4lak - Revision history

OCA at 14:33, 8 November 2023

OCA — Wed, 08 Nov 2023 14:33:42 GMT

←Older revision		Revision as of 14:33, 8 November 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4lak]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Cordyceps_militaris_CM01 Cordyceps militaris CM01]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LAK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4LAK FirstGlance]. <br>		<table><tr><td colspan='2'>[[4lak]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Cordyceps_militaris_CM01 Cordyceps militaris CM01]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LAK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4LAK FirstGlance]. <br>
-	</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>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.41Å</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=4lak FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lak OCA], [https://pdbe.org/4lak PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4lak RCSB], [https://www.ebi.ac.uk/pdbsum/4lak PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4lak ProSAT]</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=4lak FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lak OCA], [https://pdbe.org/4lak PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4lak RCSB], [https://www.ebi.ac.uk/pdbsum/4lak PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4lak ProSAT]</span></td></tr>
	</table>		</table>

OCA at 10:48, 14 December 2022

OCA — Wed, 14 Dec 2022 10:48:16 GMT

←Older revision		Revision as of 10:48, 14 December 2022
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	==Crystal structure of Cordyceps militaris IDCase D323N mutant in apo form==		==Crystal structure of Cordyceps militaris IDCase D323N mutant in apo form==
-	<StructureSection load='4lak' size='340' side='right' caption='[[4lak]], [[Resolution\|resolution]] 2.41Å' scene=''>	+	<StructureSection load='4lak' size='340' side='right'caption='[[4lak]], [[Resolution\|resolution]] 2.41Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4lak]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Cormm Cormm~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LAK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4LAK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4lak]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Cordyceps_militaris_CM01 Cordyceps militaris CM01]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LAK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4LAK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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" id="ligandDat"><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">[[4lal\|4lal]], [[4lam\|4lam]], [[4lan\|4lan]], [[4lao\|4lao]]</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=4lak FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lak OCA], [https://pdbe.org/4lak PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4lak RCSB], [https://www.ebi.ac.uk/pdbsum/4lak PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4lak ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CCM_01452 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=983644 CORMM])~~</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=4lak FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lak OCA], [~~http~~://pdbe.org/4lak PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4lak RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4lak PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4lak ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/G3J531_CORMM G3J531_CORMM]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Cormm~~]]	+	[[Category: Cordyceps militaris CM01]]
-	[[Category: Ding, J]]	+	[[Category: Large Structures]]
-	[[Category: Li, W]]	+	[[Category: Ding J]]
-	[[Category: Li, Z]]	+	[[Category: Li W]]
-	[[Category: Wang, R]]	+	[[Category: Li Z]]
-	[[Category: Xu~~, G L~~]]	+	[[Category: Wang R]]
-	[[Category: Xu, S]]	+	[[Category: Xu GL]]
-	[[Category: Zhu, J]]	+	[[Category: Xu S]]
-	~~[[Category: Decarboxylase]]~~	+	[[Category: Zhu J]]
-	~~[[Category: Dna decarboxylation]]~~	+
-	~~[[Category: Idcase]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Pyrimidine metabolism]]~~	+
-	~~[[Category: Uracil~~]]	+

OCA at 00:16, 5 August 2016

OCA — Fri, 05 Aug 2016 00:16:19 GMT

←Older revision		Revision as of 00:16, 5 August 2016
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-	{{STRUCTURE_4lak\| PDB=4lak \| SCENE= }}
-	===Crystal structure of Cordyceps militaris IDCase D323N mutant in apo form===
-	{{ABSTRACT_PUBMED_23917530}}

-	==~~About this Structure~~==	+	==Crystal structure of Cordyceps militaris IDCase D323N mutant in apo form==
-	[[4lak]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Cormm Cormm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LAK OCA].	+	<StructureSection load='4lak' size='340' side='right' caption='[[4lak]], [[Resolution\|resolution]] 2.41Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4lak]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Cormm Cormm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LAK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4LAK FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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">[[4lal\|4lal]], [[4lam\|4lam]], [[4lan\|4lan]], [[4lao\|4lao]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CCM_01452 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=983644 CORMM])</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=4lak FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lak OCA], [http://pdbe.org/4lak PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4lak RCSB], [http://www.ebi.ac.uk/pdbsum/4lak PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4lak ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	DNA methylation and demethylation regulate many crucial biological processes in mammals and are linked to many diseases. Active DNA demethylation is believed to be catalyzed by TET proteins and a putative DNA decarboxylase that may share some similarities in sequence, structure and catalytic mechanism with isoorotate decarboxylase (IDCase) that catalyzes decarboxylation of 5caU to U in fungi. We report here the structures of wild-type and mutant IDCases from Cordyceps militaris and Metarhizium anisopliae in apo form or in complexes with 5caU, U, and an inhibitor 5-nitro-uracil. IDCases adopt a typical (beta/alpha)8 barrel fold of the amidohydrolase superfamily and function as dimers. A Zn2+ is bound at the active site and coordinated by four strictly conserved residues, one Asp and three His. The substrate is recognized by several strictly conserved residues. The functional roles of the key residues at the active site are validated by mutagenesis and biochemical studies. Based on the structural and biochemical data, we present for the first time a novel catalytic mechanism of decarboxylation for IDCases, which might also apply to other members of the amidohydrolase superfamily. In addition, our biochemical data show that IDCases can catalyze decarboxylation of 5caC to C albeit with weak activity, which is the first in vitro evidence for direct decarboxylation of 5caC to C by an enzyme. These findings are valuable in the identification of potential DNA decarboxylase in mammals.Cell Research advance online publication 6 August 2013; doi:10.1038/cr.2013.107.

