6aid

From Proteopedia

(Difference between revisions)

Current revision

Structural insights into the unique polylactate degrading mechanism of Thermobifida alba cutinase

Structural highlights

6aid is a 1 chain structure with sequence from Thermobifida alba. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.3Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PETH2_THEAE Catalyzes the hydrolysis of cutin, a polyester that forms the structure of plant cuticle (PubMed:20393707, PubMed:22183084, PubMed:25910960, PubMed:33387709). Shows esterase activity towards p-nitrophenol-linked aliphatic esters (pNP-aliphatic esters) (PubMed:20393707, PubMed:22183084, PubMed:25910960, PubMed:33387709). Capable of degrading the plastic poly(ethylene terephthalate) (PET), the most abundant polyester plastic in the world (By similarity). Can also depolymerize the synthetic polyesters poly(epsilon-caprolactone) (PCL), poly(butylene succinate-co-adipate) (PBSA), poly(butylene succinate) (PBS), and poly(lactic acid) (PLA) (PubMed:20393707, PubMed:22183084).[UniProtKB:D4Q9N1]^[1] ^[2] ^[3] ^[4]

Publication Abstract from PubMed

Cutinases are enzymes known to degrade polyester-type plastics. Est119, a plastic-degrading type of cutinase from Thermobifida alba AHK119 (herein called Ta_cut), shows a broad substrate specificity toward polyesters, and can degrade substrates including polylactic acid (PLA). However, the PLA-degrading mechanism of cutinases is still poorly understood. Here, we report the structure complexes of cutinase with ethyl lactate (EL), the constitutional unit. From this complex structure, the electron density maps clearly showed one lactate (LAC) and one EL occupying different positions in the active site cleft. The binding mode of EL is assumed to show a figure prior to reaction and LAC is an after-reaction product. These complex structures demonstrate the role of active site residues in the esterase reaction and substrate recognition. The complex structures were compared with other documented complex structures of cutinases and with the structure of PETase from Ideonella sakaiensis. The amino acid residues involved in substrate interaction are highly conserved among these enzymes. Thus, mapping the precise interactions in the Ta_cut and EL complex will pave the way for understanding the plastic-degrading mechanism of cutinases and suggest ways of creating more potent enzymes by structural protein engineering. This article is protected by copyright. All rights reserved.

Structural insights into the unique polylactate-degrading mechanism of Thermobifida alba cutinase.,Kitadokoro K, Mizuki K, Matsui S, Osokoshi R, Uschara T, Kawai F, Kamitani S FEBS J. 2019 Feb 14. doi: 10.1111/febs.14781. PMID:30761732^[5]

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

References

↑ Hu X, Thumarat U, Zhang X, Tang M, Kawai F. Diversity of polyester-degrading bacteria in compost and molecular analysis of a thermoactive esterase from Thermobifida alba AHK119. Appl Microbiol Biotechnol. 2010 Jun;87(2):771-9. PMID:20393707 doi:10.1007/s00253-010-2555-x
↑ Thumarat U, Nakamura R, Kawabata T, Suzuki H, Kawai F. Biochemical and genetic analysis of a cutinase-type polyesterase from a thermophilic Thermobifida alba AHK119. Appl Microbiol Biotechnol. 2012 Jul;95(2):419-30. PMID:22183084 doi:10.1007/s00253-011-3781-6
↑ Thumarat U, Kawabata T, Nakajima M, Nakajima H, Sugiyama A, Yazaki K, Tada T, Waku T, Tanaka N, Kawai F. Comparison of genetic structures and biochemical properties of tandem cutinase-type polyesterases from Thermobifida alba AHK119. J Biosci Bioeng. 2015 Nov;120(5):491-7. PMID:25910960 doi:10.1016/j.jbiosc.2015.03.006
↑ Zhang Z, Wang W, Li D, Xiao J, Wu L, Geng X, Wu G, Zeng Z, Hu J. Decolorization of molasses alcohol wastewater by thermophilic hydrolase with practical application value. Bioresour Technol. 2021 Mar;323:124609. PMID:33387709 doi:10.1016/j.biortech.2020.124609
↑ Kitadokoro K, Mizuki K, Matsui S, Osokoshi R, Uschara T, Kawai F, Kamitani S. Structural insights into the unique polylactate-degrading mechanism of Thermobifida alba cutinase. FEBS J. 2019 Feb 14. doi: 10.1111/febs.14781. PMID:30761732 doi:http://dx.doi.org/10.1111/febs.14781

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/6aid"

@@ Line 3: / Line 3: @@
 <StructureSection load='6aid' size='340' side='right'caption='[[6aid]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6aid]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"actinobifida_alba"_locci_et_al._1967 "actinobifida alba" locci et al. 1967]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AID OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6AID FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6aid]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermobifida_alba Thermobifida alba]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AID OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6AID FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9YL:ethyl+(2R)-2-oxidanylpropanoate'>9YL</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=LAC:LACTIC+ACID'>LAC</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]] 1.3&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3vis|3vis]], [[3wyn|3wyn]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=9YL:ethyl+(2R)-2-oxidanylpropanoate'>9YL</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=LAC:LACTIC+ACID'>LAC</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">est2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=53522 "Actinobifida alba" Locci et al. 1967])</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=6aid FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6aid OCA], [https://pdbe.org/6aid PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6aid RCSB], [https://www.ebi.ac.uk/pdbsum/6aid PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6aid ProSAT]</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=6aid FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6aid OCA], [http://pdbe.org/6aid PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6aid RCSB], [http://www.ebi.ac.uk/pdbsum/6aid PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6aid ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/PETH2_THEAE PETH2_THEAE] Catalyzes the hydrolysis of cutin, a polyester that forms the structure of plant cuticle (PubMed:20393707, PubMed:22183084, PubMed:25910960, PubMed:33387709). Shows esterase activity towards p-nitrophenol-linked aliphatic esters (pNP-aliphatic esters) (PubMed:20393707, PubMed:22183084, PubMed:25910960, PubMed:33387709). Capable of degrading the plastic poly(ethylene terephthalate) (PET), the most abundant polyester plastic in the world (By similarity). Can also depolymerize the synthetic polyesters poly(epsilon-caprolactone) (PCL), poly(butylene succinate-co-adipate) (PBSA), poly(butylene succinate) (PBS), and poly(lactic acid) (PLA) (PubMed:20393707, PubMed:22183084).[UniProtKB:D4Q9N1]<ref>PMID:20393707</ref> <ref>PMID:22183084</ref> <ref>PMID:25910960</ref> <ref>PMID:33387709</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Actinobifida alba locci et al. 1967]]
 [[Category: Large Structures]]
-[[Category: Kakara, M]]
+[[Category: Thermobifida alba]]
-[[Category: Kamitani, S]]
+[[Category: Kakara M]]
-[[Category: Kawai, F]]
+[[Category: Kamitani S]]
-[[Category: Kitadokoro, K]]
+[[Category: Kawai F]]
-[[Category: Matsui, S]]
+[[Category: Kitadokoro K]]
-[[Category: Osokoshi, R]]
+[[Category: Matsui S]]
-[[Category: Thumarat, U]]
+[[Category: Osokoshi R]]
-[[Category: Hydrolase]]
+[[Category: Thumarat U]]

6aid

From Proteopedia

Current revision

Structural insights into the unique polylactate degrading mechanism of Thermobifida alba cutinase

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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