2obc - Revision history

OCA at 08:57, 25 October 2023

OCA — Wed, 25 Oct 2023 08:57:07 GMT

←Older revision		Revision as of 08:57, 25 October 2023
Line 3:		Line 3:
	<StructureSection load='2obc' size='340' side='right'caption='[[2obc]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='2obc' size='340' side='right'caption='[[2obc]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2obc]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OBC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OBC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2obc]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OBC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OBC FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=RP5:5~~-~~O-PHOSPHONO-BETA-D-RIBOFURANOSE'>RP5</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]] 3Å</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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=RP5:5-O-PHOSPHONO-BETA-D-RIBOFURANOSE'>RP5</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b></td><td class="sblockDat"><div style='overflow: auto; max~~-~~height: 3em;~~'>~~[[2g6v\|2g6v]]~~</~~div~~>~~</td></tr>~~	+
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ribD ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])~~</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=2obc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2obc OCA], [https://pdbe.org/2obc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2obc RCSB], [https://www.ebi.ac.uk/pdbsum/2obc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2obc 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=2obc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2obc OCA], [https://pdbe.org/2obc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2obc RCSB], [https://www.ebi.ac.uk/pdbsum/2obc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2obc ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[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.	+	[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 35:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Ecoli~~]]	+	[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[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: Stenmark P]]
-	[[Category: Stenmark, P]]	+
-	~~[[Category: Alpha and beta class of proteins with mainly parallell strand]]~~	+
-	~~[[Category: Htp escherichia coli protein]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Spine]]~~	+
-	~~[[Category: Structural genomic]]~~	+
-	~~[[Category: Structural proteomics in europe~~]]	+

OCA at 12:51, 9 June 2021

OCA — Wed, 09 Jun 2021 12:51:50 GMT

←Older revision		Revision as of 12:51, 9 June 2021
Line 1:		Line 1:

	==The crystal structure of RibD from Escherichia coli in complex with a substrate analogue, ribose 5-phosphate (beta form), bound to the active site of the reductase domain==		==The crystal structure of RibD from Escherichia coli in complex with a substrate analogue, ribose 5-phosphate (beta form), bound to the active site of the reductase domain==
-	<StructureSection load='2obc' size='340' side='right' caption='[[2obc]], [[Resolution\|resolution]] 3.00Å' scene=''>	+	<StructureSection load='2obc' size='340' side='right'caption='[[2obc]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2obc]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OBC OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2OBC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2obc]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OBC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OBC FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=RP5:5-O-PHOSPHONO-BETA-D-RIBOFURANOSE'>RP5</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=RP5:5-O-PHOSPHONO-BETA-D-RIBOFURANOSE'>RP5</scene></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='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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2g6v\|2g6v]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2g6v\|2g6v]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ribD ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ribD ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=2obc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2obc OCA], [~~http~~://pdbe.org/2obc PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2obc RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2obc PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2obc 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=2obc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2obc OCA], [https://pdbe.org/2obc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2obc RCSB], [https://www.ebi.ac.uk/pdbsum/2obc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2obc 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]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ob/2obc_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ob/2obc_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>
Line 36:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Ecoli]]		[[Category: Ecoli]]
		+	[[Category: Large Structures]]
	[[Category: Gurmu, D]]		[[Category: Gurmu, D]]
	[[Category: Moche, M]]		[[Category: Moche, M]]

OCA at 17:31, 9 March 2017

OCA — Thu, 09 Mar 2017 17:31:57 GMT

←Older revision		Revision as of 17:31, 9 March 2017
Line 1:		Line 1:
		+
	==The crystal structure of RibD from Escherichia coli in complex with a substrate analogue, ribose 5-phosphate (beta form), bound to the active site of the reductase domain==		==The crystal structure of RibD from Escherichia coli in complex with a substrate analogue, ribose 5-phosphate (beta form), bound to the active site of the reductase domain==
	<StructureSection load='2obc' size='340' side='right' caption='[[2obc]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='2obc' size='340' side='right' caption='[[2obc]], [[Resolution\|resolution]] 3.00Å' scene=''>
Line 7:		Line 8:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2g6v\|2g6v]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2g6v\|2g6v]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ribD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ribD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=2obc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2obc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2obc RCSB], [http://www.ebi.ac.uk/pdbsum/2obc 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=2obc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2obc OCA], [http://pdbe.org/2obc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2obc RCSB], [http://www.ebi.ac.uk/pdbsum/2obc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2obc ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	<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=2obc ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 29:		Line 30:
	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 2obc" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:44, 3 June 2015

