8j45: Difference between revisions

Latest revision as of 07:29, 21 November 2024

Crystal structure of a Pichia pastoris-expressed IsPETase variant

Structural highlights

8j45 is a 1 chain structure with sequence from Ideonella sakaiensis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.49Å
Ligands:	NAG
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PETH_PISS1 Involved in the degradation and assimilation of the plastic poly(ethylene terephthalate) (PET), which allows I.sakaiensis to use PET as its major energy and carbon source for growth. Likely acts synergistically with MHETase to depolymerize PET (PubMed:26965627). Catalyzes the hydrolysis of PET to produce mono(2-hydroxyethyl) terephthalate (MHET) as the major product (PubMed:26965627, PubMed:29235460, PubMed:29374183, PubMed:29603535, PubMed:29666242, PubMed:32269349). Also depolymerizes another semiaromatic polyester, poly(ethylene-2,5-furandicarboxylate) (PEF), which is an emerging, bioderived PET replacement with improved gas barrier properties (PubMed:29666242). In contrast, PETase does not degrade aliphatic polyesters such as polylactic acid (PLA) and polybutylene succinate (PBS) (PubMed:29666242). Is also able to hydrolyze bis(hydroxyethyl) terephthalate (BHET) to yield MHET with no further decomposition, but terephthalate (TPA) can also be observed (PubMed:26965627, PubMed:29374183, PubMed:29603535). Shows esterase activity towards p-nitrophenol-linked aliphatic esters (pNP-aliphatic esters) in vitro (PubMed:26965627, PubMed:30502092).^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7]

References

↑ Yoshida S, Hiraga K, Takehana T, Taniguchi I, Yamaji H, Maeda Y, Toyohara K, Miyamoto K, Kimura Y, Oda K. A bacterium that degrades and assimilates poly(ethylene terephthalate). Science. 2016 Mar 11;351(6278):1196-9. doi: 10.1126/science.aad6359. PMID:26965627 doi:https://dx.doi.org/10.1126/science.aad6359
↑ Han X, Liu W, Huang JW, Ma J, Zheng Y, Ko TP, Xu L, Cheng YS, Chen CC, Guo RT. Structural insight into catalytic mechanism of PET hydrolase. Nat Commun. 2017 Dec 13;8(1):2106. doi: 10.1038/s41467-017-02255-z. PMID:29235460 doi:https://dx.doi.org/10.1038/s41467-017-02255-z
↑ Joo S, Cho IJ, Seo H, Son HF, Sagong HY, Shin TJ, Choi SY, Lee SY, Kim KJ. Structural insight into molecular mechanism of poly(ethylene terephthalate) degradation. Nat Commun. 2018 Jan 26;9(1):382. doi: 10.1038/s41467-018-02881-1. PMID:29374183 doi:https://dx.doi.org/10.1038/s41467-018-02881-1
↑ Liu B, He L, Wang L, Li T, Li C, Liu H, Luo Y, Bao R. Protein Crystallography and Site-Direct Mutagenesis Analysis of the Poly(ethylene terephthalate) Hydrolase PETase from Ideonella sakaiensis. Chembiochem. 2018 Mar 30. doi: 10.1002/cbic.201800097. PMID:29603535 doi:https://dx.doi.org/10.1002/cbic.201800097
↑ Austin HP, Allen MD, Donohoe BS, Rorrer NA, Kearns FL, Silveira RL, Pollard BC, Dominick G, Duman R, El Omari K, Mykhaylyk V, Wagner A, Michener WE, Amore A, Skaf MS, Crowley MF, Thorne AW, Johnson CW, Woodcock HL, McGeehan JE, Beckham GT. Characterization and engineering of a plastic-degrading aromatic polyesterase. Proc Natl Acad Sci U S A. 2018 Apr 17. pii: 1718804115. doi:, 10.1073/pnas.1718804115. PMID:29666242 doi:https://dx.doi.org/10.1073/pnas.1718804115
↑ Liu C, Shi C, Zhu S, Wei R, Yin CC. Structural and functional characterization of polyethylene terephthalate hydrolase from Ideonella sakaiensis. Biochem Biophys Res Commun. 2019 Jan 1;508(1):289-294. doi:, 10.1016/j.bbrc.2018.11.148. Epub 2018 Nov 27. PMID:30502092 doi:https://dx.doi.org/10.1016/j.bbrc.2018.11.148
↑ Tournier V, Topham CM, Gilles A, David B, Folgoas C, Moya-Leclair E, Kamionka E, Desrousseaux ML, Texier H, Gavalda S, Cot M, Guemard E, Dalibey M, Nomme J, Cioci G, Barbe S, Chateau M, Andre I, Duquesne S, Marty A. An engineered PET depolymerase to break down and recycle plastic bottles. Nature. 2020 Apr;580(7802):216-219. doi: 10.1038/s41586-020-2149-4. Epub 2020 Apr, 8. PMID:32269349 doi:https://dx.doi.org/10.1038/s41586-020-2149-4

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OCA

[1] Yoshida S, Hiraga K, Takehana T, Taniguchi I, Yamaji H, Maeda Y, Toyohara K, Miyamoto K, Kimura Y, Oda K. A bacterium that degrades and assimilates poly(ethylene terephthalate). Science. 2016 Mar 11;351(6278):1196-9. doi: 10.1126/science.aad6359. PMID:26965627 doi:https://dx.doi.org/10.1126/science.aad6359

