4n2x - Revision history

OCA at 08:56, 20 March 2024

OCA — Wed, 20 Mar 2024 08:56:32 GMT

←Older revision		Revision as of 08:56, 20 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4n2x]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Methylobacterium_sp._CPA1 Methylobacterium sp. CPA1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4N2X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4N2X FirstGlance]. <br>		<table><tr><td colspan='2'>[[4n2x]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Methylobacterium_sp._CPA1 Methylobacterium sp. CPA1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4N2X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4N2X FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 1.7Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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=4n2x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4n2x OCA], [https://pdbe.org/4n2x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4n2x RCSB], [https://www.ebi.ac.uk/pdbsum/4n2x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4n2x 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=4n2x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4n2x OCA], [https://pdbe.org/4n2x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4n2x RCSB], [https://www.ebi.ac.uk/pdbsum/4n2x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4n2x ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/A6BM74_9HYPH A6BM74_9HYPH]		[https://www.uniprot.org/uniprot/A6BM74_9HYPH A6BM74_9HYPH]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Several pathways of biotic dechlorination can be found in enzymes, each characterized by different chlorine isotopic fractionation, which can thus serve as a signature of a particular mechanism. Unlike other dehalogenases, DL-2-haloacid dehalogenase, DL-DEX, converts both enantiomers of the substrate. Chlorine isotope effects for this enzyme are larger than in the case of other dehalogenases. Recently, the 3D structure of this enzyme became available and enabled us to model these isotope effects and seek their origin. We show that the elevated values of the chlorine kinetic isotope effects originate in part in the processes of binding and migration within the enzyme active site that precede the dehalogenation step.
-
-	Binding modes of DL-2-haloacid dehalogenase revealed by crystallography, modeling and isotope effects studies.,Siwek A, Omi R, Hirotsu K, Jitsumori K, Esaki N, Kurihara T, Paneth P Arch Biochem Biophys. 2013 Sep 23;540(1-2):26-32. doi: 10.1016/j.abb.2013.09.012. PMID:24071515<ref>PMID:24071515</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4n2x" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Dehalogenase 3D structures\|Dehalogenase 3D structures]]		*[[Dehalogenase 3D structures\|Dehalogenase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 10:28, 28 December 2022

OCA — Wed, 28 Dec 2022 10:28:58 GMT

←Older revision		Revision as of 10:28, 28 December 2022
Line 1:		Line 1:

	==Crystal Structure of DL-2-haloacid dehalogenase==		==Crystal Structure of DL-2-haloacid dehalogenase==
-	<StructureSection load='4n2x' size='340' side='right' caption='[[4n2x]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='4n2x' size='340' side='right'caption='[[4n2x]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4n2x]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Methylobacterium_sp.~~_cpa1~~ Methylobacterium sp. ~~cpa1~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4N2X OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4N2X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4n2x]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Methylobacterium_sp._CPA1 Methylobacterium sp. CPA1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4N2X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4N2X FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dl-dex ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=439332 Methylobacterium sp. CPA1])</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=4n2x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4n2x OCA], [https://pdbe.org/4n2x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4n2x RCSB], [https://www.ebi.ac.uk/pdbsum/4n2x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4n2x ProSAT]</span></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2-haloacid_dehalogenase_(configuration-inverting) 2-haloacid dehalogenase (configuration-inverting)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.8.1.10 3.8.1.10] </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=4n2x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4n2x OCA], [~~http~~://pdbe.org/4n2x PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4n2x RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4n2x PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4n2x ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A6BM74_9HYPH A6BM74_9HYPH]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 20:

	==See Also==		==See Also==
-	*[[Dehalogenase\|Dehalogenase]]	+	*[[Dehalogenase 3D structures\|Dehalogenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Methylobacterium sp. ~~cpa1~~]]	+	[[Category: Large Structures]]
-	[[Category: Esaki, N]]	+	[[Category: Methylobacterium sp. CPA1]]
-	[[Category: Hirotsu, K]]	+	[[Category: Esaki N]]
-	[[Category: Jitsumori, K]]	+	[[Category: Hirotsu K]]
-	[[Category: Kurihara, T]]	+	[[Category: Jitsumori K]]
-	[[Category: Omi, R]]	+	[[Category: Kurihara T]]
-	[[Category: Paneth, P]]	+	[[Category: Omi R]]
-	[[Category: Siwek, A]]	+	[[Category: Paneth P]]
-	~~[[Category: Dehalogenase]]~~	+	[[Category: Siwek A]]
-	~~[[Category: Hydrolase~~]]	+

