3oxa: Difference between revisions
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< | ==Crystal Structure of Ketosteroid Isomerase D40N/C69S/C81S/C97S/M116C-CN from P. putida== | ||
<StructureSection load='3oxa' size='340' side='right'caption='[[3oxa]], [[Resolution|resolution]] 1.89Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3oxa]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OXA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3OXA 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]] 1.89Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=XCN:S-CYANO-L-CYSTEINE'>XCN</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=3oxa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3oxa OCA], [https://pdbe.org/3oxa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3oxa RCSB], [https://www.ebi.ac.uk/pdbsum/3oxa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3oxa ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/SDIS_PSEPU SDIS_PSEPU] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Understanding the electrostatic forces and features within highly heterogeneous, anisotropic, and chemically complex enzyme active sites and their connection to biological catalysis remains a longstanding challenge, in part due to the paucity of incisive experimental probes of electrostatic properties within proteins. To quantitatively assess the landscape of electrostatic fields at discrete locations and orientations within an enzyme active site, we have incorporated site-specific thiocyanate vibrational probes into multiple positions within bacterial ketosteroid isomerase. A battery of X-ray crystallographic, vibrational Stark spectroscopy, and NMR studies revealed electrostatic field heterogeneity of 8 MV/cm between active site probe locations and widely differing sensitivities of discrete probes to common electrostatic perturbations from mutation, ligand binding, and pH changes. Electrostatic calculations based on active site ionization states assigned by literature precedent and computational pK(a) prediction were unable to quantitatively account for the observed vibrational band shifts. However, electrostatic models of the D40N mutant gave qualitative agreement with the observed vibrational effects when an unusual ionization of an active site tyrosine with a pK(a) near 7 was included. UV-absorbance and (13)C NMR experiments confirmed the presence of a tyrosinate in the active site, in agreement with electrostatic models. This work provides the most direct measure of the heterogeneous and anisotropic nature of the electrostatic environment within an enzyme active site, and these measurements provide incisive benchmarks for further developing accurate computational models and a foundation for future tests of electrostatics in enzymatic catalysis. | |||
Quantitative, directional measurement of electric field heterogeneity in the active site of ketosteroid isomerase.,Fafarman AT, Sigala PA, Schwans JP, Fenn TD, Herschlag D, Boxer SG Proc Natl Acad Sci U S A. 2012 Feb 7;109(6):E299-308. Epub 2012 Jan 17. PMID:22308339<ref>PMID:22308339</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3oxa" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Ketosteroid Isomerase|Ketosteroid Isomerase]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | [[Category: Large Structures]] | ||
[[ | |||
== | |||
< | |||
[[Category: Pseudomonas putida]] | [[Category: Pseudomonas putida]] | ||
[[Category: Fenn TD]] | |||
[[Category: Fenn | [[Category: Herschlag D]] | ||
[[Category: Herschlag | [[Category: Sigala PA]] | ||
[[Category: Sigala | |||
Latest revision as of 12:45, 6 September 2023
Crystal Structure of Ketosteroid Isomerase D40N/C69S/C81S/C97S/M116C-CN from P. putidaCrystal Structure of Ketosteroid Isomerase D40N/C69S/C81S/C97S/M116C-CN from P. putida
Structural highlights
FunctionPublication Abstract from PubMedUnderstanding the electrostatic forces and features within highly heterogeneous, anisotropic, and chemically complex enzyme active sites and their connection to biological catalysis remains a longstanding challenge, in part due to the paucity of incisive experimental probes of electrostatic properties within proteins. To quantitatively assess the landscape of electrostatic fields at discrete locations and orientations within an enzyme active site, we have incorporated site-specific thiocyanate vibrational probes into multiple positions within bacterial ketosteroid isomerase. A battery of X-ray crystallographic, vibrational Stark spectroscopy, and NMR studies revealed electrostatic field heterogeneity of 8 MV/cm between active site probe locations and widely differing sensitivities of discrete probes to common electrostatic perturbations from mutation, ligand binding, and pH changes. Electrostatic calculations based on active site ionization states assigned by literature precedent and computational pK(a) prediction were unable to quantitatively account for the observed vibrational band shifts. However, electrostatic models of the D40N mutant gave qualitative agreement with the observed vibrational effects when an unusual ionization of an active site tyrosine with a pK(a) near 7 was included. UV-absorbance and (13)C NMR experiments confirmed the presence of a tyrosinate in the active site, in agreement with electrostatic models. This work provides the most direct measure of the heterogeneous and anisotropic nature of the electrostatic environment within an enzyme active site, and these measurements provide incisive benchmarks for further developing accurate computational models and a foundation for future tests of electrostatics in enzymatic catalysis. Quantitative, directional measurement of electric field heterogeneity in the active site of ketosteroid isomerase.,Fafarman AT, Sigala PA, Schwans JP, Fenn TD, Herschlag D, Boxer SG Proc Natl Acad Sci U S A. 2012 Feb 7;109(6):E299-308. Epub 2012 Jan 17. PMID:22308339[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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