5xjh: Difference between revisions

Revision as of 08:04, 22 November 2023

Crystal structure of PETase from Ideonella sakaiensis

Structural highlights

5xjh 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 1.54Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PETH_IDESA

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^[1]

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

References

↑ 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

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OCA

[1] 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

[1]

@@ Line 3: / Line 3: @@
 <StructureSection load='5xjh' size='340' side='right'caption='[[5xjh]], [[Resolution|resolution]] 1.54&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5xjh]] 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=5XJH OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5XJH FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5xjh]] 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=5XJH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XJH 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]] 1.54&#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=5xjh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xjh OCA], [https://pdbe.org/5xjh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xjh RCSB], [https://www.ebi.ac.uk/pdbsum/5xjh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xjh 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=5xjh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xjh OCA], [http://pdbe.org/5xjh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xjh RCSB], [http://www.ebi.ac.uk/pdbsum/5xjh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xjh ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/PETH_IDESA PETH_IDESA]
 <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]]

5xjh: Difference between revisions

Revision as of 08:04, 22 November 2023

Crystal structure of PETase from Ideonella sakaiensis

Structural highlights

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Publication Abstract from PubMed

References

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