4rf2: Difference between revisions
m Protected "4rf2" [edit=sysop:move=sysop] |
No edit summary |
||
| (6 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
==Crystal structure of NADP+ bound ketoreductase from Lactobacillus kefir== | |||
<StructureSection load='4rf2' size='340' side='right'caption='[[4rf2]], [[Resolution|resolution]] 2.09Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4rf2]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Lentilactobacillus_kefiri Lentilactobacillus kefiri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RF2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RF2 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]] 2.089Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</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=4rf2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rf2 OCA], [https://pdbe.org/4rf2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rf2 RCSB], [https://www.ebi.ac.uk/pdbsum/4rf2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rf2 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/RADH_LENKE RADH_LENKE] NADP-dependent (R)-specific alcohol dehydrogenase (ADH) with a broad substrate specificity, able to catalyze in vitro the stereoselective reduction of several aliphatic and aromatic ketones as well as beta-keto esters to the corresponding enantiomerically pure alcohols.<ref>PMID:26644568</ref> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Mutants of Lactobacillus kefir short-chain alcohol dehydrogenase, used here as ketoreductases (KREDs), enantioselectively reduce the pharmaceutically relevant substrates 3-thiacyclopentanone and 3-oxacyclopentanone. These substrates differ by only the heteroatom (S or O) in the ring, but the KRED mutants reduce them with different enantioselectivities. Kinetic studies show that these enzymes are more efficient with 3-thiacyclopentanone than with 3-oxacyclopentanone. X-ray crystal structures of apo- and NADP+-bound selected mutants show that the substrate-binding loop conformational preferences are modified by these mutations. Quantum mechanical calculations and molecular dynamics (MD) simulations are used to investigate the mechanism of reduction by the enzyme. We have developed an MD-based method for studying the diastereomeric transition state complexes and rationalize different enantiomeric ratios. This method, which probes the stability of the catalytic arrangement within the theozyme, shows a correlation between the relative fractions of catalytically competent poses for the enantiomeric reductions and the experimental enantiomeric ratio. Some mutations, such as A94F and Y190F, induce conformational changes in the active site that enlarge the small binding pocket, facilitating accommodation of the larger S atom in this region and enhancing S-selectivity with 3-thiacyclopentanone. In contrast, in the E145S mutant and the final variant evolved for large-scale production of the intermediate for the antibiotic sulopenem, R-selectivity is promoted by shrinking the small binding pocket, thereby destabilizing the pro-S orientation. | |||
Origins of stereoselectivity in evolved ketoreductases.,Noey EL, Tibrewal N, Jimenez-Oses G, Osuna S, Park J, Bond CM, Cascio D, Liang J, Zhang X, Huisman GW, Tang Y, Houk KN Proc Natl Acad Sci U S A. 2015 Dec 7. pii: 201507910. PMID:26644568<ref>PMID:26644568</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 4rf2" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Alcohol dehydrogenase 3D structures|Alcohol dehydrogenase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Lentilactobacillus kefiri]] | |||
[[Category: Cascio D]] | |||
[[Category: Tang Y]] | |||
[[Category: Tibrewal N]] | |||
Latest revision as of 20:49, 20 September 2023
Crystal structure of NADP+ bound ketoreductase from Lactobacillus kefirCrystal structure of NADP+ bound ketoreductase from Lactobacillus kefir
Structural highlights
FunctionRADH_LENKE NADP-dependent (R)-specific alcohol dehydrogenase (ADH) with a broad substrate specificity, able to catalyze in vitro the stereoselective reduction of several aliphatic and aromatic ketones as well as beta-keto esters to the corresponding enantiomerically pure alcohols.[1] Publication Abstract from PubMedMutants of Lactobacillus kefir short-chain alcohol dehydrogenase, used here as ketoreductases (KREDs), enantioselectively reduce the pharmaceutically relevant substrates 3-thiacyclopentanone and 3-oxacyclopentanone. These substrates differ by only the heteroatom (S or O) in the ring, but the KRED mutants reduce them with different enantioselectivities. Kinetic studies show that these enzymes are more efficient with 3-thiacyclopentanone than with 3-oxacyclopentanone. X-ray crystal structures of apo- and NADP+-bound selected mutants show that the substrate-binding loop conformational preferences are modified by these mutations. Quantum mechanical calculations and molecular dynamics (MD) simulations are used to investigate the mechanism of reduction by the enzyme. We have developed an MD-based method for studying the diastereomeric transition state complexes and rationalize different enantiomeric ratios. This method, which probes the stability of the catalytic arrangement within the theozyme, shows a correlation between the relative fractions of catalytically competent poses for the enantiomeric reductions and the experimental enantiomeric ratio. Some mutations, such as A94F and Y190F, induce conformational changes in the active site that enlarge the small binding pocket, facilitating accommodation of the larger S atom in this region and enhancing S-selectivity with 3-thiacyclopentanone. In contrast, in the E145S mutant and the final variant evolved for large-scale production of the intermediate for the antibiotic sulopenem, R-selectivity is promoted by shrinking the small binding pocket, thereby destabilizing the pro-S orientation. Origins of stereoselectivity in evolved ketoreductases.,Noey EL, Tibrewal N, Jimenez-Oses G, Osuna S, Park J, Bond CM, Cascio D, Liang J, Zhang X, Huisman GW, Tang Y, Houk KN Proc Natl Acad Sci U S A. 2015 Dec 7. pii: 201507910. PMID:26644568[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
|
| ||||||||||||||||||