2g6v - Revision history

OCA at 18:49, 10 March 2021

2021-03-10T18:49:14Z

←Older revision		Revision as of 18:49, 10 March 2021
Line 1:		Line 1:

	==The crystal structure of ribD from Escherichia coli==		==The crystal structure of ribD from Escherichia coli==
-	<StructureSection load='2g6v' size='340' side='right' caption='[[2g6v]], [[Resolution\|resolution]] 2.60Å' scene=''>	+	<StructureSection load='2g6v' size='340' side='right'caption='[[2g6v]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2g6v]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2G6V OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2G6V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2g6v]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2G6V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2G6V FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ribD, ribG ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ribD, ribG ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=2g6v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2g6v OCA], [~~http~~://pdbe.org/2g6v PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2g6v RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2g6v PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2g6v 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=2g6v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2g6v OCA], [https://pdbe.org/2g6v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2g6v RCSB], [https://www.ebi.ac.uk/pdbsum/2g6v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2g6v ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/RIBD_ECOLI RIBD_ECOLI]] Converts 2,5-diamino-6-(ribosylamino)-4(3h)-pyrimidinone 5'-phosphate into 5-amino-6-(ribosylamino)-2,4(1h,3h)-pyrimidinedione 5'-phosphate.	+	[[https://www.uniprot.org/uniprot/RIBD_ECOLI RIBD_ECOLI]] Converts 2,5-diamino-6-(ribosylamino)-4(3h)-pyrimidinone 5'-phosphate into 5-amino-6-(ribosylamino)-2,4(1h,3h)-pyrimidinedione 5'-phosphate.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Gurmu, D]]		[[Category: Gurmu, D]]
	[[Category: Moche, M]]		[[Category: Moche, M]]

OCA at 06:53, 20 June 2018

2018-06-20T06:53:50Z

←Older revision		Revision as of 06:53, 20 June 2018
Line 1:		Line 1:
		+
	==The crystal structure of ribD from Escherichia coli==		==The crystal structure of ribD from Escherichia coli==
	<StructureSection load='2g6v' size='340' side='right' caption='[[2g6v]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='2g6v' size='340' side='right' caption='[[2g6v]], [[Resolution\|resolution]] 2.60Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ribD, ribG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ribD, ribG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=2g6v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2g6v OCA], [http://pdbe.org/2g6v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2g6v RCSB], [http://www.ebi.ac.uk/pdbsum/2g6v 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=2g6v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2g6v OCA], [http://pdbe.org/2g6v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2g6v RCSB], [http://www.ebi.ac.uk/pdbsum/2g6v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2g6v ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/g6/2g6v_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/g6/2g6v_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2g6v ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 02:10, 12 September 2015

2015-09-12T02:10:29Z

←Older revision		Revision as of 02:10, 12 September 2015
Line 2:		Line 2:
	<StructureSection load='2g6v' size='340' side='right' caption='[[2g6v]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='2g6v' size='340' side='right' caption='[[2g6v]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2g6v]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia~~ coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2G6V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2G6V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2g6v]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2G6V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2G6V FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ribD, ribG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 ~~Escherichia~~ coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ribD, ribG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=2g6v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2g6v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2g6v RCSB], [http://www.ebi.ac.uk/pdbsum/2g6v 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=2g6v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2g6v OCA], [http://pdbe.org/2g6v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2g6v RCSB], [http://www.ebi.ac.uk/pdbsum/2g6v PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 27:		Line 27:
	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 2g6v" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia~~ coli]]	+	[[Category: Bacillus coli migula 1895]]
	[[Category: Gurmu, D]]		[[Category: Gurmu, D]]
	[[Category: Moche, M]]		[[Category: Moche, M]]

OCA at 22:30, 25 December 2014

2014-12-25T22:30:37Z

←Older revision		Revision as of 22:30, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2g6v]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2G6V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2G6V FirstGlance]. <br>		<table><tr><td colspan='2'>[[2g6v]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2G6V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2G6V FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>	+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ribD, ribG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ribD, ribG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2g6v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2g6v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2g6v RCSB], [http://www.ebi.ac.uk/pdbsum/2g6v 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=2g6v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2g6v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2g6v RCSB], [http://www.ebi.ac.uk/pdbsum/2g6v PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RIBD_ECOLI RIBD_ECOLI]] Converts 2,5-diamino-6-(ribosylamino)-4(3h)-pyrimidinone 5'-phosphate into 5-amino-6-(ribosylamino)-2,4(1h,3h)-pyrimidinedione 5'-phosphate.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 30:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Gurmu, D.]]	+	[[Category: Gurmu, D]]
-	[[Category: Moche, M.]]	+	[[Category: Moche, M]]
-	[[Category: Nordlund, P.]]	+	[[Category: Nordlund, P]]
-	[[Category: SPINE, Structural Proteomics in Europe.]]	+	[[Category: SPINE, Structural Proteomics in Europe]]
-	[[Category: Stenmark, P.]]	+	[[Category: Stenmark, P]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 10:30, 30 September 2014

