1sff - Revision history

OCA at 08:30, 14 February 2024

2024-02-14T08:30:24Z

←Older revision		Revision as of 08:30, 14 February 2024
Line 3:		Line 3:
	<StructureSection load='1sff' size='340' side='right'caption='[[1sff]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1sff' size='340' side='right'caption='[[1sff]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1sff]] is a 4 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=1SFF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1SFF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1sff]] is a 4 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=1SFF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SFF FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=EDO:1,2~~-~~ETHANEDIOL'>EDO</scene>~~, ~~<scene name='pdbligand=IK2:4-DEOXY-4-ACETYLYAMINO-PYRIDOXAL-5-PHOSPHATE'>IK2</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.9Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[1sf2\|1sf2]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IK2:4-DEOXY-4-ACETYLYAMINO-PYRIDOXAL-5-PHOSPHATE'>IK2</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>GABT, B2662 ([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'>[https://proteopedia.org/fgij/fg.htm?mol=1sff FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sff OCA], [https://pdbe.org/1sff PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1sff RCSB], [https://www.ebi.ac.uk/pdbsum/1sff PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1sff ProSAT]</span></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class="sblockDat"><span class~~='~~plainlinks'>[http~~:~~//en.wikipedia.org/wiki/~~4-~~aminobutyrate-~~-~~2-oxoglutarate_transaminase~~ 4-~~aminobutyrate~~--2-~~oxoglutarate transaminase]~~, ~~with EC number [http~~:~~//www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.19 2.6.1.19]~~ </~~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=1sff FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sff OCA], [~~http~~://pdbe.org/1sff PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1sff RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1sff PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1sff ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/GABT_ECOLI GABT_ECOLI]] Catalyzes the transfer of the amino group from gamma-aminobutyrate (GABA) to alpha-ketoglutarate (KG) to yield succinic semialdehyde (SSA).<ref>PMID:20639325</ref>	+	[https://www.uniprot.org/uniprot/GABT_ECOLI GABT_ECOLI] Catalyzes the transfer of the amino group from gamma-aminobutyrate (GABA) to alpha-ketoglutarate (KG) to yield succinic semialdehyde (SSA).<ref>PMID:20639325</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</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=1sff 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=1sff ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The X-ray crystal structures of Escherichia coli gamma-aminobutyrate aminotransferase unbound and bound to the inhibitor aminooxyacetate are reported. The enzyme crystallizes from ammonium sulfate solutions in the P3(2)21 space group with a tetramer in the asymmetric unit. Diffraction data were collected to 2.4 A resolution for the unliganded enzyme and 1.9 A resolution for the aminooxyacetate complex. The overall structure of the enzyme is similar to those of other aminotransferase subgroup II enzymes. The ability of gamma-aminobutyrate aminotransferase to act on primary amine substrates (gamma-aminobutyrate) in the first half-reaction and alpha-amino acids in the second is proposed to be enabled by the presence of Glu211, whose side chain carboxylate alternates between interactions with Arg398 in the primary amine half-reaction and an alternative binding site in the alpha-amino acid half-reaction, in which Arg398 binds the substrate alpha-carboxylate. The specificity for a carboxylate group on the substrate side chain is due primarily to the presence of Arg141, but also requires substantial local main chain rearrangements relative to the structurally homologous enzyme dialkylglycine decarboxylase, which is specific for small alkyl side chains. No iron-sulfur cluster is found in the bacterial enzyme as was found in the pig enzyme [Storici, P., De Biase, D., Bossa, F., Bruno, S., Mozzarelli, A., Peneff, C., Silverman, R. B., and Schirmer, T. (2004) J. Biol. Chem. 279, 363-73.]. The binding of aminooxyacetate causes remarkably small changes in the active site structure, and no large domain movements are observed. Active site structure comparisons with pig gamma-aminobutyrate aminotransferase and dialkylglycine decarboxylase are discussed.
-
-	Crystal structures of unbound and aminooxyacetate-bound Escherichia coli gamma-aminobutyrate aminotransferase.,Liu W, Peterson PE, Carter RJ, Zhou X, Langston JA, Fisher AJ, Toney MD Biochemistry. 2004 Aug 31;43(34):10896-905. PMID:15323550<ref>PMID:15323550</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1sff" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 38:		Line 27:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895]]~~	+	[[Category: Escherichia coli]]
-	~~[[Category: 4-aminobutyrate--2-oxoglutarate transaminase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Carter~~, R J~~]]	+	[[Category: Carter RJ]]
-	[[Category: Fisher~~, A J~~]]	+	[[Category: Fisher AJ]]
-	[[Category: Langston~~, J A~~]]	+	[[Category: Langston JA]]
-	[[Category: Liu, W]]	+	[[Category: Liu W]]
-	[[Category: Peterson~~, P E~~]]	+	[[Category: Peterson PE]]
-	[[Category: Toney~~, M D~~]]	+	[[Category: Toney MD]]
-	[[Category: Zhou, X]]	+	[[Category: Zhou X]]
-	~~[[Category: Aminotransferase]]~~	+
-	~~[[Category: Enzyme complex]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 11:23, 24 December 2020

2020-12-24T11:23:06Z

←Older revision		Revision as of 11:23, 24 December 2020
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	==Structure of gamma-aminobutyrate aminotransferase complex with aminooxyacetate==		==Structure of gamma-aminobutyrate aminotransferase complex with aminooxyacetate==
-	<StructureSection load='1sff' size='340' side='right' caption='[[1sff]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='1sff' size='340' side='right'caption='[[1sff]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1sff]] is a 4 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=1SFF OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1SFF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1sff]] is a 4 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=1SFF OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1SFF FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IK2:4-DEOXY-4-ACETYLYAMINO-PYRIDOXAL-5-PHOSPHATE'>IK2</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IK2:4-DEOXY-4-ACETYLYAMINO-PYRIDOXAL-5-PHOSPHATE'>IK2</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1sf2\|1sf2]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1sf2\|1sf2]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GABT, B2662 ([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">GABT, B2662 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-aminobutyrate--2-oxoglutarate_transaminase 4-aminobutyrate--2-oxoglutarate transaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.19 2.6.1.19] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-aminobutyrate--2-oxoglutarate_transaminase 4-aminobutyrate--2-oxoglutarate transaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.19 2.6.1.19] </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=1sff FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sff OCA], [http://pdbe.org/1sff PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1sff RCSB], [http://www.ebi.ac.uk/pdbsum/1sff PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1sff 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=1sff FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sff OCA], [http://pdbe.org/1sff PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1sff RCSB], [http://www.ebi.ac.uk/pdbsum/1sff PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1sff ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	==See Also==		==See Also==
-	*[[Aminotransferase\|Aminotransferase]]	+	*[[Aminotransferase 3D structures\|Aminotransferase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
	[[Category: 4-aminobutyrate--2-oxoglutarate transaminase]]		[[Category: 4-aminobutyrate--2-oxoglutarate transaminase]]
		+	[[Category: Large Structures]]
	[[Category: Carter, R J]]		[[Category: Carter, R J]]
	[[Category: Fisher, A J]]		[[Category: Fisher, A J]]

OCA at 07:07, 8 March 2018

2018-03-08T07:07:29Z

←Older revision		Revision as of 07:07, 8 March 2018
Line 1:		Line 1:
		+
	==Structure of gamma-aminobutyrate aminotransferase complex with aminooxyacetate==		==Structure of gamma-aminobutyrate aminotransferase complex with aminooxyacetate==
	<StructureSection load='1sff' size='340' side='right' caption='[[1sff]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1sff' size='340' side='right' caption='[[1sff]], [[Resolution\|resolution]] 1.90Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GABT, B2662 ([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">GABT, B2662 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-aminobutyrate--2-oxoglutarate_transaminase 4-aminobutyrate--2-oxoglutarate transaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.19 2.6.1.19] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-aminobutyrate--2-oxoglutarate_transaminase 4-aminobutyrate--2-oxoglutarate transaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.19 2.6.1.19] </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=1sff FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sff OCA], [http://pdbe.org/1sff PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1sff RCSB], [http://www.ebi.ac.uk/pdbsum/1sff 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=1sff FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sff OCA], [http://pdbe.org/1sff PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1sff RCSB], [http://www.ebi.ac.uk/pdbsum/1sff PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1sff ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/sf/1sff_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/sf/1sff_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>

OCA at 15:38, 9 February 2016

2016-02-09T15:38:26Z

←Older revision		Revision as of 15:38, 9 February 2016
Line 19:		Line 19:
	<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=1sff ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 30:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1sff" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1sff" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Aminotransferase\|Aminotransferase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 23:39, 10 September 2015

2015-09-10T23:39:24Z

←Older revision		Revision as of 23:39, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1sff' size='340' side='right' caption='[[1sff]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1sff' size='340' side='right' caption='[[1sff]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1sff]] is a 4 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=1SFF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SFF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1sff]] is a 4 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=1SFF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SFF FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IK2:4-DEOXY-4-ACETYLYAMINO-PYRIDOXAL-5-PHOSPHATE'>IK2</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IK2:4-DEOXY-4-ACETYLYAMINO-PYRIDOXAL-5-PHOSPHATE'>IK2</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1sf2\|1sf2]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1sf2\|1sf2]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GABT, B2662 ([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">GABT, B2662 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-~~aminobutyrate_transaminase~~ 4-aminobutyrate transaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.19 2.6.1.19] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-aminobutyrate--2-oxoglutarate_transaminase 4-aminobutyrate--2-oxoglutarate transaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.19 2.6.1.19] </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=1sff FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sff OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1sff RCSB], [http://www.ebi.ac.uk/pdbsum/1sff 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=1sff FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sff OCA], [http://pdbe.org/1sff PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1sff RCSB], [http://www.ebi.ac.uk/pdbsum/1sff PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 29:		Line 29:
	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 1sff" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~4-aminobutyrate transaminase~~]]	+	[[Category: Bacillus coli migula 1895]]
-	[[Category: ~~Escherichia coli~~]]	+	[[Category: 4-aminobutyrate--2-oxoglutarate transaminase]]
	[[Category: Carter, R J]]		[[Category: Carter, R J]]
	[[Category: Fisher, A J]]		[[Category: Fisher, A J]]