OCA at 20:58, 11 August 2016

OCA — Thu, 11 Aug 2016 20:58:18 GMT

←Older revision		Revision as of 20:58, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal Structure of DL-2-haloacid dehalogenase==		==Crystal Structure of DL-2-haloacid dehalogenase==
	<StructureSection load='4n2x' size='340' side='right' caption='[[4n2x]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='4n2x' size='340' side='right' caption='[[4n2x]], [[Resolution\|resolution]] 1.70Å' scene=''>
Line 6:		Line 7:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dl-dex ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=439332 Methylobacterium sp. CPA1])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dl-dex ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=439332 Methylobacterium sp. CPA1])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2-haloacid_dehalogenase_(configuration-inverting) 2-haloacid dehalogenase (configuration-inverting)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.8.1.10 3.8.1.10] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2-haloacid_dehalogenase_(configuration-inverting) 2-haloacid dehalogenase (configuration-inverting)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.8.1.10 3.8.1.10] </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=4n2x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4n2x OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4n2x RCSB], [http://www.ebi.ac.uk/pdbsum/4n2x PDBsum]</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=4n2x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4n2x OCA], [http://pdbe.org/4n2x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4n2x RCSB], [http://www.ebi.ac.uk/pdbsum/4n2x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4n2x ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4n2x" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 09:33, 5 January 2015

OCA — Mon, 05 Jan 2015 09:33:32 GMT

←Older revision		Revision as of 09:33, 5 January 2015
Line 1:		Line 1:
-	~~{{STRUCTURE_4n2x~~\| ~~PDB~~=4n2x \| ~~SCENE~~= }}	+	==Crystal Structure of DL-2-haloacid dehalogenase==
-	===~~Crystal Structure of DL~~-2-haloacid dehalogenase===	+	<StructureSection load='4n2x' size='340' side='right' caption='[[4n2x]], [[Resolution\|resolution]] 1.70Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24071515}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4n2x]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Methylobacterium_sp._cpa1 Methylobacterium sp. cpa1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4N2X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4N2X FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dl-dex ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=439332 Methylobacterium sp. CPA1])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2-haloacid_dehalogenase_(configuration-inverting) 2-haloacid dehalogenase (configuration-inverting)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.8.1.10 3.8.1.10] </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=4n2x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4n2x OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4n2x RCSB], [http://www.ebi.ac.uk/pdbsum/4n2x PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Several pathways of biotic dechlorination can be found in enzymes, each characterized by different chlorine isotopic fractionation, which can thus serve as a signature of a particular mechanism. Unlike other dehalogenases, DL-2-haloacid dehalogenase, DL-DEX, converts both enantiomers of the substrate. Chlorine isotope effects for this enzyme are larger than in the case of other dehalogenases. Recently, the 3D structure of this enzyme became available and enabled us to model these isotope effects and seek their origin. We show that the elevated values of the chlorine kinetic isotope effects originate in part in the processes of binding and migration within the enzyme active site that precede the dehalogenation step.

-	~~==About this Structure==~~	+	Binding modes of DL-2-haloacid dehalogenase revealed by crystallography, modeling and isotope effects studies.,Siwek A, Omi R, Hirotsu K, Jitsumori K, Esaki N, Kurihara T, Paneth P Arch Biochem Biophys. 2013 Sep 23;540(1-2):26-32. doi: 10.1016/j.abb.2013.09.012. PMID:24071515<ref>PMID:24071515</ref>
-	~~[[4n2x]] is a 6 chain structure~~. ~~Full crystallographic information is available from [http~~:/~~/oca~~.~~weizmann~~.ac.~~il/oca-bin/ocashort?id=4N2X OCA]~~.	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group~~=~~"xtra">PMID:024071515</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
-	[[Category: Esaki, N.]]	+
-	[[Category: Hirotsu, K.]]	+	==See Also==
-	[[Category: Jitsumori, K.]]	+	*[[Dehalogenase\|Dehalogenase]]
-	[[Category: Kurihara, T.]]	+	== References ==
-	[[Category: Omi, R.]]	+	<references/>
-	[[Category: Paneth, P.]]	+	__TOC__
-	[[Category: Siwek, A.]]	+	</StructureSection>
		+	[[Category: Methylobacterium sp. cpa1]]
		+	[[Category: Esaki, N]]
		+	[[Category: Hirotsu, K]]
		+	[[Category: Jitsumori, K]]
		+	[[Category: Kurihara, T]]
		+	[[Category: Omi, R]]
		+	[[Category: Paneth, P]]
		+	[[Category: Siwek, A]]
	[[Category: Dehalogenase]]		[[Category: Dehalogenase]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 10:19, 27 November 2013

OCA — Wed, 27 Nov 2013 10:19:44 GMT

←Older revision		Revision as of 10:19, 27 November 2013
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4n2x\| PDB=4n2x \| SCENE= }}
		+	===Crystal Structure of DL-2-haloacid dehalogenase===
		+	{{ABSTRACT_PUBMED_24071515}}

-	~~The entry~~ 4n2x is ~~ON HOLD~~	+	==About this Structure==
		+	[[4n2x]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4N2X OCA].

-	~~Authors~~: ~~Siwek~~, A.~~, Omi, R.,~~ Hirotsu, K., Jitsumori, K.~~, Esaki, N.,~~ Kurihara, T., Paneth, O.	+	==Reference==
-		+	<ref group="xtra">PMID:024071515</ref><references group="xtra"/><references/>
-	~~Description~~: ~~Crystal Structure of DL-2-haloacid dehalogenase~~	+	[[Category: Esaki, N.]]
		+	[[Category: Hirotsu, K.]]
		+	[[Category: Jitsumori, K.]]
		+	[[Category: Kurihara, T.]]
		+	[[Category: Omi, R.]]
		+	[[Category: Paneth, P.]]
		+	[[Category: Siwek, A.]]
		+	[[Category: Dehalogenase]]
		+	[[Category: Hydrolase]]

OCA at 06:14, 23 October 2013

OCA — Wed, 23 Oct 2013 06:14:05 GMT

←Older revision		Revision as of 06:14, 23 October 2013
Line 3:		Line 3:
	The entry 4n2x is ON HOLD		The entry 4n2x is ON HOLD

-	Authors: ~~Agata~~ Siwek, ~~Rie~~ Omi, ~~Ken~~ Hirotsu, ~~Keiji~~ Jitsumori, ~~Noboyoshi~~ Esaki, ~~Tetsuo~~ Kurihara, ~~Piotr~~ Paneth	+	Authors: Siwek, A., Omi, R., Hirotsu, K., Jitsumori, K., Esaki, N., Kurihara, T., Paneth, O.

	Description: Crystal Structure of DL-2-haloacid dehalogenase		Description: Crystal Structure of DL-2-haloacid dehalogenase

OCA: Protected "4n2x" [edit=sysop:move=sysop]

OCA — Wed, 16 Oct 2013 07:32:54 GMT

Protected "4n2x" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:32, 16 October 2013

OCA: New page: '''Unreleased structure''' The entry 4n2x is ON HOLD Authors: Agata Siwek, Rie Omi, Ken Hirotsu, Keiji Jitsumori, Noboyoshi Esaki, Tetsuo Kurihara, Piotr Paneth Description: Crystal St...

OCA — Wed, 16 Oct 2013 07:32:53 GMT

New page: '''Unreleased structure''' The entry 4n2x is ON HOLD Authors: Agata Siwek, Rie Omi, Ken Hirotsu, Keiji Jitsumori, Noboyoshi Esaki, Tetsuo Kurihara, Piotr Paneth Description: Crystal St...

New page

'''Unreleased structure'''

The entry 4n2x is ON HOLD

Authors: Agata Siwek, Rie Omi, Ken Hirotsu, Keiji Jitsumori, Noboyoshi Esaki, Tetsuo Kurihara, Piotr Paneth

Description: Crystal Structure of DL-2-haloacid dehalogenase