyzes the flavin adenine dinucleotide (FAD)-dependent oxidative cleavage of carboxymethyl group from cmnm5U34 via an imine intermediate to generate aminomethyl uridine (nm5U34), which is subsequently methylated by S-adenosyl-L-methionine (SAM) to yield methylaminomethyl uridine (mnm5U34). RESULTS: The X-ray crystal structures of SAM/FAD-bound bifunctional MnmC from Escherichia coli and Yersinia pestis, and FAD-bound bifunctional MnmC from Yersinia pestis were determined and the catalytic functions verified in an in vitro assay. CONCLUSION: The crystal structures of MnmC from two Gram negative bacteria reveal the overall architecture of the enzyme and the relative disposition of the two independent catalytic domains: a Rossmann-fold domain containing the SAM binding site and an FAD containing domain structurally homologous to glycine oxidase from Bacillus subtilis. The structures of MnmC also reveal the detailed atomic interactions at the interdomain interface and provide spatial restraints relevant to the overall catalytic mechanism. Structural basis for hypermodification of the wobble uridine in tRNA by bifunctional enzyme MnmC.,Kim J, Almo SC BMC Struct Biol. 2013 Apr 24;13:5. doi: 10.1186/1472-6807-13-5. PMID:23617613[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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