3b12: Difference between revisions
New page: '''Unreleased structure''' The entry 3b12 is ON HOLD Authors: Omi, R, Hirotsu, K Description: Crystal Structure of the Fluoroacetate Dehalogenase D104 mutant from Burkholderia sp. FA1 ... |
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The | ==Crystal Structure of the Fluoroacetate Dehalogenase D104 mutant from Burkholderia sp. FA1 in complex with fluoroacetate== | ||
<StructureSection load='3b12' size='340' side='right'caption='[[3b12]], [[Resolution|resolution]] 1.20Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3b12]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Burkholderia_sp. Burkholderia sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B12 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3B12 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]] 1.2Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAH:FLUOROACETIC+ACID'>FAH</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=3b12 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b12 OCA], [https://pdbe.org/3b12 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3b12 RCSB], [https://www.ebi.ac.uk/pdbsum/3b12 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3b12 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/DEHA_BURSP DEHA_BURSP] Catalyzes the hydrolytic defluorination of fluoroacetate to produce glycolate. Has only very low activity towards chloroacetate.[REFERENCE:1]<ref>PMID:19218394</ref> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The high substrate specificity of fluoroacetate dehalogenase was explored by using crystallographic analysis, fluorescence spectroscopy, and theoretical computations. A crystal structure for the Asp104Ala mutant of the enzyme from Burkholderia sp. FA1 complexed with fluoroacetate was determined at 1.2 A resolution. The orientation and conformation of bound fluoroacetate is different from those in the crystal structure of the corresponding Asp110Asn mutant of the enzyme from Rhodopseudomonas palustris CGA009 reported recently (J. Am. Chem. Soc. 2011, 133, 7461). The fluorescence of the tryptophan residues of the wild-type and Trp150Phe mutant enzymes from Burkholderia sp. FA1 incubated with fluoroacetate and chloroacetate was measured to gain information on the environment of the tryptophan residues. The environments of the tryptophan residues were found to be different between the fluoroacetate- and chloroacetate-bound enzymes; this would come from different binding modes of these two substrates in the active site. Docking simulations and QM/MM optimizations were performed to predict favorable conformations and orientations of the substrates. The F atom of the substrate is oriented toward Arg108 in the most stable enzyme-fluoroacetate complex. This is a stable but unreactive conformation, in which the small OCF angle is not suitable for the S(N) 2 displacement of the F(-) ion. The cleavage of the CF bond is initiated by the conformational change of the substrate to a near attack conformation (NAC) in the active site. The second lowest energy conformation is appropriate for NAC; the CO distance and the OCF angle are reasonable for the S(N) 2 reaction. The activation energy is greatly reduced in this conformation because of three hydrogen bonds between the leaving F atom and surrounding amino acid residues. Chloroacetate cannot reach the reactive conformation, due to the longer CCl bond; this results in an increase of the activation energy despite the weaker CCl bond. | |||
Substrate Specificity of Fluoroacetate Dehalogenase: An Insight from Crystallographic Analysis, Fluorescence Spectroscopy, and Theoretical Computations.,Nakayama T, Kamachi T, Jitsumori K, Omi R, Hirotsu K, Esaki N, Kurihara T, Yoshizawa K Chemistry. 2012 Jun 1. doi: 10.1002/chem.201103369. PMID:22674735<ref>PMID:22674735</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3b12" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Dehalogenase 3D structures|Dehalogenase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Burkholderia sp]] | |||
[[Category: Large Structures]] | |||
[[Category: Hirotsu K]] | |||
[[Category: Omi R]] | |||
Latest revision as of 11:51, 11 October 2023
Crystal Structure of the Fluoroacetate Dehalogenase D104 mutant from Burkholderia sp. FA1 in complex with fluoroacetateCrystal Structure of the Fluoroacetate Dehalogenase D104 mutant from Burkholderia sp. FA1 in complex with fluoroacetate
Structural highlights
FunctionDEHA_BURSP Catalyzes the hydrolytic defluorination of fluoroacetate to produce glycolate. Has only very low activity towards chloroacetate.[REFERENCE:1][1] Publication Abstract from PubMedThe high substrate specificity of fluoroacetate dehalogenase was explored by using crystallographic analysis, fluorescence spectroscopy, and theoretical computations. A crystal structure for the Asp104Ala mutant of the enzyme from Burkholderia sp. FA1 complexed with fluoroacetate was determined at 1.2 A resolution. The orientation and conformation of bound fluoroacetate is different from those in the crystal structure of the corresponding Asp110Asn mutant of the enzyme from Rhodopseudomonas palustris CGA009 reported recently (J. Am. Chem. Soc. 2011, 133, 7461). The fluorescence of the tryptophan residues of the wild-type and Trp150Phe mutant enzymes from Burkholderia sp. FA1 incubated with fluoroacetate and chloroacetate was measured to gain information on the environment of the tryptophan residues. The environments of the tryptophan residues were found to be different between the fluoroacetate- and chloroacetate-bound enzymes; this would come from different binding modes of these two substrates in the active site. Docking simulations and QM/MM optimizations were performed to predict favorable conformations and orientations of the substrates. The F atom of the substrate is oriented toward Arg108 in the most stable enzyme-fluoroacetate complex. This is a stable but unreactive conformation, in which the small OCF angle is not suitable for the S(N) 2 displacement of the F(-) ion. The cleavage of the CF bond is initiated by the conformational change of the substrate to a near attack conformation (NAC) in the active site. The second lowest energy conformation is appropriate for NAC; the CO distance and the OCF angle are reasonable for the S(N) 2 reaction. The activation energy is greatly reduced in this conformation because of three hydrogen bonds between the leaving F atom and surrounding amino acid residues. Chloroacetate cannot reach the reactive conformation, due to the longer CCl bond; this results in an increase of the activation energy despite the weaker CCl bond. Substrate Specificity of Fluoroacetate Dehalogenase: An Insight from Crystallographic Analysis, Fluorescence Spectroscopy, and Theoretical Computations.,Nakayama T, Kamachi T, Jitsumori K, Omi R, Hirotsu K, Esaki N, Kurihara T, Yoshizawa K Chemistry. 2012 Jun 1. doi: 10.1002/chem.201103369. PMID:22674735[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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