4f8b: Difference between revisions

Latest revision as of 10:50, 6 November 2024

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

Structural highlights

4f8b is a 5 chain structure with sequence from Bacillus subtilis subsp. subtilis str. 168. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.502Å
Ligands:	GD1, MG, PE4, PO4
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.^[1] ^[2]

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^[3]

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

References

↑ Van Lanen SG, Reader JS, Swairjo MA, de Crecy-Lagard V, Lee B, Iwata-Reuyl D. From cyclohydrolase to oxidoreductase: discovery of nitrile reductase activity in a common fold. Proc Natl Acad Sci U S A. 2005 Mar 22;102(12):4264-9. Epub 2005 Mar 14. PMID:15767583 doi:https://dx.doi.org/0408056102
↑ Lee BW, Van Lanen SG, Iwata-Reuyl D. Mechanistic studies of Bacillus subtilis QueF, the nitrile oxidoreductase involved in queuosine biosynthesis. Biochemistry. 2007 Nov 6;46(44):12844-54. Epub 2007 Oct 11. PMID:17929836 doi:https://dx.doi.org/10.1021/bi701265r
↑ Chikwana VM, Stec B, Lee BW, de Crecy-Lagard V, Iwata-Reuyl D, Swairjo MA. Structural Basis of Biological Nitrile Reduction. J Biol Chem. 2012 Jul 11. PMID:22787148 doi:10.1074/jbc.M112.388538

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Van Lanen SG, Reader JS, Swairjo MA, de Crecy-Lagard V, Lee B, Iwata-Reuyl D. From cyclohydrolase to oxidoreductase: discovery of nitrile reductase activity in a common fold. Proc Natl Acad Sci U S A. 2005 Mar 22;102(12):4264-9. Epub 2005 Mar 14. PMID:15767583 doi:https://dx.doi.org/0408056102

[2] Lee BW, Van Lanen SG, Iwata-Reuyl D. Mechanistic studies of Bacillus subtilis QueF, the nitrile oxidoreductase involved in queuosine biosynthesis. Biochemistry. 2007 Nov 6;46(44):12844-54. Epub 2007 Oct 11. PMID:17929836 doi:https://dx.doi.org/10.1021/bi701265r

[3] Chikwana VM, Stec B, Lee BW, de Crecy-Lagard V, Iwata-Reuyl D, Swairjo MA. Structural Basis of Biological Nitrile Reduction. J Biol Chem. 2012 Jul 11. PMID:22787148 doi:10.1074/jbc.M112.388538

[1]

[2]

[3]

@@ Line 1: / Line 1: @@
-[[Image:4f8b.jpg|left|200px]]
-{{STRUCTURE_4f8b|  PDB=4f8b  |  SCENE=  }}
+==Crystal Structure of the Covalent Thioimide Intermediate of Unimodular Nitrile Reductase QueF==
+<StructureSection load='4f8b' size='340' side='right'caption='[[4f8b]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+== 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>
+</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>
+</table>
+== 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>
+<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.
-===Crystal Structure of the Covalent Thioimide Intermediate of Unimodular Nitrile Reductase QueF===
+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>
-==About this Structure==
+</div>
-[[4f8b]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis Bacillus subtilis subsp. subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4F8B OCA].
+<div class="pdbe-citations 4f8b" style="background-color:#fffaf0;"></div>
-[[Category: Bacillus subtilis subsp. subtilis]]
+== References ==
-[[Category: Stec, B.]]
+<references/>
-[[Category: Swairjo, M A.]]
+__TOC__
-[[Category: 7-cyano-7-deazaguanine]]
+</StructureSection>
-[[Category: Beta barrel]]
+[[Category: Bacillus subtilis subsp. subtilis str. 168]]
-[[Category: Nadph]]
+[[Category: Large Structures]]
-[[Category: Oxidoreductase]]
+[[Category: Stec B]]
-[[Category: Protein thioimide complex]]
+[[Category: Swairjo MA]]
-[[Category: Pterin binding fold]]
-[[Category: Trna modification enzyme]]
-[[Category: Tunnel fold]]

4f8b: Difference between revisions

Latest revision as of 10:50, 6 November 2024

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

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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