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5eht

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Revision as of 06:58, 22 April 2020

Indirect contributions of mutations underlie optimization of new enzyme function

Structural highlights

5eht is a 1 chain structure with sequence from "bacillus_cereus_var._thuringiensis"_smith_et_al._1952 "bacillus cereus var. thuringiensis" smith et al. 1952. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
NonStd Res:
Related:	5eh9
Gene:	aiiA ("Bacillus cereus var. thuringiensis" Smith et al. 1952)
Activity:	Quorum-quenching N-acyl-homoserine lactonase, with EC number 3.1.1.81
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[AHLL_BACTU] Catalyzes hydrolysis of N-hexanoyl-(S)-homoserine lactone, but not the R-enantiomer. Hydrolyzes short- and long-chain N-acyl homoserine lactones with or without 3-oxo substitution at C3, has maximum activity on C10-AHL.^[1]

Publication Abstract from PubMed

How remote mutations can lead to changes in enzyme function at a molecular level is a central question in evolutionary biochemistry and biophysics. Here, we combine laboratory evolution with biochemical, structural, genetic, and computational analysis to dissect the molecular basis for the functional optimization of phosphotriesterase activity in a bacterial lactonase (AiiA) from the metallo-beta-lactamase (MBL) superfamily. We show that a 1000-fold increase in phosphotriesterase activity is caused by a more favorable catalytic binding position of the paraoxon substrate in the evolved enzyme that resulted from conformational tinkering of the active site through peripheral mutations. A nonmutated active site residue, Phe68, was displaced by approximately 3 A through the indirect effects of two second-shell trajectory mutations, allowing molecular interactions between the residue and paraoxon. Comparative mutational scanning, i.e., examining the effects of alanine mutagenesis on different genetic backgrounds, revealed significant changes in the functional roles of Phe68 and other nonmutated active site residues caused by the indirect effects of trajectory mutations. Our work provides a quantitative measurement of the impact of second-shell mutations on the catalytic contributions of nonmutated residues and unveils the underlying intramolecular network of strong epistatic mutational relationships between active site residues and more remote residues. Defining these long-range conformational and functional epistatic relationships has allowed us to better understand the subtle, but cumulatively significant, role of second- and third-shell mutations in evolution.

Conformational Tinkering Drives Evolution of a Promiscuous Activity through Indirect Mutational Effects.,Yang G, Hong N, Baier F, Jackson CJ, Tokuriki N Biochemistry. 2016 Aug 16;55(32):4583-93. doi: 10.1021/acs.biochem.6b00561. Epub , 2016 Aug 2. PMID:27444875^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Thomas PW, Stone EM, Costello AL, Tierney DL, Fast W. The quorum-quenching lactonase from Bacillus thuringiensis is a metalloprotein. Biochemistry. 2005 May 24;44(20):7559-69. PMID:15895999 doi:http://dx.doi.org/10.1021/bi050050m
↑ Yang G, Hong N, Baier F, Jackson CJ, Tokuriki N. Conformational Tinkering Drives Evolution of a Promiscuous Activity through Indirect Mutational Effects. Biochemistry. 2016 Aug 16;55(32):4583-93. doi: 10.1021/acs.biochem.6b00561. Epub , 2016 Aug 2. PMID:27444875 doi:http://dx.doi.org/10.1021/acs.biochem.6b00561

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5eht"

@@ Line 1: / Line 1: @@
 ==Indirect contributions of mutations underlie optimization of new enzyme function==
-<StructureSection load='5eht' size='340' side='right' caption='[[5eht]], [[Resolution|resolution]] 1.29&Aring;' scene=''>
+<StructureSection load='5eht' size='340' side='right'caption='[[5eht]], [[Resolution|resolution]] 1.29&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5eht]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EHT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5EHT FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5eht]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_cereus_var._thuringiensis"_smith_et_al._1952 "bacillus cereus var. thuringiensis" smith et al. 1952]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EHT OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5EHT FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5eh9|5eh9]]</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">aiiA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1428 "Bacillus cereus var. thuringiensis" Smith et al. 1952])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Quorum-quenching_N-acyl-homoserine_lactonase Quorum-quenching N-acyl-homoserine lactonase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.81 3.1.1.81] </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=5eht FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5eht OCA], [http://pdbe.org/5eht PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5eht RCSB], [http://www.ebi.ac.uk/pdbsum/5eht PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5eht ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5eht FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5eht OCA], [http://pdbe.org/5eht PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5eht RCSB], [http://www.ebi.ac.uk/pdbsum/5eht PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5eht ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 25: / Line 26: @@
 __TOC__
 </StructureSection>
+[[Category: Bacillus cereus var. thuringiensis smith et al. 1952]]
+[[Category: Large Structures]]
 [[Category: Quorum-quenching N-acyl-homoserine lactonase]]
 [[Category: Hong, N S]]

5eht

From Proteopedia

Revision as of 06:58, 22 April 2020

Indirect contributions of mutations underlie optimization of new enzyme function

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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