2014-09-30T10:30:10Z

←Older revision		Revision as of 10:30, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2g6v.~~png~~\|~~left~~\|200px]]	+	==The crystal structure of ribD from Escherichia coli==
		+	<StructureSection load='2g6v' size='340' side='right' caption='[[2g6v]], [[Resolution\|resolution]] 2.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2g6v]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2G6V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2G6V FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ribD, ribG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2g6v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2g6v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2g6v RCSB], [http://www.ebi.ac.uk/pdbsum/2g6v PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/g6/2g6v_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	We have determined the crystal structure of the bi-functional deaminase/reductase enzyme from Escherichia coli (EcRibD) that catalyzes two consecutive reactions during riboflavin biosynthesis. The polypeptide chain of EcRibD is folded into two domains where the 3D structure of the N-terminal domain (1-145) is similar to cytosine deaminase and the C-terminal domain (146-367) is similar to dihydrofolate reductase. We showed that EcRibD is dimeric and compared our structure to tetrameric RibG, an ortholog from Bacillus subtilis (BsRibG). We have also determined the structure of EcRibD in two binary complexes with the oxidized cofactor (NADP(+)) and with the substrate analogue ribose-5-phosphate (RP5) and superposed these two in order to mimic the ternary complex. Based on this superposition we propose that the invariant Asp200 initiates the reductive reaction by abstracting a proton from the bound substrate and that the pro-R proton from C4 of the cofactor is transferred to C1 of the substrate. A highly flexible loop is found in the reductase active site (159-173) that appears to control cofactor and substrate binding to the reductase active site and was therefore compared to the corresponding Met20 loop of E. coli dihydrofolate reductase (EcDHFR). Lys152, identified by comparing substrate analogue (RP5) coordination in the reductase active site of EcRibD with the homologous reductase from Methanocaldococcus jannaschii (MjaRED), is invariant among bacterial RibD enzymes and could contribute to the various pathways taken during riboflavin biosynthesis in bacteria and yeast.

-	~~{{STRUCTURE_2g6v\| PDB=2g6v \| SCENE= }}~~	+	The crystal structure of the bifunctional deaminase/reductase RibD of the riboflavin biosynthetic pathway in Escherichia coli: implications for the reductive mechanism.,Stenmark P, Moche M, Gurmu D, Nordlund P J Mol Biol. 2007 Oct 12;373(1):48-64. Epub 2006 Dec 8. PMID:17765262<ref>PMID:17765262</ref>

-	~~===The crystal structure~~ of ~~ribD from Escherichia coli===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17765262}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2g6v]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Escherichia_coli Escherichia coli]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2G6V OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:017765262<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Gurmu, D.]]		[[Category: Gurmu, D.]]

OCA: Protected "2g6v" [edit=sysop:move=sysop]

2013-01-07T14:57:59Z

Protected "2g6v" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:57, 7 January 2013

OCA at 14:57, 7 January 2013

2013-01-07T14:57:57Z

←Older revision		Revision as of 14:57, 7 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2g6v.png\|left\|200px]]		[[Image:2g6v.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2g6v", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_2g6v\| PDB=2g6v \| SCENE= }}		{{STRUCTURE_2g6v\| PDB=2g6v \| SCENE= }}

	===The crystal structure of ribD from Escherichia coli===		===The crystal structure of ribD from Escherichia coli===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17765262}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17765262 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17765262}}		{{ABSTRACT_PUBMED_17765262}}

	==About this Structure==		==About this Structure==
-	~~2G6V~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2G6V OCA].	+	[[2g6v]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2G6V OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17765262~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017765262</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Gurmu, D.]]		[[Category: Gurmu, D.]]
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	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Structural proteomics in europe]]		[[Category: Structural proteomics in europe]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 09:46:54 2009''

OCA at 07:46, 18 February 2009

2009-02-18T07:46:54Z

←Older revision		Revision as of 07:46, 18 February 2009
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	==About this Structure==		==About this Structure==
-	2G6V is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2G6V OCA].	+	2G6V is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2G6V OCA].

