View source for 5jyx


==Crystal structure of the covalent thioimide intermediate of the archaeosine synthase QueF-Like==
<StructureSection load='5jyx' size='340' side='right'caption='[[5jyx]], [[Resolution|resolution]] 2.74&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5jyx]] is a 15 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrobaculum_calidifontis_JCM_11548 Pyrobaculum calidifontis JCM 11548]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JYX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JYX FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.74&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GD1:2-AMINO-5-[(Z)-IMINOMETHYL]-3,7-DIHYDRO-4H-PYRROLO[2,3-D]PYRIMIDIN-4-ONE'>GD1</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=5jyx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jyx OCA], [https://pdbe.org/5jyx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jyx RCSB], [https://www.ebi.ac.uk/pdbsum/5jyx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jyx ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/QUEFL_PYRCJ QUEFL_PYRCJ] Is responsible for the final step in the biosynthesis of archaeosine, a modified nucleoside present in the dihydrouridine loop (D-loop) of archaeal tRNA (PubMed:22032275, PubMed:28383498). Catalyzes the conversion of 7-cyano-7-deazaguanine (preQ0)-modified tRNA to archaeosine-tRNA, transforming a nitrile group to a formamidine group. Can use neither glutamine nor asparagine as amino donor in vitro, is only able to utilize free ammonium (PubMed:28383498). However, the enzyme might function in vivo with a partner that serves to generate ammonium.<ref>PMID:22032275</ref> <ref>PMID:28383498</ref> 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The tunneling-fold (T-fold) structural superfamily has emerged as a versatile protein scaffold of diverse catalytic activities. This is especially evident in the pathways to the 7-deazaguanosine modified nucleosides of tRNA queuosine and archaeosine. Four members of the T-fold superfamily have been confirmed in these pathways and here we report the crystal structure of a fifth enzyme; the recently discovered amidinotransferase QueF-Like (QueF-L), responsible for the final step in the biosynthesis of archaeosine in the D-loop of tRNA in a subset of Crenarchaeota. QueF-L catalyzes the conversion of the nitrile group of the 7-cyano-7-deazaguanine (preQ0 ) base of preQ0 -modified tRNA to a formamidino group. The structure, determined in the presence of preQ0 , reveals a symmetric T-fold homodecamer of two head-to-head facing pentameric subunits, with 10 active sites at the inter-monomer interfaces. Bound preQ0 forms a stable covalent thioimide bond with a conserved active site cysteine similar to the intermediate previously observed in the nitrile reductase QueF. Despite distinct catalytic functions, phylogenetic distributions, and only 19% sequence identity, the two enzymes share a common preQ0 binding pocket, and likely a common mechanism of thioimide formation. However, due to tight twisting of its decamer, QueF-L lacks the NADPH binding site present in QueF. A large positively charged molecular surface and a docking model suggest simultaneous binding of multiple tRNA molecules and structure-specific recognition of the D-loop by a surface groove. The structure sheds light on the mechanism of nitrile amidation, and the evolution of diverse chemistries in a common fold. Proteins 2016; 85:103-116. (c) 2016 Wiley Periodicals, Inc.

Crystal structure of the archaeosine synthase QueF-like-Insights into amidino transfer and tRNA recognition by the tunnel fold.,Mei X, Alvarez J, Bon Ramos A, Samanta U, Iwata-Reuyl D, Swairjo MA Proteins. 2017 Jan;85(1):103-116. doi: 10.1002/prot.25202. Epub 2016 Nov 20. PMID:27802572<ref>PMID:27802572</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 5jyx" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Pyrobaculum calidifontis JCM 11548]]
[[Category: Mei X]]
[[Category: Swairjo MA]]