OCA — Wed, 03 Jun 2015 06:44:43 GMT

←Older revision		Revision as of 06:44, 3 June 2015
Line 2:		Line 2:
	<StructureSection load='2obc' size='340' side='right' caption='[[2obc]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='2obc' size='340' side='right' caption='[[2obc]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2obc]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli_k-12 Escherichia coli k-12~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OBC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OBC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2obc]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OBC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OBC FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=RP5:5-O-PHOSPHONO-BETA-D-RIBOFURANOSE'>RP5</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=RP5:5-O-PHOSPHONO-BETA-D-RIBOFURANOSE'>RP5</scene></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='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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2g6v\|2g6v]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2g6v\|2g6v]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ribD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ~~Escherichia coli K-12~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ribD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=2obc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2obc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2obc RCSB], [http://www.ebi.ac.uk/pdbsum/2obc 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=2obc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2obc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2obc RCSB], [http://www.ebi.ac.uk/pdbsum/2obc PDBsum]</span></td></tr>
	</table>		</table>
Line 21:		Line 21:
	</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/chain_selection.php?pdb_ID=2ata ConSurf].
	<div style="clear:both"></div>		<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.
		+
		+	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>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia coli k-12~~]]	+	[[Category: Ecoli]]
	[[Category: Gurmu, D]]		[[Category: Gurmu, D]]
	[[Category: Moche, M]]		[[Category: Moche, M]]

OCA at 14:46, 25 December 2014

OCA — Thu, 25 Dec 2014 14:46:27 GMT

←Older revision		Revision as of 14:46, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2obc]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OBC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OBC FirstGlance]. <br>		<table><tr><td colspan='2'>[[2obc]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OBC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OBC FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=RP5:5-O-PHOSPHONO-BETA-D-RIBOFURANOSE'>RP5</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=RP5:5-O-PHOSPHONO-BETA-D-RIBOFURANOSE'>RP5</scene></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 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>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2g6v\|2g6v]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2g6v\|2g6v]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ribD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 Escherichia coli K-12])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ribD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 Escherichia coli K-12])</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=2obc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2obc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2obc RCSB], [http://www.ebi.ac.uk/pdbsum/2obc 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=2obc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2obc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2obc RCSB], [http://www.ebi.ac.uk/pdbsum/2obc 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 22:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Escherichia coli k-12]]		[[Category: Escherichia coli k-12]]
-	[[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: Alpha and beta class of proteins with mainly parallell strand]]		[[Category: Alpha and beta class of proteins with mainly parallell strand]]
	[[Category: Htp escherichia coli protein]]		[[Category: Htp escherichia coli protein]]

OCA at 20:00, 30 September 2014

OCA — Tue, 30 Sep 2014 20:00:20 GMT

←Older revision		Revision as of 20:00, 30 September 2014
Line 1:		Line 1:
-	~~[[Image:2obc.png\|left\|200px]]~~	+	==The crystal structure of RibD from Escherichia coli in complex with a substrate analogue, ribose 5-phosphate (beta form), bound to the active site of the reductase domain==
-		+	<StructureSection load='2obc' size='340' side='right' caption='[[2obc]], [[Resolution\|resolution]] 3.00Å' scene=''>
-	~~{{STRUCTURE_2obc\| PDB=2obc \| SCENE= }}~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[2obc]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OBC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OBC FirstGlance]. <br>
-	===The crystal structure of RibD from Escherichia coli in complex with a substrate analogue, ribose 5-phosphate (beta form), bound to the active site of the reductase domain===	+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=RP5:5-O-PHOSPHONO-BETA-D-RIBOFURANOSE'>RP5</scene><br>
-		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	~~{{ABSTRACT_PUBMED_017765262}}~~	+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2g6v\|2g6v]]</td></tr>
-		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ribD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 Escherichia coli K-12])</td></tr>
-	==~~About this Structure~~==	+	<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=2obc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2obc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2obc RCSB], [http://www.ebi.ac.uk/pdbsum/2obc PDBsum]</span></td></tr>
-	[[2obc]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OBC OCA].	+	<table>
-		+	== Evolutionary Conservation ==
-	==~~Reference~~==	+	[[Image:Consurf_key_small.gif\|200px\|right]]
-	<~~ref group~~="~~xtra~~">~~PMID~~:~~017765262~~</~~ref~~><~~references group~~="~~xtra~~"/>	+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ob/2obc_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>
		+	__TOC__
		+	</StructureSection>
	[[Category: Escherichia coli k-12]]		[[Category: Escherichia coli k-12]]
	[[Category: Gurmu, D.]]		[[Category: Gurmu, D.]]

