6yra - Revision history

OCA at 13:33, 24 January 2024

OCA — Wed, 24 Jan 2024 13:33:57 GMT

←Older revision		Revision as of 13:33, 24 January 2024
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-	====	+	==Crystal structure of ATP-dependent caprolactamase from Pseudomonas jessenii==
-	<StructureSection load='6yra' size='340' side='right'caption='[[6yra]]' scene=''>	+	<StructureSection load='6yra' size='340' side='right'caption='[[6yra]], [[Resolution\|resolution]] 4.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6yra]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_jessenii Pseudomonas jessenii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YRA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YRA FirstGlance]. <br>
-	</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=6yra FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yra OCA], [https://pdbe.org/6yra PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yra RCSB], [https://www.ebi.ac.uk/pdbsum/6yra PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yra ProSAT]</span></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]] 4Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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=6yra FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yra OCA], [https://pdbe.org/6yra PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yra RCSB], [https://www.ebi.ac.uk/pdbsum/6yra PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yra ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A2W0FH34_9PSED A0A2W0FH34_9PSED]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Caprolactamase is the first enzyme in the caprolactam degradation pathway of Pseudomonas jessenii. It is composed of two subunits (CapA and CapB) and sequence-related to other ATP-dependent enzymes involved in lactam hydrolysis, like 5-oxoprolinases and hydantoinases. Low sequence similarity also exists with ATP-dependent acetone- and acetophenone carboxylases. The caprolactamase was produced in Escherichia coli, isolated by His-tag affinity chromatography, and subjected to functional and structural studies. Activity toward caprolactam required ATP and was dependent on the presence of bicarbonate in the assay buffer. The hydrolysis product was identified as 6-aminocaproic acid. Quantum mechanical modeling indicated that the hydrolysis of caprolactam was highly disfavored (DeltaG(0) '= 23 kJ/mol), which explained the ATP dependence. A crystal structure showed that the enzyme exists as an (alphabeta)(2) tetramer and revealed an ATP-binding site in CapA and a Zn-coordinating site in CapB. Mutations in the ATP-binding site of CapA (D11A and D295A) significantly reduced product formation. Mutants with substitutions in the metal binding site of CapB (D41A, H99A, D101A, and H124A) were inactive and less thermostable than the wild-type enzyme. These residues proved to be essential for activity and on basis of the experimental findings we propose possible mechanisms for ATP-dependent lactam hydrolysis.
		+
		+	Catalytic and structural properties of ATP-dependent caprolactamase from Pseudomonas jessenii.,Marjanovic A, Rozeboom HJ, de Vries MS, Mayer C, Otzen M, Wijma HJ, Janssen DB Proteins. 2021 Sep;89(9):1079-1098. doi: 10.1002/prot.26082. Epub 2021 May 6. PMID:33826169<ref>PMID:33826169</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6yra" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Pseudomonas jessenii]]
		+	[[Category: Janssen DB]]
		+	[[Category: Rozeboom HJ]]

OCA at 08:20, 21 April 2021

OCA — Wed, 21 Apr 2021 08:20:35 GMT

←Older revision		Revision as of 08:20, 21 April 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 6yra ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='6yra' size='340' side='right'caption='[[6yra]]' scene=''>
-	~~Authors~~: ~~Rozeboom, H~~.J.~~, Janssen, D~~.B.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure of ATP~~-~~dependent caprolactamase from Pseudomonas jessenii~~	+	</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=6yra FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yra OCA], [https://pdbe.org/6yra PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yra RCSB], [https://www.ebi.ac.uk/pdbsum/6yra PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yra ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[Category: ~~Janssen, D.B~~]]	+	__TOC__
-	[[Category: ~~Rozeboom, H.J~~]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA at 04:13, 13 May 2020

OCA — Wed, 13 May 2020 04:13:33 GMT

←Older revision		Revision as of 04:13, 13 May 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6yra is ON HOLD	+	The entry 6yra is ON HOLD until Paper Publication

	Authors: Rozeboom, H.J., Janssen, D.B.		Authors: Rozeboom, H.J., Janssen, D.B.

OCA: Protected "6yra" [edit=sysop:move=sysop]

OCA — Wed, 29 Apr 2020 05:26:39 GMT

Protected "6yra" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:26, 29 April 2020

OCA: New page: '''Unreleased structure''' The entry 6yra is ON HOLD Authors: Rozeboom, H.J., Janssen, D.B. Description: Crystal structure of ATP-dependent caprolactamase from Pseudomonas jessenii [[C...

OCA — Wed, 29 Apr 2020 05:26:37 GMT

New page: '''Unreleased structure''' The entry 6yra is ON HOLD Authors: Rozeboom, H.J., Janssen, D.B. Description: Crystal structure of ATP-dependent caprolactamase from Pseudomonas jessenii [[C...

New page

'''Unreleased structure'''

The entry 6yra is ON HOLD

Authors: Rozeboom, H.J., Janssen, D.B.

Description: Crystal structure of ATP-dependent caprolactamase from Pseudomonas jessenii
[[Category: Unreleased Structures]]
[[Category: Janssen, D.B]]
[[Category: Rozeboom, H.J]]