5yns

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of PETase R280A mutant from Ideonella sakaiensis

Structural highlights

5yns 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 1.36Å
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]

Publication Abstract from PubMed

Plastics, including poly(ethylene terephthalate) (PET), possess many desirable characteristics and thus are widely used in daily life. However, non-biodegradability, once thought to be an advantage offered by plastics, is causing major environmental problem. Recently, a PET-degrading bacterium, Ideonella sakaiensis, was identified and suggested for possible use in degradation and/or recycling of PET. However, the molecular mechanism of PET degradation is not known. Here we report the crystal structure of I. sakaiensis PETase (IsPETase) at 1.5 A resolution. IsPETase has a Ser-His-Asp catalytic triad at its active site and contains an optimal substrate binding site to accommodate four monohydroxyethyl terephthalate (MHET) moieties of PET. Based on structural and site-directed mutagenesis experiments, the detailed process of PET degradation into MHET, terephthalic acid, and ethylene glycol is suggested. Moreover, other PETase candidates potentially having high PET-degrading activities are suggested based on phylogenetic tree analysis of 69 PETase-like proteins.

Structural insight into molecular mechanism of poly(ethylene terephthalate) degradation.,Joo S, Cho IJ, Seo H, Son HF, Sagong HY, Shin TJ, Choi SY, Lee SY, Kim KJ Nat Commun. 2018 Jan 26;9(1):382. doi: 10.1038/s41467-018-02881-1. PMID:29374183^[8]

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

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:http://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:http://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:http://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:http://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:http://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:http://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:http://dx.doi.org/10.1038/s41586-020-2149-4
↑ 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:http://dx.doi.org/10.1038/s41467-018-02881-1

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/5yns"

Categories: Ideonella sakaiensis | Large Structures | Joo S | Kim K-J

@@ Line 3: / Line 3: @@
 <StructureSection load='5yns' size='340' side='right'caption='[[5yns]], [[Resolution|resolution]] 1.36&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5yns]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Idesa Idesa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YNS OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5YNS FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5yns]] 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=5YNS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YNS FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ISF6_4831 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1547922 IDESA])</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]] 1.36&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Poly(ethylene_terephthalate)_hydrolase Poly(ethylene terephthalate) hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.101 3.1.1.101] </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=5yns FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yns OCA], [https://pdbe.org/5yns PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yns RCSB], [https://www.ebi.ac.uk/pdbsum/5yns PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yns ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5yns FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yns OCA], [http://pdbe.org/5yns PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yns RCSB], [http://www.ebi.ac.uk/pdbsum/5yns PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yns 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>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 21: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Idesa]]
+[[Category: Ideonella sakaiensis]]
 [[Category: Large Structures]]
-[[Category: Joo, S]]
+[[Category: Joo S]]
-[[Category: Kim, K J]]
+[[Category: Kim K-J]]
-[[Category: Hydrolase]]

5yns

From Proteopedia

Current revision

Crystal structure of PETase R280A mutant from Ideonella sakaiensis

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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