7lc5: Difference between revisions

Revision as of 10:38, 22 May 2024

Crystal structure of epoxyqueuosine reductase QueH from Thermotoga maritima

Structural highlights

7lc5 is a 1 chain structure with sequence from Thermotoga maritima MSB8. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.5Å
Ligands:	CL, FE, SF4
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

QUEH_THEMA 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_02089]^[1]

Publication Abstract from PubMed

Queuosine is a structurally unique and functionally important tRNA modification, widely distributed in eukaryotes and bacteria. The final step of queuosine biosynthesis is the reduction/deoxygenation of epoxyqueuosine to form the cyclopentene motif of the nucleobase. The chemistry is performed by the structurally and functionally characterized cobalamin-dependent QueG. However, the queG gene is absent from several bacteria that otherwise retain queuosine biosynthesis machinery. Members of the IPR003828 family (previously known as DUF208) have been recently identified as nonorthologous replacements of QueG, and this family was renamed QueH. Here, we present the structural characterization of QueH from Thermotoga maritima. The structure reveals an unusual active site architecture with a [4Fe-4S] metallocluster along with an adjacent coordinated iron metal. The juxtaposition of the cofactor and coordinated metal ion predicts a unique mechanism for a two-electron reduction/deoxygenation of epoxyqueuosine. To support the structural characterization, in vitro biochemical and genomic analyses are presented. Overall, this work reveals new diversity in the chemistry of iron/sulfur-dependent enzymes and novel insight into the last step of this widely conserved tRNA modification.

Epoxyqueuosine Reductase QueH in the Biosynthetic Pathway to tRNA Queuosine Is a Unique Metalloenzyme.,Li Q, Zallot R, MacTavish BS, Montoya A, Payan DJ, Hu Y, Gerlt JA, Angerhofer A, de Crecy-Lagard V, Bruner SD Biochemistry. 2021 Oct 26;60(42):3152-3161. doi: 10.1021/acs.biochem.1c00164., Epub 2021 Oct 15. PMID:34652139^[2]

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

References

↑ Zallot R, Ross R, Chen WH, Bruner SD, Limbach PA, de Crecy-Lagard V. Identification of a Novel Epoxyqueuosine Reductase Family by Comparative Genomics. ACS Chem Biol. 2017 Mar 17;12(3):844-851. doi: 10.1021/acschembio.6b01100. Epub, 2017 Feb 8. PMID:28128549 doi:https://dx.doi.org/10.1021/acschembio.6b01100
↑ Li Q, Zallot R, MacTavish BS, Montoya A, Payan DJ, Hu Y, Gerlt JA, Angerhofer A, de Crecy-Lagard V, Bruner SD. Epoxyqueuosine Reductase QueH in the Biosynthetic Pathway to tRNA Queuosine Is a Unique Metalloenzyme. Biochemistry. 2021 Oct 26;60(42):3152-3161. doi: 10.1021/acs.biochem.1c00164., Epub 2021 Oct 15. PMID:34652139 doi:https://dx.doi.org/10.1021/acs.biochem.1c00164

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OCA

[1] Zallot R, Ross R, Chen WH, Bruner SD, Limbach PA, de Crecy-Lagard V. Identification of a Novel Epoxyqueuosine Reductase Family by Comparative Genomics. ACS Chem Biol. 2017 Mar 17;12(3):844-851. doi: 10.1021/acschembio.6b01100. Epub, 2017 Feb 8. PMID:28128549 doi:https://dx.doi.org/10.1021/acschembio.6b01100

[2] Li Q, Zallot R, MacTavish BS, Montoya A, Payan DJ, Hu Y, Gerlt JA, Angerhofer A, de Crecy-Lagard V, Bruner SD. Epoxyqueuosine Reductase QueH in the Biosynthetic Pathway to tRNA Queuosine Is a Unique Metalloenzyme. Biochemistry. 2021 Oct 26;60(42):3152-3161. doi: 10.1021/acs.biochem.1c00164., Epub 2021 Oct 15. PMID:34652139 doi:https://dx.doi.org/10.1021/acs.biochem.1c00164

[1]

[2]

@@ Line 3: / Line 3: @@
 <StructureSection load='7lc5' size='340' side='right'caption='[[7lc5]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[7lc5]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7LC5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7LC5 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[7lc5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima_MSB8 Thermotoga maritima MSB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7LC5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7LC5 FirstGlance]. <br>
-</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=FE:FE+(III)+ION'>FE</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]] 1.5&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Epoxyqueuosine_reductase Epoxyqueuosine reductase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.17.99.6 1.17.99.6] </span></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=FE:FE+(III)+ION'>FE</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=7lc5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7lc5 OCA], [https://pdbe.org/7lc5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7lc5 RCSB], [https://www.ebi.ac.uk/pdbsum/7lc5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7lc5 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/QUEH_THEMA QUEH_THEMA]] 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_02089]<ref>PMID:28128549</ref>
+[https://www.uniprot.org/uniprot/QUEH_THEMA QUEH_THEMA] 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_02089]<ref>PMID:28128549</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Epoxyqueuosine reductase]]
 [[Category: Large Structures]]
-[[Category: Bruner, S D]]
+[[Category: Thermotoga maritima MSB8]]
-[[Category: Li, Q]]
+[[Category: Bruner SD]]
-[[Category: Iron-sulfur cluster]]
+[[Category: Li Q]]
-[[Category: Oxidoreductase]]
-[[Category: Queh]]
-[[Category: Queuosine]]
-[[Category: Trna]]

7lc5: Difference between revisions

Revision as of 10:38, 22 May 2024

Crystal structure of epoxyqueuosine reductase QueH from Thermotoga maritima

Structural highlights

Function

Publication Abstract from PubMed

References

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