	==Reference==		==Reference==
-	The crystal structure of the bifunctional deaminase/reductase RibD of the riboflavin biosynthetic pathway in Escherichia coli: implications for the reductive mechanism., Stenmark P, Moche M, Gurmu D, Nordlund P, J Mol Biol. 2007 Oct 12;373(1):48-64. Epub 2006 Dec 8. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/17765262 17765262]~~	+	<ref group="xtra">PMID:17765262</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Single protein]]
	[[Category: Gurmu, D.]]		[[Category: Gurmu, D.]]
	[[Category: Moche, M.]]		[[Category: Moche, M.]]
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	[[Category: Structural proteomics in europe]]		[[Category: Structural proteomics in europe]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue Jul 29 16~~:06:~~13 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 09:46:54 2009''

OCA at 13:06, 29 July 2008

2008-07-29T13:06:16Z

←Older revision		Revision as of 13:06, 29 July 2008
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-	[[Image:2g6v.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:2g6v.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_2g6v\| PDB=2g6v \| SCENE= }}		{{STRUCTURE_2g6v\| PDB=2g6v \| SCENE= }}

-	~~'''~~The crystal structure of ribD from Escherichia coli~~'''~~	+	===The crystal structure of ribD from Escherichia coli===


-	~~==Overview==~~	+	<!--
-	~~We have determined the crystal structure of the bi-functional deaminase/reductase enzyme from Escherichia coli (EcRibD) that catalyzes two consecutive reactions during riboflavin biosynthesis.~~ The polypeptide chain of EcRibD is folded into two domains where the 3D structure of the N-terminal domain (1-145) is similar to cytosine deaminase and the C-terminal domain (146-367) is similar to dihydrofolate reductase. We showed that EcRibD is dimeric and compared our structure to tetrameric RibG, ~~an ortholog from Bacillus subtilis (BsRibG). We have also determined~~ the ~~structure of EcRibD in two binary complexes with the oxidized cofactor (NADP(+)) and with the substrate analogue ribose-5-phosphate (RP5) and superposed these two in order~~ to ~~mimic~~ the ternary complex. Based on this superposition we propose that the invariant Asp200 initiates the reductive reaction by abstracting a proton from the bound substrate and that the pro-R proton from C4 of the cofactor is transferred to C1 of the substrate. A highly flexible loop is found in the reductase active site (~~159-173) that~~ appears ~~to control cofactor and substrate binding to the reductase active site and was therefore compared to the corresponding Met20 loop of E~~. ~~coli dihydrofolate reductase (EcDHFR)~~. ~~Lys152, identified by comparing substrate analogue (RP5) coordination in the reductase active site of EcRibD with the homologous reductase from Methanocaldococcus jannaschii (MjaRED~~), is ~~invariant among bacterial RibD enzymes and could contribute to~~ the ~~various pathways taken during riboflavin biosynthesis in bacteria and yeast~~.	+	The line below this paragraph, {{ABSTRACT_PUBMED_17765262}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 17765262 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_17765262}}

	==About this Structure==		==About this Structure==
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	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Structural proteomics in europe]]		[[Category: Structural proteomics in europe]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun Apr 13 08~~:19:22 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 16:06:13 2008''

OCA at 05:19, 13 April 2008

2008-04-13T05:19:22Z

←Older revision		Revision as of 05:19, 13 April 2008
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	[[Image:2g6v.gif\|left\|200px]]		[[Image:2g6v.gif\|left\|200px]]

-	~~{{Structure~~	+	<!--
-	~~\|PDB= 2g6v \|SIZE=350\|CAPTION= <scene name='initialview01'>2g6v</scene>~~, ~~resolution 2~~.~~60Å~~	+	The line below this paragraph, containing "STRUCTURE_2g6v", creates the "Structure Box" on the page.
-	~~\|SITE=~~	+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	~~\|LIGAND= <~~scene ~~name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>~~	+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	~~\|ACTIVITY=~~	+	or leave the SCENE parameter empty for the default display.
-	~~\|GENE= ribD, ribG ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])~~	+	-->
-	~~\|DOMAIN=~~	+	{{STRUCTURE_2g6v\| PDB=2g6v \| SCENE= }}
-	\|~~RELATEDENTRY~~=	+
-	\|~~RESOURCES~~=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2g6v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2g6v OCA], [http://www.ebi.ac.uk/pdbsum/2g6v PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2g6v RCSB]</span>	+
-	}}	+

	'''The crystal structure of ribD from Escherichia coli'''		'''The crystal structure of ribD from Escherichia coli'''
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	[[Category: SPINE, Structural Proteomics in Europe.]]		[[Category: SPINE, Structural Proteomics in Europe.]]
	[[Category: Stenmark, P.]]		[[Category: Stenmark, P.]]
-	[[Category: ~~hydrolase~~]]	+	[[Category: Hydrolase]]
-	[[Category: ~~oxidoreductase~~]]	+	[[Category: Oxidoreductase]]
-	[[Category: ~~ribd~~ apo structure]]	+	[[Category: Ribd apo structure]]
-	[[Category: ~~spine~~]]	+	[[Category: Spine]]
-	[[Category: ~~structural~~ genomic]]	+	[[Category: Structural genomic]]
-	[[Category: ~~structural~~ proteomics in europe]]	+	[[Category: Structural proteomics in europe]]
-		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Apr 13 08:19:22 2008''
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Mar 31 03~~:12:37 2008''	+