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

OCA — Mon, 07 Jan 2013 15:00:06 GMT

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

←Older revision

Revision as of 15:00, 7 January 2013

OCA at 15:00, 7 January 2013

OCA — Mon, 07 Jan 2013 15:00:04 GMT

←Older revision		Revision as of 15:00, 7 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2obc.png\|left\|200px]]		[[Image:2obc.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2obc", 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_2obc\| PDB=2obc \| SCENE= }}		{{STRUCTURE_2obc\| PDB=2obc \| SCENE= }}

	===The crystal structure of RibD from Escherichia coli in complex with a substrate analogue, ribose 5-phosphate (beta form), bound to the active site of the reductase domain===		===The crystal structure of RibD from Escherichia coli in complex with a substrate analogue, ribose 5-phosphate (beta form), bound to the active site of the reductase domain===

		+	{{ABSTRACT_PUBMED_017765262}}

	==About this Structure==		==About this Structure==
-	~~2OBC~~ 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=2OBC OCA].	+	[[2obc]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OBC OCA].
-	[[Category: Escherichia coli]]	+
		+	==Reference==
		+	<ref group="xtra">PMID:017765262</ref><references group="xtra"/>
		+	[[Category: Escherichia coli k-12]]
	[[Category: Gurmu, D.]]		[[Category: Gurmu, D.]]
	[[Category: Moche, M.]]		[[Category: Moche, M.]]
Line 23:		Line 20:
	[[Category: Alpha and beta class of proteins with mainly parallell strand]]		[[Category: Alpha and beta class of proteins with mainly parallell strand]]
	[[Category: Htp escherichia coli protein]]		[[Category: Htp escherichia coli protein]]
		+	[[Category: Hydrolase]]
		+	[[Category: Oxidoreductase]]
	[[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 Tue Feb 17 19:04:27 2009''

OCA at 17:04, 17 February 2009

OCA — Tue, 17 Feb 2009 17:04:29 GMT

←Older revision		Revision as of 17:04, 17 February 2009
Line 1:		Line 1:
-	[[Image:2obc.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:2obc.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_2obc\| PDB=2obc \| SCENE= }}		{{STRUCTURE_2obc\| PDB=2obc \| SCENE= }}

-	~~'''~~The crystal structure of RibD from Escherichia coli in complex with a substrate analogue, ribose 5-phosphate (beta form), bound to the active site of the reductase domain~~'''~~	+	===The crystal structure of RibD from Escherichia coli in complex with a substrate analogue, ribose 5-phosphate (beta form), bound to the active site of the reductase domain===


	==About this Structure==		==About this Structure==
-	2OBC 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=2OBC OCA].	+	2OBC 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=2OBC OCA].
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Single protein]]
	[[Category: Gurmu, D.]]		[[Category: Gurmu, D.]]
	[[Category: Moche, M.]]		[[Category: Moche, M.]]
Line 26:		Line 26:
	[[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~~:20:~~46 2008~~''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 19:04:27 2009''

OCA at 05:20, 13 April 2008

OCA — Sun, 13 Apr 2008 05:20:47 GMT

←Older revision		Revision as of 05:20, 13 April 2008
Line 1:		Line 1:
	[[Image:2obc.gif\|left\|200px]]		[[Image:2obc.gif\|left\|200px]]

-	{{Structure	+	<!--
-	\|PDB~~= 2obc \|SIZE=350\|CAPTION= <~~scene ~~name='initialview01'>2obc</scene>~~, ~~resolution 3~~.~~00Å~~	+	The line below this paragraph, containing "STRUCTURE_2obc", 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>, <scene name='pdbligand=RP5:RIBOSE~~-5-~~PHOSPHATE,+PYRANOSE+FORM'>RP5</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 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])~~	+	-->
-	~~\|DOMAIN=~~	+	{{STRUCTURE_2obc\| PDB=2obc \| SCENE= }}
-	~~\|RELATEDENTRY=[[2g6v\|2G6V]]~~	+
-	\|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2obc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2obc OCA], [http://www.ebi.ac.uk/pdbsum/2obc PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2obc RCSB]</span>	+
-	}}	+

	'''The crystal structure of RibD from Escherichia coli in complex with a substrate analogue, ribose 5-phosphate (beta form), bound to the active site of the reductase domain'''		'''The crystal structure of RibD from Escherichia coli in complex with a substrate analogue, ribose 5-phosphate (beta form), bound to the active site of the reductase domain'''
Line 24:		Line 21:
	[[Category: SPINE, Structural Proteomics in Europe.]]		[[Category: SPINE, Structural Proteomics in Europe.]]
	[[Category: Stenmark, P.]]		[[Category: Stenmark, P.]]
-	[[Category: ~~alpha~~ and beta class of proteins with mainly parallell strand]]	+	[[Category: Alpha and beta class of proteins with mainly parallell strand]]
-	[[Category: ~~beta-form)]]~~	+	[[Category: Htp escherichia coli protein]]
-	~~[[Category: htp~~ escherichia coli protein]]	+	[[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 08:20:46 2008''
-	~~[[Category: substrate analogue complex (ribose 5-phosphate]]~~	+
-		+
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Mar 31 04~~:15:23 2008''	+