4ccy: Difference between revisions
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== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4ccy]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CCY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4CCY FirstGlance]. <br> | <table><tr><td colspan='2'>[[4ccy]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CCY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4CCY FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr> | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.04Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=4ccy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ccy OCA], [https://pdbe.org/4ccy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ccy RCSB], [https://www.ebi.ac.uk/pdbsum/4ccy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ccy ProSAT]</span></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=4ccy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ccy OCA], [https://pdbe.org/4ccy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ccy RCSB], [https://www.ebi.ac.uk/pdbsum/4ccy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ccy ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[https://www.uniprot.org/uniprot/YBFK_BACSU YBFK_BACSU] Shows carboxylesterase activity in vitro. | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Naproxen esterase (NP) from Bacillus subtilis Thai I-8 is a carboxylesterase that catalyzes the enantioselective hydrolysis of naproxenmethylester to produce S-naproxen (E>200). It is a homolog of CesA (98% sequence identity) and CesB (64% identity), both produced by B. subtilis strain 168. CesB can be used for the enantioselective hydrolysis of 1,2-O-isopropylideneglycerol (solketal) esters (E>200 for IPG-caprylate). Crystal structures of NP and CesB, determined to a resolution of 1.75A and 2.04A, respectively, showed that both proteins have a canonical alpha/beta hydrolase fold with an extra N-terminal helix stabilizing the cap subdomain. The active site in both enzymes is located in a deep hydrophobic groove and includes the catalytic triad residues Ser130, His274, and Glu245. A product analog, presumably 2-(2-hydroxyethoxy)acetic acid, was bound in the NP active site. The enzymes have different enantioselectivities, which previously were shown to result from only a few amino acid substitutions in the cap domain. Modeling of a substrate in the active site of NP allowed explaining the different enantioselectivities. In addition, Ala156 may be a determinant of enantioselectivity as well, since its side chain appears to interfere with the binding of certain R-enantiomers in the active site of NP. However, the exchange route for substrate and product between the active site and the solvent is not obvious from the structures. Flexibility of the cap domain might facilitate such exchange. Interestingly, both carboxylesterases show higher structural similarity to meta-cleavage compound (MCP) hydrolases than to other alpha/beta hydrolase fold esterases. | |||
Crystal structures of two Bacillus carboxylesterases with different enantioselectivities.,Rozeboom HJ, Godinho LF, Nardini M, Quax WJ, Dijkstra BW Biochim Biophys Acta. 2014 Mar;1844(3):567-75. doi: 10.1016/j.bbapap.2014.01.003., Epub 2014 Jan 11. PMID:24418394<ref>PMID:24418394</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 4ccy" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
*[[Carboxylesterase 3D structures|Carboxylesterase 3D structures]] | *[[Carboxylesterase 3D structures|Carboxylesterase 3D structures]] | ||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
Latest revision as of 15:07, 20 December 2023
Crystal structure of carboxylesterase CesB (YbfK) from Bacillus subtilisCrystal structure of carboxylesterase CesB (YbfK) from Bacillus subtilis
Structural highlights
FunctionYBFK_BACSU Shows carboxylesterase activity in vitro. Publication Abstract from PubMedNaproxen esterase (NP) from Bacillus subtilis Thai I-8 is a carboxylesterase that catalyzes the enantioselective hydrolysis of naproxenmethylester to produce S-naproxen (E>200). It is a homolog of CesA (98% sequence identity) and CesB (64% identity), both produced by B. subtilis strain 168. CesB can be used for the enantioselective hydrolysis of 1,2-O-isopropylideneglycerol (solketal) esters (E>200 for IPG-caprylate). Crystal structures of NP and CesB, determined to a resolution of 1.75A and 2.04A, respectively, showed that both proteins have a canonical alpha/beta hydrolase fold with an extra N-terminal helix stabilizing the cap subdomain. The active site in both enzymes is located in a deep hydrophobic groove and includes the catalytic triad residues Ser130, His274, and Glu245. A product analog, presumably 2-(2-hydroxyethoxy)acetic acid, was bound in the NP active site. The enzymes have different enantioselectivities, which previously were shown to result from only a few amino acid substitutions in the cap domain. Modeling of a substrate in the active site of NP allowed explaining the different enantioselectivities. In addition, Ala156 may be a determinant of enantioselectivity as well, since its side chain appears to interfere with the binding of certain R-enantiomers in the active site of NP. However, the exchange route for substrate and product between the active site and the solvent is not obvious from the structures. Flexibility of the cap domain might facilitate such exchange. Interestingly, both carboxylesterases show higher structural similarity to meta-cleavage compound (MCP) hydrolases than to other alpha/beta hydrolase fold esterases. Crystal structures of two Bacillus carboxylesterases with different enantioselectivities.,Rozeboom HJ, Godinho LF, Nardini M, Quax WJ, Dijkstra BW Biochim Biophys Acta. 2014 Mar;1844(3):567-75. doi: 10.1016/j.bbapap.2014.01.003., Epub 2014 Jan 11. PMID:24418394[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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