5zrq - Revision history

OCA at 09:05, 22 November 2023

OCA — Wed, 22 Nov 2023 09:05:03 GMT

←Older revision		Revision as of 09:05, 22 November 2023
Line 1:		Line 1:

	==Crystal structure of PET-degrading cutinase Cut190 S176A/S226P/R228S mutant in Zn(2+)-bound state==		==Crystal structure of PET-degrading cutinase Cut190 S176A/S226P/R228S mutant in Zn(2+)-bound state==
-	<StructureSection load='5zrq' size='340' side='right' caption='[[5zrq]], [[Resolution\|resolution]] 1.12Å' scene=''>	+	<StructureSection load='5zrq' size='340' side='right'caption='[[5zrq]], [[Resolution\|resolution]] 1.12Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zrq]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"saccharomonospora_internatus"_(agre_et_al._1974)_greiner-mai_et_al._1988 "saccharomonospora internatus" (agre et al. 1974) greiner-mai et al. 1988~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZRQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ZRQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zrq]] is a 1 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=5ZRQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZRQ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=CA:CALCIUM+ION'>CA</scene~~>, ~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.12Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~MHO~~:~~S-OXYMETHIONINE~~'>~~MHO~~</scene><~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MHO:S-OXYMETHIONINE'>MHO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<~~tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td><~~td class~~=~~"sblockDat"~~>~~[[5zno\|5zno]], [[5zrr\|5zrr]], [[5zrs\|5zrs]]~~</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=5zrq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zrq OCA], [https://pdbe.org/5zrq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zrq RCSB], [https://www.ebi.ac.uk/pdbsum/5zrq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zrq ProSAT]</span></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td><td class="sblockDat">Cut190, SAMN02982918_2340 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1852 "Saccharomonospora internatus" (Agre et al. 1974) Greiner-Mai et al. 1988])</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=5zrq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zrq OCA], [~~http~~://pdbe.org/5zrq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5zrq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5zrq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5zrq ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/W0TJ64_9PSEU W0TJ64_9PSEU]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5zrq" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5zrq" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Cutinase 3D structures\|Cutinase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bekker~~, G J~~]]	+	[[Category: Large Structures]]
-	[[Category: Inaba, S]]	+	[[Category: Saccharomonospora viridis]]
-	[[Category: Ishii, K]]	+	[[Category: Bekker GJ]]
-	[[Category: Ito, N]]	+	[[Category: Inaba S]]
-	[[Category: Kamiya, N]]	+	[[Category: Ishii K]]
-	[[Category: Kawai, F]]	+	[[Category: Ito N]]
-	[[Category: Numoto, N]]	+	[[Category: Kamiya N]]
-	[[Category: Oda, M]]	+	[[Category: Kawai F]]
-	[[Category: Uchiyama, S]]	+	[[Category: Numoto N]]
-	[[Category: Yamagami, Y]]	+	[[Category: Oda M]]
-	~~[[Category: Alpha/beta-hydrolase fold]]~~	+	[[Category: Uchiyama S]]
-	~~[[Category: Hydrolase]]~~	+	[[Category: Yamagami Y]]
-	~~[[Category: Polyesterase]]~~	+
-	~~[[Category: Protein engineering]]~~	+
-	~~[[Category: Thermostability~~]]	+

