1r8g - Revision history

OCA at 06:10, 17 April 2024

2024-04-17T06:10:26Z

←Older revision		Revision as of 06:10, 17 April 2024
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	<StructureSection load='1r8g' size='340' side='right'caption='[[1r8g]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='1r8g' size='340' side='right'caption='[[1r8g]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1r8g]] 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=1R8G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1R8G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1r8g]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1R8G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1R8G 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='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.15Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>YBDK, B0581 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~562~~ "~~Bacillus coli~~" ~~Migula 1895])~~</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></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=1r8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r8g OCA], [https://pdbe.org/1r8g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1r8g RCSB], [https://www.ebi.ac.uk/pdbsum/1r8g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1r8g 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=1r8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r8g OCA], [https://pdbe.org/1r8g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1r8g RCSB], [https://www.ebi.ac.uk/pdbsum/1r8g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1r8g ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/GCS2_ECOLI GCS2_ECOLI]] ATP-dependent carboxylate-amine ligase which exhibits weak glutamate--cysteine ligase activity. However, because of the low catalytic rate, the question remains whether L-cysteine is the actual biological substrate.[HAMAP-Rule:MF_01609]<ref>PMID:15211520</ref>	+	[https://www.uniprot.org/uniprot/GCS2_ECOLI GCS2_ECOLI] ATP-dependent carboxylate-amine ligase which exhibits weak glutamate--cysteine ligase activity. However, because of the low catalytic rate, the question remains whether L-cysteine is the actual biological substrate.[HAMAP-Rule:MF_01609]<ref>PMID:15211520</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 20:		Line 20:
	</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=1r8g 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=1r8g ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The Escherichia coli open reading frame YbdK encodes a member of a large bacterial protein family of unknown biological function. The sequences within this family are remotely related to the sequence of gamma-glutamate-cysteine ligase (gamma-GCS), an enzyme in the glutathione biosynthetic pathway. A gene encoding gamma-GCS in E. coli is already known. The 2.15 A resolution crystal structure of YbdK reveals an overall fold similar to that of glutamine synthetase (GS), a nitrogen metabolism enzyme that ligates glutamate and ammonia to yield glutamine. GS and gamma-GCS perform related chemical reactions and require ATP and Mg2+ for their activity. The Mg2+-dependent binding of ATP to YbdK was confirmed by fluorescence spectroscopy employing 2'(or 3')-O-(trinitrophenyl)adenosine 5'-triphosphate, and yielding a dissociation constant of 3 +/- 0.5 microM. The structure of YbdK contains a crevice that corresponds to the binding sites of ATP, Mg2+ and glutamate in GS. Many of the GS residues that coordinate the metal ions and interact with glutamic acid and the phosphoryl and ribosyl groups of ATP are also present in YbdK. GS amino acids that have been associated with ammonia binding have no obvious counterparts in YbdK, consistent with a substrate specificity that is different from that of GS. Ligase activity between glutamic acid and each of the twenty amino acid residues was tested on high performance liquid chromatography (HPLC) by following the hydrolysis of ATP to ADP. Catalysis was observed only with cysteine. A pyruvate kinase/lactic acid dehydrogenase coupled assay was used to rule out GS activity and to determine that YbdK exhibits gamma-GCS activity. The catalytic rate was found to be approximately 500-fold slower than that reported for authentic gamma-GCS.
-
-	YbdK is a carboxylate-amine ligase with a gamma-glutamyl:Cysteine ligase activity: crystal structure and enzymatic assays.,Lehmann C, Doseeva V, Pullalarevu S, Krajewski W, Howard A, Herzberg O Proteins. 2004 Aug 1;56(2):376-83. PMID:15211520<ref>PMID:15211520</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1r8g" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Doseeva, V]]	+	[[Category: Doseeva V]]
-	[[Category: Herzberg, O]]	+	[[Category: Herzberg O]]
-	[[Category: Howard, A]]	+	[[Category: Howard A]]
-	[[Category: Krajewski, W]]	+	[[Category: Krajewski W]]
-	[[Category: Lehmann, C]]	+	[[Category: Lehmann C]]
-	[[Category: Pullalarevu, S]]	+	[[Category: Pullalarevu S]]
-	~~[[Category: S2F, Structure 2.Function Project]]~~	+
-	~~[[Category: Carboxylate-amine ligase]]~~	+
-	~~[[Category: Hypothetical protein]]~~	+
-	~~[[Category: Ligase]]~~	+
-	~~[[Category: S2f]]~~	+
-	~~[[Category: Structural genomic]]~~	+
-	~~[[Category: Structure 2 function project]]~~	+
-	~~[[Category: Unknown function]]~~	+
-	~~[[Category: Ybdk~~]]	+

