This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

3awi

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 14:58, 4 August 2016

Bifunctional tRNA modification enzyme MnmC from Escherichia coli

Structural highlights

3awi is a 6 chain structure with sequence from Ecoli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Gene:	mnmC, yfcK, b2324, JW5380 (ECOLI)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[MNMC_ECOLI] 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.^[1] ^[2]

Publication Abstract from PubMed

Posttranscriptional modifications of bases within the tRNA anticodon significantly affect the decoding system. In bacteria and eukaryotes, uridines at the wobble position (U34) of some tRNAs are modified to 5-methyluridine derivatives (xm(5) U). These xm(5) U34-containing tRNAs read codons ending with A or G, while tRNAs with the unmodified U34 are able to read all four synonymous codons of a family box. In Escherichia coli, the bifunctional enzyme MnmC catalyzes the two consecutive reactions that convert 5-carboxymethylaminomethyl uridine (cmnm(5) U) to 5-methylaminomethyl uridine (mnm(5) U). The C-terminal domain of MnmC (MnmC1) is responsible for the FAD-dependent deacetylation of cmnm(5) U to 5-aminomethyl uridine (nm(5) U), while the N-terminal domain (MnmC2) catalyzes the subsequent S-adenosyl-L-methionine-dependent methylation of nm(5) U, leading to the final product, mnm(5) U34. Here, we determined the crystal structure of E. coli MnmC containing FAD, at 3.0 A resolution. The structure of the MnmC1 domain can be classified in the FAD-dependent glutathione reductase 2 (GR(2) ) structural family, including the glycine oxidase ThiO, while the MnmC2 domain adopts the canonical class I methyltransferase fold. A structural comparison with ThiO revealed the residues that may be involved in cmnm(5) U recognition, supporting previous mutational analyses. The catalytic sites of the two reactions are both surrounded by conserved basic residues for possible anticodon binding, and are located far away from each other, on opposite sides of the protein. These results suggest that, although the MnmC1 and MnmC2 domains are physically linked, they could catalyze the two consecutive reactions in a rather independent manner.

Crystal structure of the bifunctional tRNA modification enzyme MnmC from Escherichia coli.,Kitamura A, Sengoku T, Nishimoto M, Yokoyama S, Bessho Y Protein Sci. 2011 May 13. doi: 10.1002/pro.659. PMID:21574198^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Bujnicki JM, Oudjama Y, Roovers M, Owczarek S, Caillet J, Droogmans L. Identification of a bifunctional enzyme MnmC involved in the biosynthesis of a hypermodified uridine in the wobble position of tRNA. RNA. 2004 Aug;10(8):1236-42. Epub 2004 Jul 9. PMID:15247431 doi:http://dx.doi.org/10.1261/rna.7470904
↑ Roovers M, Oudjama Y, Kaminska KH, Purta E, Caillet J, Droogmans L, Bujnicki JM. Sequence-structure-function analysis of the bifunctional enzyme MnmC that catalyses the last two steps in the biosynthesis of hypermodified nucleoside mnm5s2U in tRNA. Proteins. 2008 Jun;71(4):2076-85. doi: 10.1002/prot.21918. PMID:18186482 doi:http://dx.doi.org/10.1002/prot.21918
↑ Kitamura A, Sengoku T, Nishimoto M, Yokoyama S, Bessho Y. Crystal structure of the bifunctional tRNA modification enzyme MnmC from Escherichia coli. Protein Sci. 2011 May 13. doi: 10.1002/pro.659. PMID:21574198 doi:10.1002/pro.659

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3awi"

@@ Line 1: / Line 1: @@
 ==Bifunctional tRNA modification enzyme MnmC from Escherichia coli==
 <StructureSection load='3awi' size='340' side='right' caption='[[3awi]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
@@ Line 5: / Line 6: @@
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">mnmC, yfcK, b2324, JW5380 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=3awi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3awi OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3awi RCSB], [http://www.ebi.ac.uk/pdbsum/3awi PDBsum]</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=3awi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3awi OCA], [http://pdbe.org/3awi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3awi RCSB], [http://www.ebi.ac.uk/pdbsum/3awi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3awi ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 17: / Line 18: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3awi" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>

3awi

From Proteopedia

Revision as of 14:58, 4 August 2016

Bifunctional tRNA modification enzyme MnmC from Escherichia coli

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox