7e8q: Difference between revisions
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==Crystal structure of a Flavin-dependent Monooxygenase HadA F441V mutant complexed with reduced FAD and 4-nitrophenol== | |||
<StructureSection load='7e8q' size='340' side='right'caption='[[7e8q]], [[Resolution|resolution]] 2.30Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[7e8q]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Ralstonia_pickettii Ralstonia pickettii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7E8Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7E8Q 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]] 2.3Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FDA:DIHYDROFLAVINE-ADENINE+DINUCLEOTIDE'>FDA</scene>, <scene name='pdbligand=NPO:P-NITROPHENOL'>NPO</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=7e8q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7e8q OCA], [https://pdbe.org/7e8q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7e8q RCSB], [https://www.ebi.ac.uk/pdbsum/7e8q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7e8q ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/Q53008_RALPI Q53008_RALPI] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
HadA is a flavin-dependent monooxygenase catalyzing hydroxylation plus dehalogenation/denitration which is useful for biodetoxification and bio-detection. In this study, the X-ray structure of wild-type HadA (HadAWT) co-complexed with reduced FAD (FADH(-)) and 4-nitrophenol (4NP) (HadAWT-FADH(-)-4NP) was solved at 2.3 A resolution, providing the first full package (with flavin and substrate bound) structure of a monooxygenase of this type. Residues Arg101, Gln158, Arg161, Thr193, Asp254, Arg233, and Arg439 constitute a flavin binding pocket, while the 4NP binding pocket contains the aromatic sidechain of Phe206, which provides pi-pi stacking and also is a part of the hydrophobic pocket formed by Phe155, Phe286, Thr449 and Leu457. Based on site-directed mutagenesis and stopped-flow experiments, Thr193, Asp254 and His290 are important for C4a-hydroperoxyflavin formation with His290, also serving as a catalytic base for hydroxylation. We also identified a novel structural motif of quadruple pi-stacking (pi-pi-pi-pi) provided by two 4NP and two Phe441 from two subunits. This motif promotes 4NP binding in a non-productive dead-end complex which prevents C4a-hydroperoxy-FAD formation when HadA is pre-mixed with aromatic substrates. We also solved the structure of the HadAPhe441Val-FADH(-)-4NP complex at 2.3 A resolution. Although 4NP can still bind to this variant, the quadruple pi-stacking motif was disrupted. All HadAPhe441 variants lack substrate inhibition behavior, confirming that quadruple pi-stacking is a main cause of dead-end complex formation. Moreover, the activities of these HadAPhe441 variants were improved by 20%, suggesting that insights gained from the flavin-dependent monooxygenases illustrated here should be useful for future improvement of HadA's biocatalytic applications. | |||
Structural Insights into a Flavin-dependent Dehalogenase HadA Explain Catalysis and Substrate Inhibition via Quadruple pi-stacking.,Pimviriyakul P, Jaruwat A, Chitnumsub P, Chaiyen P J Biol Chem. 2021 Jul 9:100952. doi: 10.1016/j.jbc.2021.100952. PMID:34252455<ref>PMID:34252455</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 7e8q" style="background-color:#fffaf0;"></div> | ||
[[Category: Chaiyen | |||
[[Category: Chitnumsub | ==See Also== | ||
[[Category: Pimviriyakul | *[[Monooxygenase 3D structures|Monooxygenase 3D structures]] | ||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Ralstonia pickettii]] | |||
[[Category: Chaiyen P]] | |||
[[Category: Chitnumsub P]] | |||
[[Category: Jaruwat A]] | |||
[[Category: Pimviriyakul P]] | |||
Latest revision as of 19:48, 29 November 2023
Crystal structure of a Flavin-dependent Monooxygenase HadA F441V mutant complexed with reduced FAD and 4-nitrophenolCrystal structure of a Flavin-dependent Monooxygenase HadA F441V mutant complexed with reduced FAD and 4-nitrophenol
Structural highlights
FunctionPublication Abstract from PubMedHadA is a flavin-dependent monooxygenase catalyzing hydroxylation plus dehalogenation/denitration which is useful for biodetoxification and bio-detection. In this study, the X-ray structure of wild-type HadA (HadAWT) co-complexed with reduced FAD (FADH(-)) and 4-nitrophenol (4NP) (HadAWT-FADH(-)-4NP) was solved at 2.3 A resolution, providing the first full package (with flavin and substrate bound) structure of a monooxygenase of this type. Residues Arg101, Gln158, Arg161, Thr193, Asp254, Arg233, and Arg439 constitute a flavin binding pocket, while the 4NP binding pocket contains the aromatic sidechain of Phe206, which provides pi-pi stacking and also is a part of the hydrophobic pocket formed by Phe155, Phe286, Thr449 and Leu457. Based on site-directed mutagenesis and stopped-flow experiments, Thr193, Asp254 and His290 are important for C4a-hydroperoxyflavin formation with His290, also serving as a catalytic base for hydroxylation. We also identified a novel structural motif of quadruple pi-stacking (pi-pi-pi-pi) provided by two 4NP and two Phe441 from two subunits. This motif promotes 4NP binding in a non-productive dead-end complex which prevents C4a-hydroperoxy-FAD formation when HadA is pre-mixed with aromatic substrates. We also solved the structure of the HadAPhe441Val-FADH(-)-4NP complex at 2.3 A resolution. Although 4NP can still bind to this variant, the quadruple pi-stacking motif was disrupted. All HadAPhe441 variants lack substrate inhibition behavior, confirming that quadruple pi-stacking is a main cause of dead-end complex formation. Moreover, the activities of these HadAPhe441 variants were improved by 20%, suggesting that insights gained from the flavin-dependent monooxygenases illustrated here should be useful for future improvement of HadA's biocatalytic applications. Structural Insights into a Flavin-dependent Dehalogenase HadA Explain Catalysis and Substrate Inhibition via Quadruple pi-stacking.,Pimviriyakul P, Jaruwat A, Chitnumsub P, Chaiyen P J Biol Chem. 2021 Jul 9:100952. doi: 10.1016/j.jbc.2021.100952. PMID:34252455[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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