OCA at 10:37, 28 July 2021

2021-07-28T10:37:07Z

←Older revision		Revision as of 10:37, 28 July 2021
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	<StructureSection load='1r8g' size='340' side='right'caption='[[1r8g]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='1r8g' size='340' side='right'caption='[[1r8g]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1r8g]] 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=1R8G OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1R8G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1r8g]] 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=1R8G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1R8G 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">YBDK, B0581 ([~~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">YBDK, B0581 ([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~~://proteopedia.org/fgij/fg.htm?mol=1r8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r8g OCA], [~~http~~://pdbe.org/1r8g PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1r8g RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1r8g PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1r8g 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=1r8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r8g OCA], [https://pdbe.org/1r8g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1r8g RCSB], [https://www.ebi.ac.uk/pdbsum/1r8g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1r8g ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/GCS2_ECOLI GCS2_ECOLI]] ATP-dependent carboxylate-amine ligase which exhibits weak glutamate--cysteine ligase activity. However, because of the low catalytic rate, the question remains whether L-cysteine is the actual biological substrate.[HAMAP-Rule:MF_01609]<ref>PMID:15211520</ref>	+	[[https://www.uniprot.org/uniprot/GCS2_ECOLI GCS2_ECOLI]] ATP-dependent carboxylate-amine ligase which exhibits weak glutamate--cysteine ligase activity. However, because of the low catalytic rate, the question remains whether L-cysteine is the actual biological substrate.[HAMAP-Rule:MF_01609]<ref>PMID:15211520</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 13:21, 16 December 2020

2020-12-16T13:21:23Z

←Older revision		Revision as of 13:21, 16 December 2020
Line 1:		Line 1:

	==Structure and function of YbdK==		==Structure and function of YbdK==
-	<StructureSection load='1r8g' size='340' side='right' caption='[[1r8g]], [[Resolution\|resolution]] 2.15Å' scene=''>	+	<StructureSection load='1r8g' size='340' side='right'caption='[[1r8g]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1r8g]] 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=1R8G OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1R8G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1r8g]] 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=1R8G OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1R8G 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">YBDK, B0581 ([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">YBDK, B0581 ([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=1r8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r8g OCA], [http://pdbe.org/1r8g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1r8g RCSB], [http://www.ebi.ac.uk/pdbsum/1r8g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1r8g ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1r8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r8g OCA], [http://pdbe.org/1r8g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1r8g RCSB], [http://www.ebi.ac.uk/pdbsum/1r8g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1r8g ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Doseeva, V]]		[[Category: Doseeva, V]]
	[[Category: Herzberg, O]]		[[Category: Herzberg, O]]

OCA at 07:47, 28 February 2018

2018-02-28T07:47:03Z

←Older revision		Revision as of 07:47, 28 February 2018
Line 1:		Line 1:
		+
	==Structure and function of YbdK==		==Structure and function of YbdK==
	<StructureSection load='1r8g' size='340' side='right' caption='[[1r8g]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='1r8g' size='340' side='right' caption='[[1r8g]], [[Resolution\|resolution]] 2.15Å' 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">YBDK, B0581 ([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">YBDK, B0581 ([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=1r8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r8g OCA], [http://pdbe.org/1r8g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1r8g RCSB], [http://www.ebi.ac.uk/pdbsum/1r8g 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=1r8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r8g OCA], [http://pdbe.org/1r8g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1r8g RCSB], [http://www.ebi.ac.uk/pdbsum/1r8g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1r8g 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/r8/1r8g_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/r8/1r8g_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=1r8g ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 23:48, 11 September 2015

