4f8b: Difference between revisions

Revision as of 04:40, 7 October 2022

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.
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: @@
 ==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=''>
+<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 [http://en.wikipedia.org/wiki/Bacsu Bacsu]. 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 [http://oca.weizmann.ac.il/oca-docs/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"><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='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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4fgc|4fgc]]</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='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=4f8b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4f8b OCA], [http://pdbe.org/4f8b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4f8b RCSB], [http://www.ebi.ac.uk/pdbsum/4f8b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4f8b 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: 7-cyano-7-deazaguanine]]
-[[Category: Beta barrel]]
-[[Category: Nadph]]
-[[Category: Protein thioimide complex]]
-[[Category: Pterin binding fold]]
-[[Category: Trna modification enzyme]]
-[[Category: Tunnel fold]]

4f8b: Difference between revisions

Revision as of 04:40, 7 October 2022

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

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools