4dbf - Revision history

OCA at 13:42, 8 November 2023

2023-11-08T13:42:47Z

← Older revision		Revision as of 13:42, 8 November 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4dbf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Corynebacterium_glutamicum Corynebacterium glutamicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DBF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DBF FirstGlance]. <br>		<table><tr><td colspan='2'>[[4dbf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Corynebacterium_glutamicum Corynebacterium glutamicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DBF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DBF FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.9Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=4dbf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dbf OCA], [https://pdbe.org/4dbf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dbf RCSB], [https://www.ebi.ac.uk/pdbsum/4dbf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dbf 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=4dbf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dbf OCA], [https://pdbe.org/4dbf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dbf RCSB], [https://www.ebi.ac.uk/pdbsum/4dbf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dbf ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/Q8NQY2_CORGL Q8NQY2_CORGL]]		[https://www.uniprot.org/uniprot/Q8NQY2_CORGL Q8NQY2_CORGL]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 08:10, 21 September 2022

2022-09-21T08:10:01Z

← Older revision		Revision as of 08:10, 21 September 2022
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	<StructureSection load='4dbf' size='340' side='right'caption='[[4dbf]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='4dbf' size='340' side='right'caption='[[4dbf]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4dbf]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"micrococcus_glutamicus"_kinoshita_et_al._1958 "micrococcus glutamicus" kinoshita et al. 1958~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DBF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4DBF FirstGlance]. <br>		<table><tr><td colspan='2'>[[4dbf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Corynebacterium_glutamicum Corynebacterium glutamicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DBF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DBF FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>~~</td></tr>~~		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4dbh\|4dbh]]~~</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=4dbf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dbf OCA], [https://pdbe.org/4dbf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dbf RCSB], [https://www.ebi.ac.uk/pdbsum/4dbf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dbf 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=4dbf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dbf OCA], [~~http~~://pdbe.org/4dbf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4dbf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4dbf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4dbf ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[[https://www.uniprot.org/uniprot/Q8NQY2_CORGL Q8NQY2_CORGL]]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Micrococcus glutamicus kinoshita et al. 1958~~]]		[[Category: Corynebacterium glutamicum]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Gao~~, Y Y~~]]		[[Category: Gao YY]]
	[[Category: Ran~~, T T~~]]		[[Category: Ran TT]]
	[[Category: Wang~~, M T~~]]		[[Category: Wang MT]]
	[[Category: Wang~~, W W~~]]		[[Category: Wang WW]]
	[[Category: Xu~~, D Q]]~~		[[Category: Xu DQ]]
	~~[[Category: Isomerase]]~~
	~~[[Category: Oxaloacetate decarboxylase~~]]

OCA at 07:49, 27 March 2019

2019-03-27T07:49:24Z

← Older revision		Revision as of 07:49, 27 March 2019
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	==Crystal structures of Cg1458==		==Crystal structures of Cg1458==
	<StructureSection load='4dbf' size='340' side='right' caption='[[4dbf]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='4dbf' size='340' side='right'caption='[[4dbf]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4dbf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_glutamicus"_kinoshita_et_al._1958 "micrococcus glutamicus" kinoshita et al. 1958]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DBF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DBF FirstGlance]. <br>		<table><tr><td colspan='2'>[[4dbf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_glutamicus"_kinoshita_et_al._1958 "micrococcus glutamicus" kinoshita et al. 1958]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DBF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DBF FirstGlance]. <br>
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	</StructureSection>		</StructureSection>
	[[Category: Micrococcus glutamicus kinoshita et al. 1958]]		[[Category: Micrococcus glutamicus kinoshita et al. 1958]]
			[[Category: Large Structures]]
	[[Category: Gao, Y Y]]		[[Category: Gao, Y Y]]
	[[Category: Ran, T T]]		[[Category: Ran, T T]]

OCA at 02:55, 11 December 2016

2016-12-11T02:55:02Z

← Older revision		Revision as of 02:55, 11 December 2016
Line 1:		Line 1:

	==Crystal structures of Cg1458==		==Crystal structures of Cg1458==
	<StructureSection load='4dbf' size='340' side='right' caption='[[4dbf]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='4dbf' size='340' side='right' caption='[[4dbf]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4dbf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Corynebacterium_glutamicum Corynebacterium glutamicum~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DBF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DBF FirstGlance]. <br>		<table><tr><td colspan='2'>[[4dbf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_glutamicus"_kinoshita_et_al._1958 "micrococcus glutamicus" kinoshita et al. 1958]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DBF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DBF FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4dbh\|4dbh]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4dbh\|4dbh]]</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=4dbf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dbf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4dbf RCSB], [http://www.ebi.ac.uk/pdbsum/4dbf 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=4dbf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dbf OCA], [http://pdbe.org/4dbf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4dbf RCSB], [http://www.ebi.ac.uk/pdbsum/4dbf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4dbf ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	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 4dbf" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Corynebacterium glutamicum~~]]		[[Category: Micrococcus glutamicus kinoshita et al. 1958]]
	[[Category: Gao, Y Y]]		[[Category: Gao, Y Y]]
	[[Category: Ran, T T]]		[[Category: Ran, T T]]

OCA at 15:24, 9 December 2014

2014-12-09T15:24:38Z

← Older revision		Revision as of 15:24, 9 December 2014
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	[[~~Image~~:~~4dbf~~.~~jpg~~\|~~left~~\|~~200px~~]]		==Crystal structures of Cg1458==
			<StructureSection load='4dbf' size='340' side='right' caption='[[4dbf]], [[Resolution\|resolution]] 1.90Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[4dbf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Corynebacterium_glutamicum Corynebacterium glutamicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DBF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DBF FirstGlance]. <br>
			</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
			<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4dbh\|4dbh]]</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=4dbf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dbf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4dbf RCSB], [http://www.ebi.ac.uk/pdbsum/4dbf PDBsum]</span></td></tr>
			</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Cg1458 was recently characterized as a novel soluble oxaloacetate decarboxylase. However, sequence alignment identified that Cg1458 has no similarity with other oxaloacetate decarboxylases and instead belongs to the fumarylacetoacetate hydrolase (FAH) family. Differences in the function of Cg1458 and other FAH proteins may suggest a different catalytic mechanism. To help elucidate the catalytic mechanism of Cg1458, crystal structures of Cg1458 in both the open and closed conformations have been determined for the first time up to a resolution of 1.9 A and 2.0 A, respectively. Comparison of both structures and detailed biochemical studies confirmed the presence of a catalytic lid domain which is missing in the native enzyme structure. In this lid domain, a Glu-His dyad was found critical in mediating enzymatic catalysis. Based on structure modeling and comparison as well as large-scale sequence alignment studies, we further determined that the catalytic mechanism of Cg1458 is actually through a Glu-His-Water triad, and this catalytic triad is common among FAH family proteins that catalyze the cleavage of the C-C bond of the substrate. Two sequence motifs, HxxE and Hxx***xxE have been identified as the basis for this mechanism.

	~~{{STRUCTURE_4dbf\| PDB=4dbf \| SCENE= }}~~		Crystal structures of Cg1458 reveal a catalytic lid domain and a common catalytic mechanism for FAH family.,Ran T, Gao Y, Marsh M, Zhu W, Wang M, Mao X, Xu L, Xu D, Wang W Biochem J. 2012 Oct 10. PMID:23046410<ref>PMID:23046410</ref>

	~~===Crystal structures~~ of ~~Cg1458===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_23046410}}~~		== References ==
			<references/>
	==~~About this Structure~~==		__TOC__
	~~[[4dbf]] is a 2 chain structure with sequence from [http:~~//~~en.wikipedia.org/wiki/Corynebacterium_glutamicum Corynebacterium glutamicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DBF OCA].~~		</StructureSection>
	[[Category: Corynebacterium glutamicum]]		[[Category: Corynebacterium glutamicum]]
	[[Category: Gao, Y Y.]]		[[Category: Gao, Y Y]]
	[[Category: Ran, T T.]]		[[Category: Ran, T T]]
	[[Category: Wang, M T.]]		[[Category: Wang, M T]]
	[[Category: Wang, W W.]]		[[Category: Wang, W W]]
	[[Category: Xu, D Q.]]		[[Category: Xu, D Q]]
	[[Category: Isomerase]]		[[Category: Isomerase]]
	[[Category: Oxaloacetate decarboxylase]]		[[Category: Oxaloacetate decarboxylase]]

OCA at 14:32, 28 November 2012

2012-11-28T14:32:00Z

← Older revision		Revision as of 14:32, 28 November 2012
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	~~'''Unreleased structure'''~~		[[Image:4dbf.jpg\|left\|200px]]

	~~The entry~~ 4dbf ~~is ON HOLD~~ ~~until Paper Publication~~		{{STRUCTURE_4dbf\| PDB=4dbf \| SCENE= }}

	~~Authors: Ran, T.T., Xu, D.Q., Wang, W.W., Gao, Y.Y., Wang, M.T.~~		===Crystal structures of Cg1458===

	~~Description~~: ~~Crystal structures of Cg1458~~		{{ABSTRACT_PUBMED_23046410}}

			==About this Structure==
			[[4dbf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Corynebacterium_glutamicum Corynebacterium glutamicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DBF OCA].
			[[Category: Corynebacterium glutamicum]]
			[[Category: Gao, Y Y.]]
			[[Category: Ran, T T.]]
			[[Category: Wang, M T.]]
			[[Category: Wang, W W.]]
			[[Category: Xu, D Q.]]
			[[Category: Isomerase]]
			[[Category: Oxaloacetate decarboxylase]]

OCA at 05:22, 30 May 2012

2012-05-30T05:22:18Z

← Older revision		Revision as of 05:22, 30 May 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 4dbf is ON HOLD		The entry 4dbf is ON HOLD until Paper Publication

	Authors: Ran, T.T., Xu, D.Q., Wang, W.W., Gao, Y.Y., Wang, M.T.		Authors: Ran, T.T., Xu, D.Q., Wang, W.W., Gao, Y.Y., Wang, M.T.

	Description: Crystal structures of Cg1458		Description: Crystal structures of Cg1458

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

2012-01-25T06:10:31Z

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

← Older revision	Revision as of 06:10, 25 January 2012
(No difference)

OCA: New page: '''Unreleased structure''' The entry 4dbf is ON HOLD Authors: Ran, T.T., Xu, D.Q., Wang, W.W., Gao, Y.Y., Wang, M.T. Description: Crystal structures of Cg1458

2012-01-25T06:10:30Z

New page: '''Unreleased structure''' The entry 4dbf is ON HOLD Authors: Ran, T.T., Xu, D.Q., Wang, W.W., Gao, Y.Y., Wang, M.T. Description: Crystal structures of Cg1458

New page

'''Unreleased structure'''

The entry 4dbf is ON HOLD

Authors: Ran, T.T., Xu, D.Q., Wang, W.W., Gao, Y.Y., Wang, M.T.

Description: Crystal structures of Cg1458