2015-09-11T23:48:45Z

←Older revision		Revision as of 23:48, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1r8g' size='340' side='right' caption='[[1r8g]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='1r8g' size='340' side='right' caption='[[1r8g]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1r8g]] 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=1R8G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1R8G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1r8g]] 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=1R8G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1R8G 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">YBDK, B0581 ([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">YBDK, B0581 ([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=1r8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r8g OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1r8g RCSB], [http://www.ebi.ac.uk/pdbsum/1r8g 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=1r8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r8g OCA], [http://pdbe.org/1r8g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1r8g RCSB], [http://www.ebi.ac.uk/pdbsum/1r8g PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~CAAL_ECOLI CAAL_ECOLI~~]] ATP-dependent carboxylate-amine ligase which exhibits weak glutamate--cysteine ligase activity. However, because of the low catalytic rate, the question remains whether L-cysteine is the actual biological substrate.<ref>PMID:15211520</ref>	+	[[http://www.uniprot.org/uniprot/GCS2_ECOLI GCS2_ECOLI]] ATP-dependent carboxylate-amine ligase which exhibits weak glutamate--cysteine ligase activity. However, because of the low catalytic rate, the question remains whether L-cysteine is the actual biological substrate.[HAMAP-Rule:MF_01609]<ref>PMID:15211520</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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 1r8g" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia~~ coli]]	+	[[Category: Bacillus coli migula 1895]]
	[[Category: Doseeva, V]]		[[Category: Doseeva, V]]
	[[Category: Herzberg, O]]		[[Category: Herzberg, O]]

OCA at 21:01, 25 December 2014

2014-12-25T21:01:49Z

←Older revision		Revision as of 21:01, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1r8g]] 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=1R8G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1R8G FirstGlance]. <br>		<table><tr><td colspan='2'>[[1r8g]] 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=1R8G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1R8G 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">YBDK, B0581 ([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">YBDK, B0581 ([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=1r8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r8g OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1r8g RCSB], [http://www.ebi.ac.uk/pdbsum/1r8g 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=1r8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r8g OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1r8g RCSB], [http://www.ebi.ac.uk/pdbsum/1r8g PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CAAL_ECOLI CAAL_ECOLI]] ATP-dependent carboxylate-amine ligase which exhibits weak glutamate--cysteine ligase activity. However, because of the low catalytic rate, the question remains whether L-cysteine is the actual biological substrate.<ref>PMID:15211520</ref>
	== 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: Doseeva, V.]]	+	[[Category: Doseeva, V]]
-	[[Category: Herzberg, O.]]	+	[[Category: Herzberg, O]]
-	[[Category: Howard, A.]]	+	[[Category: Howard, A]]
-	[[Category: Krajewski, W.]]	+	[[Category: Krajewski, W]]
-	[[Category: Lehmann, C.]]	+	[[Category: Lehmann, C]]
-	[[Category: Pullalarevu, S.]]	+	[[Category: Pullalarevu, S]]
-	[[Category: S2F, Structure 2.Function Project.]]	+	[[Category: S2F, Structure 2.Function Project]]
	[[Category: Carboxylate-amine ligase]]		[[Category: Carboxylate-amine ligase]]
	[[Category: Hypothetical protein]]		[[Category: Hypothetical protein]]