-	~~==Reference==~~	+	Crystal structures of isoorotate decarboxylases reveal a novel catalytic mechanism of 5-carboxyl-uracil decarboxylation and shed light on the search for DNA decarboxylase.,Xu S, Li W, Zhu J, Wang R, Li Z, Xu GL, Ding J Cell Res. 2013 Aug 6. doi: 10.1038/cr.2013.107. PMID:23917530<ref>PMID:23917530</ref>
-	<ref ~~group="xtra"~~>PMID:~~023917530~~</ref><~~references group~~="~~xtra~~"/><references/>	+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4lak" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Cormm]]		[[Category: Cormm]]
-	[[Category: Ding, J.]]	+	[[Category: Ding, J]]
-	[[Category: Li, W.]]	+	[[Category: Li, W]]
-	[[Category: Li, Z.]]	+	[[Category: Li, Z]]
-	[[Category: Wang, R.]]	+	[[Category: Wang, R]]
-	[[Category: Xu, G L.]]	+	[[Category: Xu, G L]]
-	[[Category: Xu, S.]]	+	[[Category: Xu, S]]
-	[[Category: Zhu, J.]]	+	[[Category: Zhu, J]]
	[[Category: Decarboxylase]]		[[Category: Decarboxylase]]
	[[Category: Dna decarboxylation]]		[[Category: Dna decarboxylation]]

OCA at 04:22, 13 February 2014

OCA — Thu, 13 Feb 2014 04:22:34 GMT

←Older revision		Revision as of 04:22, 13 February 2014
Line 4:		Line 4:

	==About this Structure==		==About this Structure==
-	[[4lak]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Cordyceps_militaris_cm01 Cordyceps militaris cm01~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LAK OCA].	+	[[4lak]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Cormm Cormm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LAK OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:023917530</ref><references group="xtra"/><references/>		<ref group="xtra">PMID:023917530</ref><references group="xtra"/><references/>
-	[[Category: ~~Cordyceps militaris cm01~~]]	+	[[Category: Cormm]]
	[[Category: Ding, J.]]		[[Category: Ding, J.]]
	[[Category: Li, W.]]		[[Category: Li, W.]]

OCA at 07:22, 2 October 2013

OCA — Wed, 02 Oct 2013 07:22:34 GMT

←Older revision		Revision as of 07:22, 2 October 2013
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4lak\| PDB=4lak \| SCENE= }}
		+	===Crystal structure of Cordyceps militaris IDCase D323N mutant in apo form===
		+	{{ABSTRACT_PUBMED_23917530}}

-	~~The entry~~ 4lak is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
		+	[[4lak]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Cordyceps_militaris_cm01 Cordyceps militaris cm01]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LAK OCA].

-	~~Authors~~: Xu, S., Li, W., ~~Zhu~~, J., ~~Ding~~, J.	+	==Reference==
-		+	<ref group="xtra">PMID:023917530</ref><references group="xtra"/><references/>
-	~~Description~~: ~~Crystal structure of fungi enzyme A D323N mutant~~	+	[[Category: Cordyceps militaris cm01]]
		+	[[Category: Ding, J.]]
		+	[[Category: Li, W.]]
		+	[[Category: Li, Z.]]
		+	[[Category: Wang, R.]]
		+	[[Category: Xu, G L.]]
		+	[[Category: Xu, S.]]
		+	[[Category: Zhu, J.]]
		+	[[Category: Decarboxylase]]
		+	[[Category: Dna decarboxylation]]
		+	[[Category: Idcase]]
		+	[[Category: Lyase]]
		+	[[Category: Pyrimidine metabolism]]
		+	[[Category: Uracil]]

OCA at 20:06, 7 August 2013

OCA — Wed, 07 Aug 2013 20:06:20 GMT

←Older revision		Revision as of 20:06, 7 August 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4lak is ON HOLD	+	The entry 4lak is ON HOLD until Paper Publication

	Authors: Xu, S., Li, W., Zhu, J., Ding, J.		Authors: Xu, S., Li, W., Zhu, J., Ding, J.

	Description: Crystal structure of fungi enzyme A D323N mutant		Description: Crystal structure of fungi enzyme A D323N mutant

OCA at 15:07, 10 July 2013

OCA — Wed, 10 Jul 2013 15:07:46 GMT

←Older revision		Revision as of 15:07, 10 July 2013
Line 3:		Line 3:
	The entry 4lak is ON HOLD		The entry 4lak is ON HOLD

-	Authors: Xu, S, Li, W, Zhu, J, Ding, J	+	Authors: Xu, S., Li, W., Zhu, J., Ding, J.

	Description: Crystal structure of fungi enzyme A D323N mutant		Description: Crystal structure of fungi enzyme A D323N mutant

OCA: Protected "4lak" [edit=sysop:move=sysop]

OCA — Sun, 30 Jun 2013 09:11:08 GMT

Protected "4lak" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:11, 30 June 2013

OCA: New page: '''Unreleased structure''' The entry 4lak is ON HOLD Authors: Xu, S, Li, W, Zhu, J, Ding, J Description: Crystal structure of fungi enzyme A D323N mutant

OCA — Sun, 30 Jun 2013 09:11:06 GMT

New page: '''Unreleased structure''' The entry 4lak is ON HOLD Authors: Xu, S, Li, W, Zhu, J, Ding, J Description: Crystal structure of fungi enzyme A D323N mutant

New page

'''Unreleased structure'''

The entry 4lak is ON HOLD

Authors: Xu, S, Li, W, Zhu, J, Ding, J

Description: Crystal structure of fungi enzyme A D323N mutant