4fgc: Difference between revisions

Revision as of 19:47, 19 October 2022

Crystal Structure of Active Site Mutant C55A of Nitrile Reductase QueF, Bound to Substrate PreQ0

Structural highlights

4fgc 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.
Ligands:	CA, PE4, PQ0
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: @@
 ==Crystal Structure of Active Site Mutant C55A of Nitrile Reductase QueF, Bound to Substrate PreQ0==
-<StructureSection load='4fgc' size='340' side='right' caption='[[4fgc]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+<StructureSection load='4fgc' size='340' side='right'caption='[[4fgc]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4fgc]] is a 5 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=4FGC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FGC FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4fgc]] 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=4FGC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FGC FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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=PQ0:2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDINE-5-CARBONITRILE'>PQ0</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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=PQ0:2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDINE-5-CARBONITRILE'>PQ0</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4f8b|4f8b]]</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=4fgc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fgc OCA], [https://pdbe.org/4fgc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4fgc RCSB], [https://www.ebi.ac.uk/pdbsum/4fgc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4fgc ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BSU13750, queF, ykvM ([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/Oxidoreductase Oxidoreductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.1.13 1.7.1.13] </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=4fgc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fgc OCA], [http://pdbe.org/4fgc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4fgc RCSB], [http://www.ebi.ac.uk/pdbsum/4fgc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4fgc ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://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 ==
@@ Line 25: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Bacsu]]
+[[Category: Bacillus subtilis subsp. subtilis str. 168]]
-[[Category: Oxidoreductase]]
+[[Category: Large Structures]]
-[[Category: Stec, B]]
+[[Category: Stec B]]
-[[Category: Swairjo, M A]]
+[[Category: Swairjo MA]]
-[[Category: Beta barrel]]
-[[Category: Nadph binding]]
-[[Category: Pterin binding fold]]
-[[Category: Trna modification enzyme]]
-[[Category: Tunnel fold]]

4fgc: Difference between revisions

Revision as of 19:47, 19 October 2022

Crystal Structure of Active Site Mutant C55A of Nitrile Reductase QueF, Bound to Substrate PreQ0

Structural highlights

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Publication Abstract from PubMed

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