OCA at 15:57, 29 September 2014

2014-09-29T15:57:55Z

←Older revision		Revision as of 15:57, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1r8g.~~png~~\|~~left~~\|200px]]	+	==Structure and function of YbdK==
		+	<StructureSection load='1r8g' size='340' side='right' caption='[[1r8g]], [[Resolution\|resolution]] 2.15Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1r8g]] 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=1R8G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1R8G 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">YBDK, B0581 ([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=1r8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r8g OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1r8g RCSB], [http://www.ebi.ac.uk/pdbsum/1r8g 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/r8/1r8g_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 ==
		+	The Escherichia coli open reading frame YbdK encodes a member of a large bacterial protein family of unknown biological function. The sequences within this family are remotely related to the sequence of gamma-glutamate-cysteine ligase (gamma-GCS), an enzyme in the glutathione biosynthetic pathway. A gene encoding gamma-GCS in E. coli is already known. The 2.15 A resolution crystal structure of YbdK reveals an overall fold similar to that of glutamine synthetase (GS), a nitrogen metabolism enzyme that ligates glutamate and ammonia to yield glutamine. GS and gamma-GCS perform related chemical reactions and require ATP and Mg2+ for their activity. The Mg2+-dependent binding of ATP to YbdK was confirmed by fluorescence spectroscopy employing 2'(or 3')-O-(trinitrophenyl)adenosine 5'-triphosphate, and yielding a dissociation constant of 3 +/- 0.5 microM. The structure of YbdK contains a crevice that corresponds to the binding sites of ATP, Mg2+ and glutamate in GS. Many of the GS residues that coordinate the metal ions and interact with glutamic acid and the phosphoryl and ribosyl groups of ATP are also present in YbdK. GS amino acids that have been associated with ammonia binding have no obvious counterparts in YbdK, consistent with a substrate specificity that is different from that of GS. Ligase activity between glutamic acid and each of the twenty amino acid residues was tested on high performance liquid chromatography (HPLC) by following the hydrolysis of ATP to ADP. Catalysis was observed only with cysteine. A pyruvate kinase/lactic acid dehydrogenase coupled assay was used to rule out GS activity and to determine that YbdK exhibits gamma-GCS activity. The catalytic rate was found to be approximately 500-fold slower than that reported for authentic gamma-GCS.

-	~~{{STRUCTURE_1r8g\| PDB=1r8g \| SCENE= }}~~	+	YbdK is a carboxylate-amine ligase with a gamma-glutamyl:Cysteine ligase activity: crystal structure and enzymatic assays.,Lehmann C, Doseeva V, Pullalarevu S, Krajewski W, Howard A, Herzberg O Proteins. 2004 Aug 1;56(2):376-83. PMID:15211520<ref>PMID:15211520</ref>

-	~~===Structure and function~~ of ~~YbdK===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15211520}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1r8g]] 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=1R8G OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:015211520<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Doseeva, V.]]		[[Category: Doseeva, V.]]

OCA: Protected "1r8g" [edit=sysop:move=sysop]

2013-01-04T10:16:28Z

Protected "1r8g" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:16, 4 January 2013

OCA at 10:16, 4 January 2013

2013-01-04T10:16:23Z

←Older revision		Revision as of 10:16, 4 January 2013
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-	{{Seed}}
	[[Image:1r8g.png\|left\|200px]]		[[Image:1r8g.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1r8g", 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_1r8g\| PDB=1r8g \| SCENE= }}		{{STRUCTURE_1r8g\| PDB=1r8g \| SCENE= }}

	===Structure and function of YbdK===		===Structure and function of YbdK===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15211520}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15211520 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15211520}}		{{ABSTRACT_PUBMED_15211520}}

	==About this Structure==		==About this Structure==
-	~~1R8G~~ 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=1R8G OCA].	+	[[1r8g]] 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=1R8G OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15211520~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015211520</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Doseeva, V.]]		[[Category: Doseeva, V.]]
Line 34:		Line 22:
	[[Category: Carboxylate-amine ligase]]		[[Category: Carboxylate-amine ligase]]
	[[Category: Hypothetical protein]]		[[Category: Hypothetical protein]]
		+	[[Category: Ligase]]
	[[Category: S2f]]		[[Category: S2f]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
Line 39:		Line 28:
	[[Category: Unknown function]]		[[Category: Unknown function]]
	[[Category: Ybdk]]		[[Category: Ybdk]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 07:11:27 2009''

OCA at 05:11, 18 February 2009

2009-02-18T05:11:29Z

←Older revision		Revision as of 05:11, 18 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1R8G 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=1R8G OCA].	+	1R8G 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=1R8G OCA].

	==Reference==		==Reference==
-	YbdK is a carboxylate-amine ligase with a gamma-glutamyl:Cysteine ligase activity: crystal structure and enzymatic assays., Lehmann C, Doseeva V, Pullalarevu S, Krajewski W, Howard A, Herzberg O, Proteins. 2004 Aug 1;56(2):376-83. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/15211520 15211520]~~	+	<ref group="xtra">PMID:15211520</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Single protein]]
	[[Category: Doseeva, V.]]		[[Category: Doseeva, V.]]
	[[Category: Herzberg, O.]]		[[Category: Herzberg, O.]]
Line 41:		Line 40:
	[[Category: Ybdk]]		[[Category: Ybdk]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue Jul 29 13~~:54:~~15 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 07:11:27 2009''