OCA at 08:36, 26 September 2018

OCA — Wed, 26 Sep 2018 08:36:36 GMT

←Older revision		Revision as of 08:36, 26 September 2018
Line 3:		Line 3:
	<StructureSection load='5zrq' size='340' side='right' caption='[[5zrq]], [[Resolution\|resolution]] 1.12Å' scene=''>		<StructureSection load='5zrq' size='340' side='right' caption='[[5zrq]], [[Resolution\|resolution]] 1.12Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zrq]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZRQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZRQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zrq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"saccharomonospora_internatus"_(agre_et_al._1974)_greiner-mai_et_al._1988 "saccharomonospora internatus" (agre et al. 1974) greiner-mai et al. 1988]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZRQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZRQ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MHO:S-OXYMETHIONINE'>MHO</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MHO:S-OXYMETHIONINE'>MHO</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5zno\|5zno]], [[5zrr\|5zrr]], [[5zrs\|5zrs]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5zno\|5zno]], [[5zrr\|5zrr]], [[5zrs\|5zrs]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Cut190, SAMN02982918_2340 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1852 "Saccharomonospora internatus" (Agre et al. 1974) Greiner-Mai et al. 1988])</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=5zrq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zrq OCA], [http://pdbe.org/5zrq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zrq RCSB], [http://www.ebi.ac.uk/pdbsum/5zrq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zrq 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=5zrq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zrq OCA], [http://pdbe.org/5zrq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zrq RCSB], [http://www.ebi.ac.uk/pdbsum/5zrq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zrq ProSAT]</span></td></tr>
	</table>		</table>

OCA at 07:29, 12 September 2018

OCA — Wed, 12 Sep 2018 07:29:09 GMT

←Older revision		Revision as of 07:29, 12 September 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5zrq is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of PET-degrading cutinase Cut190 S176A/S226P/R228S mutant in Zn(2+)-bound state==
		+	<StructureSection load='5zrq' size='340' side='right' caption='[[5zrq]], [[Resolution\|resolution]] 1.12Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5zrq]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZRQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZRQ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MHO:S-OXYMETHIONINE'>MHO</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5zno\|5zno]], [[5zrr\|5zrr]], [[5zrs\|5zrs]]</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=5zrq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zrq OCA], [http://pdbe.org/5zrq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zrq RCSB], [http://www.ebi.ac.uk/pdbsum/5zrq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zrq ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	A cutinase-type polyesterase from Saccharomonospora viridis AHK190 (Cut190) has been shown to degrade the inner block of polyethylene terephthalate. A unique feature of Cut190 is that its function and stability are regulated by Ca(2+) binding. Our previous crystal structure analysis of Cut190S226P showed that one Ca(2+) binds to the enzyme, which induces large conformational changes in several loop regions to stabilize an open conformation [Miyakawa, T., et al. (2015) Appl. Microbiol. Biotechnol. 99, 4297]. In this study, to analyze the substrate recognition mechanism of Cut190, we determined the crystal structure of the inactive form of a Cut190 mutant, Cut190S176A, in complex with calcium ions and/or substrates. We found that three calcium ions bind to Cut190S176A, which is supported by analysis using native mass spectrometry experiments and 3D Reference Interaction Site Model calculations. The complex structures with the two substrates, monoethyl succinate and monoethyl adipate (engaged and open forms), presumably correspond to the pre- and post-reaction states, as the ester bond is close to the active site and pointing outward from the active site, respectively, for the two complexes. Ca(2+) binding induces the pocket to open, enabling the substrate to access the pocket more easily. Molecular dynamics simulations suggest that a post-reaction state in the engaged form presumably exists between the experimentally observed forms, indicating that the substrate would be cleaved in the engaged form and then requires the enzyme to change to the open form to release the product, a process that Ca(2+) can greatly accelerate.

-	~~Authors:~~ Numoto, N., Kamiya, N., Bekker~~, G.J.~~, Yamagami, Y., Inaba, S., Ishii, K., Uchiyama, S., Kawai, F., Ito, N., Oda, M.	+	Structural Dynamics of the PET-Degrading Cutinase-like Enzyme from Saccharomonospora viridis AHK190 in Substrate-Bound States Elucidates the Ca(2+)-Driven Catalytic Cycle.,Numoto N, Kamiya N, Bekker GJ, Yamagami Y, Inaba S, Ishii K, Uchiyama S, Kawai F, Ito N, Oda M Biochemistry. 2018 Sep 11;57(36):5289-5300. doi: 10.1021/acs.biochem.8b00624., Epub 2018 Aug 27. PMID:30110540<ref>PMID:30110540</ref>