[2] Han X, Liu W, Huang JW, Ma J, Zheng Y, Ko TP, Xu L, Cheng YS, Chen CC, Guo RT. Structural insight into catalytic mechanism of PET hydrolase. Nat Commun. 2017 Dec 13;8(1):2106. doi: 10.1038/s41467-017-02255-z. PMID:29235460 doi:https://dx.doi.org/10.1038/s41467-017-02255-z

[3] Joo S, Cho IJ, Seo H, Son HF, Sagong HY, Shin TJ, Choi SY, Lee SY, Kim KJ. Structural insight into molecular mechanism of poly(ethylene terephthalate) degradation. Nat Commun. 2018 Jan 26;9(1):382. doi: 10.1038/s41467-018-02881-1. PMID:29374183 doi:https://dx.doi.org/10.1038/s41467-018-02881-1

[4] Liu B, He L, Wang L, Li T, Li C, Liu H, Luo Y, Bao R. Protein Crystallography and Site-Direct Mutagenesis Analysis of the Poly(ethylene terephthalate) Hydrolase PETase from Ideonella sakaiensis. Chembiochem. 2018 Mar 30. doi: 10.1002/cbic.201800097. PMID:29603535 doi:https://dx.doi.org/10.1002/cbic.201800097

[5] Austin HP, Allen MD, Donohoe BS, Rorrer NA, Kearns FL, Silveira RL, Pollard BC, Dominick G, Duman R, El Omari K, Mykhaylyk V, Wagner A, Michener WE, Amore A, Skaf MS, Crowley MF, Thorne AW, Johnson CW, Woodcock HL, McGeehan JE, Beckham GT. Characterization and engineering of a plastic-degrading aromatic polyesterase. Proc Natl Acad Sci U S A. 2018 Apr 17. pii: 1718804115. doi:, 10.1073/pnas.1718804115. PMID:29666242 doi:https://dx.doi.org/10.1073/pnas.1718804115

[6] Liu C, Shi C, Zhu S, Wei R, Yin CC. Structural and functional characterization of polyethylene terephthalate hydrolase from Ideonella sakaiensis. Biochem Biophys Res Commun. 2019 Jan 1;508(1):289-294. doi:, 10.1016/j.bbrc.2018.11.148. Epub 2018 Nov 27. PMID:30502092 doi:https://dx.doi.org/10.1016/j.bbrc.2018.11.148

[7] Tournier V, Topham CM, Gilles A, David B, Folgoas C, Moya-Leclair E, Kamionka E, Desrousseaux ML, Texier H, Gavalda S, Cot M, Guemard E, Dalibey M, Nomme J, Cioci G, Barbe S, Chateau M, Andre I, Duquesne S, Marty A. An engineered PET depolymerase to break down and recycle plastic bottles. Nature. 2020 Apr;580(7802):216-219. doi: 10.1038/s41586-020-2149-4. Epub 2020 Apr, 8. PMID:32269349 doi:https://dx.doi.org/10.1038/s41586-020-2149-4

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 8j45 is ON HOLD
+==Crystal structure of a Pichia pastoris-expressed IsPETase variant==
+<StructureSection load='8j45' size='340' side='right'caption='[[8j45]], [[Resolution|resolution]] 1.49&Aring;' scene=''>
-Authors:
+== Structural highlights ==
+<table><tr><td colspan='2'>[[8j45]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Ideonella_sakaiensis Ideonella sakaiensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8J45 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8J45 FirstGlance]. <br>
-Description:
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.49&#8491;</td></tr>
-[[Category: Unreleased Structures]]
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=8j45 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8j45 OCA], [https://pdbe.org/8j45 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8j45 RCSB], [https://www.ebi.ac.uk/pdbsum/8j45 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8j45 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PETH_PISS1 PETH_PISS1] Involved in the degradation and assimilation of the plastic poly(ethylene terephthalate) (PET), which allows I.sakaiensis to use PET as its major energy and carbon source for growth. Likely acts synergistically with MHETase to depolymerize PET (PubMed:26965627). Catalyzes the hydrolysis of PET to produce mono(2-hydroxyethyl) terephthalate (MHET) as the major product (PubMed:26965627, PubMed:29235460, PubMed:29374183, PubMed:29603535, PubMed:29666242, PubMed:32269349). Also depolymerizes another semiaromatic polyester, poly(ethylene-2,5-furandicarboxylate) (PEF), which is an emerging, bioderived PET replacement with improved gas barrier properties (PubMed:29666242). In contrast, PETase does not degrade aliphatic polyesters such as polylactic acid (PLA) and polybutylene succinate (PBS) (PubMed:29666242). Is also able to hydrolyze bis(hydroxyethyl) terephthalate (BHET) to yield MHET with no further decomposition, but terephthalate (TPA) can also be observed (PubMed:26965627, PubMed:29374183, PubMed:29603535). Shows esterase activity towards p-nitrophenol-linked aliphatic esters (pNP-aliphatic esters) in vitro (PubMed:26965627, PubMed:30502092).<ref>PMID:26965627</ref> <ref>PMID:29235460</ref> <ref>PMID:29374183</ref> <ref>PMID:29603535</ref> <ref>PMID:29666242</ref> <ref>PMID:30502092</ref> <ref>PMID:32269349</ref>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Ideonella sakaiensis]]
+[[Category: Large Structures]]
+[[Category: Chen C-C]]
+[[Category: Guo R-T]]
+[[Category: He HL]]
+[[Category: Huang J-W]]
+[[Category: Li X]]
+[[Category: Long X]]
+[[Category: Niu D]]

8j45: Difference between revisions

Latest revision as of 07:29, 21 November 2024

Crystal structure of a Pichia pastoris-expressed IsPETase variant

Structural highlights

Function

References

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