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| | ==Crystal structure of epoxyqueuosine reductase with a tRNA-TYR epoxyqueuosine-modified tRNA stem loop== | | ==Crystal structure of epoxyqueuosine reductase with a tRNA-TYR epoxyqueuosine-modified tRNA stem loop== |
| - | <StructureSection load='5d0b' size='340' side='right' caption='[[5d0b]], [[Resolution|resolution]] 2.65Å' scene=''> | + | <StructureSection load='5d0b' size='340' side='right'caption='[[5d0b]], [[Resolution|resolution]] 2.65Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5d0b]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacsu Bacsu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D0B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5D0B FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5d0b]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168] and [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D0B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5D0B FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.645Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=56B:2-AMINO-5-({[(1S,4S,5R)-4,5-DIHYDROXYCYCLOPENT-2-EN-1-YL]AMINO}METHYL)-7-(5-O-PHOSPHONO-BETA-D-RIBOFURANOSYL)-3,7-DIHYDRO-4H-PYRROLO[2,3-D]PYRIMIDIN-4-ONE'>56B</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=56B:2-AMINO-5-({[(1S,4S,5R)-4,5-DIHYDROXYCYCLOPENT-2-EN-1-YL]AMINO}METHYL)-7-(5-O-PHOSPHONO-BETA-D-RIBOFURANOSYL)-3,7-DIHYDRO-4H-PYRROLO[2,3-D]PYRIMIDIN-4-ONE'>56B</scene>, <scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5d08|5d08]], [[5d0a|5d0a]]</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=5d0b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d0b OCA], [https://pdbe.org/5d0b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5d0b RCSB], [https://www.ebi.ac.uk/pdbsum/5d0b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5d0b ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">queG, ygaP, yhbA, BSU08910 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224308 BACSU])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Epoxyqueuosine_reductase Epoxyqueuosine reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.17.99.6 1.17.99.6] </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=5d0b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d0b OCA], [http://pdbe.org/5d0b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5d0b RCSB], [http://www.ebi.ac.uk/pdbsum/5d0b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5d0b ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/QUEG_BACSU QUEG_BACSU]] Catalyzes the conversion of epoxyqueuosine (oQ) to queuosine (Q), which is a hypermodified base found in the wobble positions of tRNA(Asp), tRNA(Asn), tRNA(His) and tRNA(Tyr).[HAMAP-Rule:MF_00916]<ref>PMID:21502530</ref> | + | [https://www.uniprot.org/uniprot/QUEG_BACSU QUEG_BACSU] Catalyzes the conversion of epoxyqueuosine (oQ) to queuosine (Q), which is a hypermodified base found in the wobble positions of tRNA(Asp), tRNA(Asn), tRNA(His) and tRNA(Tyr).[HAMAP-Rule:MF_00916]<ref>PMID:21502530</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacsu]] | + | [[Category: Bacillus subtilis subsp. subtilis str. 168]] |
| - | [[Category: Epoxyqueuosine reductase]] | + | [[Category: Escherichia coli]] |
| - | [[Category: Bandarian, V]] | + | [[Category: Large Structures]] |
| - | [[Category: Dowling, D P]] | + | [[Category: Bandarian V]] |
| - | [[Category: Drennan, C L]] | + | [[Category: Dowling DP]] |
| - | [[Category: Kohrer, C]] | + | [[Category: Drennan CL]] |
| - | [[Category: Miles, Z D]] | + | [[Category: Kohrer C]] |
| - | [[Category: B12]]
| + | [[Category: Miles ZD]] |
| - | [[Category: Heat-domain]]
| + | |
| - | [[Category: Oxidoreductase-rna complex]]
| + | |
| - | [[Category: Queuosine]]
| + | |
| - | [[Category: Trna modification]]
| + | |
| Structural highlights
5d0b is a 3 chain structure with sequence from Bacillus subtilis subsp. subtilis str. 168 and Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 2.645Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
QUEG_BACSU Catalyzes the conversion of epoxyqueuosine (oQ) to queuosine (Q), which is a hypermodified base found in the wobble positions of tRNA(Asp), tRNA(Asn), tRNA(His) and tRNA(Tyr).[HAMAP-Rule:MF_00916][1]
Publication Abstract from PubMed
Queuosine (Q) was discovered in the wobble position of a transfer RNA (tRNA) 47 years ago, yet the final biosynthetic enzyme responsible for Q-maturation, epoxyqueuosine (oQ) reductase (QueG), was only recently identified. QueG is a cobalamin (Cbl)-dependent, [4Fe-4S] cluster-containing protein that produces the hypermodified nucleoside Q in situ on four tRNAs. To understand how QueG is able to perform epoxide reduction, an unprecedented reaction for a Cbl-dependent enzyme, we have determined a series of high resolution structures of QueG from Bacillus subtilis Our structure of QueG bound to a tRNATyr anticodon stem loop shows how this enzyme uses a HEAT-like domain to recognize the appropriate anticodons and position the hypermodified nucleoside into the enzyme active site. We find Q bound directly above the Cbl, consistent with a reaction mechanism that involves the formation of a covalent Cbl-tRNA intermediate. Using protein film electrochemistry, we show that two [4Fe-4S] clusters adjacent to the Cbl have redox potentials in the range expected for Cbl reduction, suggesting how Cbl can be activated for nucleophilic attack on oQ. Together, these structural and electrochemical data inform our understanding of Cbl dependent nucleic acid modification.
Molecular basis of cobalamin-dependent RNA modification.,Dowling DP, Miles ZD, Kohrer C, Maiocco SJ, Elliott SJ, Bandarian V, Drennan CL Nucleic Acids Res. 2016 Sep 15. pii: gkw806. PMID:27638883[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Miles ZD, McCarty RM, Molnar G, Bandarian V. Discovery of epoxyqueuosine (oQ) reductase reveals parallels between halorespiration and tRNA modification. Proc Natl Acad Sci U S A. 2011 May 3;108(18):7368-72. doi:, 10.1073/pnas.1018636108. Epub 2011 Apr 18. PMID:21502530 doi:http://dx.doi.org/10.1073/pnas.1018636108
- ↑ Dowling DP, Miles ZD, Kohrer C, Maiocco SJ, Elliott SJ, Bandarian V, Drennan CL. Molecular basis of cobalamin-dependent RNA modification. Nucleic Acids Res. 2016 Sep 15. pii: gkw806. PMID:27638883 doi:http://dx.doi.org/10.1093/nar/gkw806
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