-	~~Description: Crystal structure~~ of ~~PET~~-~~degrading cutinase Cut190 S176A~~/~~S226P~~/~~R228S mutant in Zn(2+)-bound state~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: ~~Ito~~, N]]	+	<div class="pdbe-citations 5zrq" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Bekker, G J]]
		+	[[Category: Inaba, S]]
	[[Category: Ishii, K]]		[[Category: Ishii, K]]
		+	[[Category: Ito, N]]
	[[Category: Kamiya, N]]		[[Category: Kamiya, N]]
-	[[Category: ~~Inaba~~, S]]	+	[[Category: Kawai, F]]
	[[Category: Numoto, N]]		[[Category: Numoto, N]]
-	[[Category: Uchiyama, S]]
-	[[Category: Bekker, G.J]]
	[[Category: Oda, M]]		[[Category: Oda, M]]
-	[[Category: ~~Kawai~~, F]]	+	[[Category: Uchiyama, S]]
	[[Category: Yamagami, Y]]		[[Category: Yamagami, Y]]
		+	[[Category: Alpha/beta-hydrolase fold]]
		+	[[Category: Hydrolase]]
		+	[[Category: Polyesterase]]
		+	[[Category: Protein engineering]]
		+	[[Category: Thermostability]]

OCA at 03:50, 16 May 2018

OCA — Wed, 16 May 2018 03:50:32 GMT

←Older revision		Revision as of 03:50, 16 May 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5zrq is ON HOLD	+	The entry 5zrq is ON HOLD until Paper Publication

	Authors: Numoto, N., Kamiya, N., Bekker, G.J., Yamagami, Y., Inaba, S., Ishii, K., Uchiyama, S., Kawai, F., Ito, N., Oda, M.		Authors: Numoto, N., Kamiya, N., Bekker, G.J., Yamagami, Y., Inaba, S., Ishii, K., Uchiyama, S., Kawai, F., Ito, N., Oda, M.
Line 12:		Line 12:
	[[Category: Inaba, S]]		[[Category: Inaba, S]]
	[[Category: Numoto, N]]		[[Category: Numoto, N]]
-	[[Category: Bekker, G.J]]
	[[Category: Uchiyama, S]]		[[Category: Uchiyama, S]]
		+	[[Category: Bekker, G.J]]
	[[Category: Oda, M]]		[[Category: Oda, M]]
	[[Category: Kawai, F]]		[[Category: Kawai, F]]
	[[Category: Yamagami, Y]]		[[Category: Yamagami, Y]]

OCA: Protected "5zrq" [edit=sysop:move=sysop]

OCA — Wed, 02 May 2018 06:35:24 GMT

Protected "5zrq" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:35, 2 May 2018

OCA: New page: '''Unreleased structure''' The entry 5zrq is ON HOLD Authors: Numoto, N., Kamiya, N., Bekker, G.J., Yamagami, Y., Inaba, S., Ishii, K., Uchiyama, S., Kawai, F., Ito, N., Oda, M. Descri...

OCA — Wed, 02 May 2018 06:35:23 GMT

New page: '''Unreleased structure''' The entry 5zrq is ON HOLD Authors: Numoto, N., Kamiya, N., Bekker, G.J., Yamagami, Y., Inaba, S., Ishii, K., Uchiyama, S., Kawai, F., Ito, N., Oda, M. Descri...

New page

'''Unreleased structure'''

The entry 5zrq is ON HOLD

Authors: Numoto, N., Kamiya, N., Bekker, G.J., Yamagami, Y., Inaba, S., Ishii, K., Uchiyama, S., Kawai, F., Ito, N., Oda, M.

Description: Crystal structure of PET-degrading cutinase Cut190 S176A/S226P/R228S mutant in Zn(2+)-bound state
[[Category: Unreleased Structures]]
[[Category: Ito, N]]
[[Category: Ishii, K]]
[[Category: Kamiya, N]]
[[Category: Inaba, S]]
[[Category: Numoto, N]]
[[Category: Bekker, G.J]]
[[Category: Uchiyama, S]]
[[Category: Oda, M]]
[[Category: Kawai, F]]
[[Category: Yamagami, Y]]