6u3k: Difference between revisions
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<StructureSection load='6u3k' size='340' side='right'caption='[[6u3k]], [[Resolution|resolution]] 1.80Å' scene=''> | <StructureSection load='6u3k' size='340' side='right'caption='[[6u3k]], [[Resolution|resolution]] 1.80Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[6u3k]] is a 1 chain structure with sequence from [ | <table><tr><td colspan='2'>[[6u3k]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodopseudomonas_palustris_HaA2 Rhodopseudomonas palustris HaA2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6U3K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6U3K FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=PQS:4-(pyridin-2-yl)benzoic+acid'>PQS</scene> | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=PQS:4-(pyridin-2-yl)benzoic+acid'>PQS</scene></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6u3k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u3k OCA], [https://pdbe.org/6u3k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6u3k RCSB], [https://www.ebi.ac.uk/pdbsum/6u3k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6u3k ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/Q2IU02_RHOP2 Q2IU02_RHOP2] | |||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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</div> | </div> | ||
<div class="pdbe-citations 6u3k" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 6u3k" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Cytochrome P450 3D structures|Cytochrome P450 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: | [[Category: Rhodopseudomonas palustris HaA2]] | ||
[[Category: Bell | [[Category: Bell SG]] | ||
[[Category: Bruning | [[Category: Bruning JB]] | ||
[[Category: Podgorski | [[Category: Podgorski MN]] | ||
Latest revision as of 10:43, 11 October 2023
The crystal structure of 4-(pyridin-2-yl)benzoate-bound CYP199A4The crystal structure of 4-(pyridin-2-yl)benzoate-bound CYP199A4
Structural highlights
FunctionPublication Abstract from PubMedThe cytochrome P450 superfamily of heme monooxygenases catalyzes important chemical reactions across nature. The changes in the optical spectra of these enzymes, induced by the addition of substrates or inhibitors, are critical for assessing how these molecules bind to the P450, enhancing or inhibiting the catalytic cycle. Here we use the bacterial CYP199A4 enzyme (Uniprot entry Q2IUO2 ), from Rhodopseudomonas palustris HaA2, and a range of substituted benzoic acids to investigate different binding modes. 4-Methoxybenzoic acid elicits an archetypal type I spectral response due to a >/=95% switch from the low- to high-spin state with concomitant dissociation of the sixth aqua ligand. 4-(Pyridin-3-yl)- and 4-(pyridin-2-yl)benzoic acid induced different type II ultraviolet-visible (UV-vis) spectral responses in CYP199A4. The former induced a greater red shift in the Soret wavelength (424 nm vs 422 nm) along with a larger overall absorbance change and other differences in the alpha-, beta-, and delta-bands. There were also variations in the ferrous UV-vis spectra of these two substrate-bound forms with a spectrum indicative of Fe-N bond formation with 4-(pyridin-3-yl)benzoic acid. The crystal structures of CYP199A4, with the pyridinyl compounds bound, revealed that while the nitrogen of 4-(pyridin-3-yl)benzoic acid is coordinated to the heme, with 4-(pyridin-2-yl)benzoic acid an aqua ligand remains. Continuous wave and pulse electron paramagnetic resonance data in frozen solution revealed that the substrates are bound in the active site in a form consistent with the crystal structures. The redox potential of each CYP199A4-substrate combination was measured, allowing correlation among binding modes, spectroscopic properties, and the observed biochemical activity. Biophysical Techniques for Distinguishing Ligand Binding Modes in Cytochrome P450 Monooxygenases.,Podgorski MN, Harbort JS, Coleman T, Stok JE, Yorke JA, Wong LL, Bruning JB, Bernhardt PV, De Voss JJ, Harmer JR, Bell SG Biochemistry. 2020 Feb 24. doi: 10.1021/acs.biochem.0c00027. PMID:32058707[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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