OCA at 14:43, 20 September 2023

2023-09-20T14:43:21Z

←Older revision		Revision as of 14:43, 20 September 2023
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-	'''Unreleased structure'''

-	~~The entry~~ 8h7c is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of a de novo enzyme, ferric enterobactin esterase Syn-F4 (K4T) - Pt derivative==
		+	<StructureSection load='8h7c' size='340' side='right'caption='[[8h7c]], [[Resolution\|resolution]] 2.15Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8h7c]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8H7C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8H7C FirstGlance]. <br>
		+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.15Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PC4:TETRACHLOROPLATINATE(II)'>PC4</scene>, <scene name='pdbligand=PT:PLATINUM+(II)+ION'>PT</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=8h7c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8h7c OCA], [https://pdbe.org/8h7c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8h7c RCSB], [https://www.ebi.ac.uk/pdbsum/8h7c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8h7c ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Producing novel enzymes that are catalytically active in vitro and biologically functional in vivo is a key goal of synthetic biology. Previously, we reported Syn-F4, the first de novo protein that meets both criteria. Syn-F4 hydrolyzed the siderophore ferric enterobactin, and expression of Syn-F4 allowed an inviable strain of Escherichia coli (Deltafes) to grow in iron-limited medium. Here, we describe the crystal structure of Syn-F4. Syn-F4 forms a dimeric 4-helix bundle. Each monomer comprises two long alpha-helices, and the loops of the Syn-F4 dimer are on the same end of the bundle (syn topology). Interestingly, there is a penetrated hole in the central region of the Syn-F4 structure. Extensive mutagenesis experiments in a previous study showed that five residues (Glu26, His74, Arg77, Lys78, and Arg85) were essential for enzymatic activity in vivo. All these residues are located around the hole in the central region of the Syn-F4 structure, suggesting a putative active site with a catalytic dyad (Glu26-His74). The complete inactivity of purified proteins with mutations at the five residues supports the putative active site and reaction mechanism. Molecular dynamics and docking simulations of the ferric enterobactin siderophore binding to the Syn-F4 structure demonstrate the dynamic property of the putative active site. The structure and active site of Syn-F4 are completely different from native enterobactin esterase enzymes, thereby demonstrating that proteins designed de novo can provide life-sustaining catalytic activities using structures and mechanisms dramatically different from those that arose in nature.

-	~~Authors~~:	+	Crystal structure and activity of a de novo enzyme, ferric enterobactin esterase Syn-F4.,Kurihara K, Umezawa K, Donnelly AE, Sperling B, Liao G, Hecht MH, Arai R Proc Natl Acad Sci U S A. 2023 Sep 19;120(38):e2218281120. doi: , 10.1073/pnas.2218281120. Epub 2023 Sep 11. PMID:37695900<ref>PMID:37695900</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 8h7c" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Synthetic construct]]
		+	[[Category: Arai R]]
		+	[[Category: Donnelly AE]]
		+	[[Category: Hecht MH]]
		+	[[Category: Kurihara K]]
		+	[[Category: Umezawa K]]

OCA at 08:44, 30 November 2022

2022-11-30T08:44:54Z

←Older revision		Revision as of 08:44, 30 November 2022
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 8h7c is ON HOLD	+	The entry 8h7c is ON HOLD until Paper Publication

	Authors:		Authors:

OCA at 05:32, 3 November 2022

2022-11-03T05:32:58Z

←Older revision		Revision as of 05:32, 3 November 2022
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	The entry 8h7c is ON HOLD		The entry 8h7c is ON HOLD

-	Authors: ~~Kurihara, K., Umezawa, K., Donnelly, A.E., Hecht, M.H., Arai, R.~~	+	Authors:

-	Description: ~~Crystal structure of a de novo enzyme, ferric enterobactin esterase Syn-F4 (K4T) -Pt derivative~~	+	Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Donnelly, A.E]]
-	[[Category: Arai, R]]
-	[[Category: Kurihara, K]]
-	[[Category: Hecht, M.H]]
-	[[Category: Umezawa, K]]

OCA: Protected "8h7c" [edit=sysop:move=sysop]

2022-10-26T04:15:23Z

Protected "8h7c" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:15, 26 October 2022

OCA: New page: '''Unreleased structure''' The entry 8h7c is ON HOLD Authors: Kurihara, K., Umezawa, K., Donnelly, A.E., Hecht, M.H., Arai, R. Description: Crystal structure of a de novo enzyme, ferri...

2022-10-26T04:15:21Z

New page: '''Unreleased structure''' The entry 8h7c is ON HOLD Authors: Kurihara, K., Umezawa, K., Donnelly, A.E., Hecht, M.H., Arai, R. Description: Crystal structure of a de novo enzyme, ferri...

New page

'''Unreleased structure'''

The entry 8h7c is ON HOLD

Authors: Kurihara, K., Umezawa, K., Donnelly, A.E., Hecht, M.H., Arai, R.

Description: Crystal structure of a de novo enzyme, ferric enterobactin esterase Syn-F4 (K4T) -Pt derivative
[[Category: Unreleased Structures]]
[[Category: Donnelly, A.E]]
[[Category: Arai, R]]
[[Category: Kurihara, K]]
[[Category: Hecht, M.H]]
[[Category: Umezawa, K]]

8h7c - Revision history

OCA at 14:43, 20 September 2023

OCA at 08:44, 30 November 2022

OCA at 05:32, 3 November 2022

OCA: Protected "8h7c" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 8h7c is ON HOLD Authors: Kurihara, K., Umezawa, K., Donnelly, A.E., Hecht, M.H., Arai, R. Description: Crystal structure of a de novo enzyme, ferri...