8z2j: Difference between revisions
New page: '''Unreleased structure''' The entry 8z2j is ON HOLD until Paper Publication Authors: Numoto, N., Kondo, F., Bekker, G.J., Liao, Z., Yamashita, M., Iida, A., Ito, N., Kamiya, N., Oda, M... |
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==Substrate analog a012 bound form of PET-degrading cutinase mutant Cut190**SS_S176A== | |||
<StructureSection load='8z2j' size='340' side='right'caption='[[8z2j]], [[Resolution|resolution]] 1.89Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[8z2j]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomonospora_viridis Saccharomonospora viridis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8Z2J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8Z2J 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=A1L0M:(4-methoxycarbonylphenyl)-(2-phenylmethoxyethoxy)phosphinic+acid'>A1L0M</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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=8z2j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8z2j OCA], [https://pdbe.org/8z2j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8z2j RCSB], [https://www.ebi.ac.uk/pdbsum/8z2j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8z2j ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/W0TJ64_9PSEU W0TJ64_9PSEU] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
We previously revealed the structural basis of Ca(2+) dependent regulation of a polyethylene terephthalate (PET)-degrading enzyme, Cut190, and proposed a unique reaction cycle in which the enzyme repeatedly binds and releases Ca(2+). Here, we report crystal structures of Cut190 mutants with high thermal stability complexed with PET-like ligands that contain aromatic rings. The structural information has allowed us to perform further computational analyses using a PET-trimer bound model. Our multicanonical molecular dynamics simulations and subsequent analyses of the free energy landscapes revealed a novel intermediate form that occurs during the enzymatic reaction cycle. Furthermore, the computational analyses were used to investigate the effect of the point mutations F77L and F81L in the Ca(2+)-binding site, which showed that the former stabilizes the engaged and open forms to improve transition between the open and active forms, while the latter extremely increases the open form. Subsequent experiments showed that the F77L mutation increased the activity, while the F81L mutation decreased the activity. Our computational analysis has enabled us to explore the dynamics of Cut190 on a completely new level, providing key insights into how the balance between the various conformations influences the reaction cycle and ultimately how to improve the reaction cycle. | |||
Structural dynamics of the Ca(2+)-regulated cutinase towards structure-based improvement of PET degradation activity.,Numoto N, Kondo F, Bekker GJ, Liao Z, Yamashita M, Iida A, Ito N, Kamiya N, Oda M Int J Biol Macromol. 2024 Oct 15;281(Pt 4):136597. doi: , 10.1016/j.ijbiomac.2024.136597. PMID:39419144<ref>PMID:39419144</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 8z2j" style="background-color:#fffaf0;"></div> | ||
[[Category: Bekker | == References == | ||
[[Category: | <references/> | ||
[[Category: | __TOC__ | ||
[[Category: Kondo | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Saccharomonospora viridis]] | ||
[[Category: | [[Category: Bekker GJ]] | ||
[[Category: Yamashita | [[Category: Iida A]] | ||
[[Category: Ito N]] | |||
[[Category: Kamiya N]] | |||
[[Category: Kondo F]] | |||
[[Category: Liao Z]] | |||
[[Category: Numoto N]] | |||
[[Category: Oda M]] | |||
[[Category: Yamashita M]] | |||
Latest revision as of 11:12, 6 November 2024
Substrate analog a012 bound form of PET-degrading cutinase mutant Cut190**SS_S176ASubstrate analog a012 bound form of PET-degrading cutinase mutant Cut190**SS_S176A
Structural highlights
FunctionPublication Abstract from PubMedWe previously revealed the structural basis of Ca(2+) dependent regulation of a polyethylene terephthalate (PET)-degrading enzyme, Cut190, and proposed a unique reaction cycle in which the enzyme repeatedly binds and releases Ca(2+). Here, we report crystal structures of Cut190 mutants with high thermal stability complexed with PET-like ligands that contain aromatic rings. The structural information has allowed us to perform further computational analyses using a PET-trimer bound model. Our multicanonical molecular dynamics simulations and subsequent analyses of the free energy landscapes revealed a novel intermediate form that occurs during the enzymatic reaction cycle. Furthermore, the computational analyses were used to investigate the effect of the point mutations F77L and F81L in the Ca(2+)-binding site, which showed that the former stabilizes the engaged and open forms to improve transition between the open and active forms, while the latter extremely increases the open form. Subsequent experiments showed that the F77L mutation increased the activity, while the F81L mutation decreased the activity. Our computational analysis has enabled us to explore the dynamics of Cut190 on a completely new level, providing key insights into how the balance between the various conformations influences the reaction cycle and ultimately how to improve the reaction cycle. Structural dynamics of the Ca(2+)-regulated cutinase towards structure-based improvement of PET degradation activity.,Numoto N, Kondo F, Bekker GJ, Liao Z, Yamashita M, Iida A, Ito N, Kamiya N, Oda M Int J Biol Macromol. 2024 Oct 15;281(Pt 4):136597. doi: , 10.1016/j.ijbiomac.2024.136597. PMID:39419144[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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