4f8b: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4f8b]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4F8B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4F8B FirstGlance]. <br>
<table><tr><td colspan='2'>[[4f8b]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4F8B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4F8B FirstGlance]. <br>
</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PE4:2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL'>PE4</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2.502&#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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PE4:2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL'>PE4</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=4f8b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4f8b OCA], [https://pdbe.org/4f8b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4f8b RCSB], [https://www.ebi.ac.uk/pdbsum/4f8b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4f8b ProSAT]</span></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=4f8b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4f8b OCA], [https://pdbe.org/4f8b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4f8b RCSB], [https://www.ebi.ac.uk/pdbsum/4f8b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4f8b ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[https://www.uniprot.org/uniprot/QUEF_BACSU QUEF_BACSU] Catalyzes the NADPH-dependent reduction of 7-cyano-7-deazaguanine (preQ0) to 7-aminomethyl-7-deazaguanine (preQ1), a late step in the queuosine pathway.<ref>PMID:15767583</ref> <ref>PMID:17929836</ref>  
[https://www.uniprot.org/uniprot/QUEF_BACSU QUEF_BACSU] Catalyzes the NADPH-dependent reduction of 7-cyano-7-deazaguanine (preQ0) to 7-aminomethyl-7-deazaguanine (preQ1), a late step in the queuosine pathway.<ref>PMID:15767583</ref> <ref>PMID:17929836</ref>  
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The enzyme QueF catalyzes the reduction of the nitrile group of 7-cyano-7-deazaguanine (preQ0) to 7-aminomethyl-7-deazaguanine (preQ1), the only nitrile reduction reaction known in Biology. We describe here two crystal structures of Bacillus subtilis QueF, one of the wild-type enzyme in complex with the substrate preQ0, trapped as a covalent thioimide, a putative intermediate in the reaction, and the second of the Cys55Ala mutant in complex with the substrate preQ0 bound non-covalently. The QueF enzyme forms an asymmetric tunnel-fold homodecamer of two head-to-head facing pentameric subunits, harboring ten active sites at the inter-subunit interfaces. In both structures a preQ0 molecule is bound at eight sites, and in the wild-type enzyme it forms a thioimide covalent linkage to the catalytic residue Cys55. Both structural and transient kinetic data show that preQ0 binding, not thioimide formation, induces a large conformational change in and closure of the active site. Based on these data we propose a mechanism for the activation of the Cys55 nucleophile and subsequent hydride transfer.
Structural Basis of Biological Nitrile Reduction.,Chikwana VM, Stec B, Lee BW, de Crecy-Lagard V, Iwata-Reuyl D, Swairjo MA J Biol Chem. 2012 Jul 11. PMID:22787148<ref>PMID:22787148</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 4f8b" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>

Revision as of 15:18, 14 March 2024

Crystal Structure of the Covalent Thioimide Intermediate of Unimodular Nitrile Reductase QueF

4f8b, resolution 2.50Å

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