OCA at 07:47, 25 December 2014

2014-12-25T07:47:48Z

←Older revision		Revision as of 07:47, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1sff]] is a 4 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=1SFF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SFF FirstGlance]. <br>		<table><tr><td colspan='2'>[[1sff]] is a 4 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=1SFF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SFF FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IK2:4-DEOXY-4-ACETYLYAMINO-PYRIDOXAL-5-PHOSPHATE'>IK2</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IK2:4-DEOXY-4-ACETYLYAMINO-PYRIDOXAL-5-PHOSPHATE'>IK2</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1sf2\|1sf2]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1sf2\|1sf2]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GABT, B2662 ([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">GABT, B2662 ([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>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-aminobutyrate_transaminase 4-aminobutyrate transaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.19 2.6.1.19] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-aminobutyrate_transaminase 4-aminobutyrate transaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.19 2.6.1.19] </span></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=1sff FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sff OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1sff RCSB], [http://www.ebi.ac.uk/pdbsum/1sff 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=1sff FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sff OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1sff RCSB], [http://www.ebi.ac.uk/pdbsum/1sff PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/GABT_ECOLI GABT_ECOLI]] Catalyzes the transfer of the amino group from gamma-aminobutyrate (GABA) to alpha-ketoglutarate (KG) to yield succinic semialdehyde (SSA).<ref>PMID:20639325</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 35:
	[[Category: 4-aminobutyrate transaminase]]		[[Category: 4-aminobutyrate transaminase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Carter, R J.]]	+	[[Category: Carter, R J]]
-	[[Category: Fisher, A J.]]	+	[[Category: Fisher, A J]]
-	[[Category: Langston, J A.]]	+	[[Category: Langston, J A]]
-	[[Category: Liu, W.]]	+	[[Category: Liu, W]]
-	[[Category: Peterson, P E.]]	+	[[Category: Peterson, P E]]
-	[[Category: Toney, M D.]]	+	[[Category: Toney, M D]]
-	[[Category: Zhou, X.]]	+	[[Category: Zhou, X]]
	[[Category: Aminotransferase]]		[[Category: Aminotransferase]]
	[[Category: Enzyme complex]]		[[Category: Enzyme complex]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 14:44, 29 September 2014

2014-09-29T14:44:00Z

←Older revision		Revision as of 14:44, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1sff.~~png~~\|~~left~~\|200px]]	+	==Structure of gamma-aminobutyrate aminotransferase complex with aminooxyacetate==
		+	<StructureSection load='1sff' size='340' side='right' caption='[[1sff]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1sff]] is a 4 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=1SFF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SFF FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IK2:4-DEOXY-4-ACETYLYAMINO-PYRIDOXAL-5-PHOSPHATE'>IK2</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1sf2\|1sf2]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GABT, B2662 ([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>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-aminobutyrate_transaminase 4-aminobutyrate transaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.19 2.6.1.19] </span></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=1sff FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sff OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1sff RCSB], [http://www.ebi.ac.uk/pdbsum/1sff 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/sf/1sff_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 X-ray crystal structures of Escherichia coli gamma-aminobutyrate aminotransferase unbound and bound to the inhibitor aminooxyacetate are reported. The enzyme crystallizes from ammonium sulfate solutions in the P3(2)21 space group with a tetramer in the asymmetric unit. Diffraction data were collected to 2.4 A resolution for the unliganded enzyme and 1.9 A resolution for the aminooxyacetate complex. The overall structure of the enzyme is similar to those of other aminotransferase subgroup II enzymes. The ability of gamma-aminobutyrate aminotransferase to act on primary amine substrates (gamma-aminobutyrate) in the first half-reaction and alpha-amino acids in the second is proposed to be enabled by the presence of Glu211, whose side chain carboxylate alternates between interactions with Arg398 in the primary amine half-reaction and an alternative binding site in the alpha-amino acid half-reaction, in which Arg398 binds the substrate alpha-carboxylate. The specificity for a carboxylate group on the substrate side chain is due primarily to the presence of Arg141, but also requires substantial local main chain rearrangements relative to the structurally homologous enzyme dialkylglycine decarboxylase, which is specific for small alkyl side chains. No iron-sulfur cluster is found in the bacterial enzyme as was found in the pig enzyme [Storici, P., De Biase, D., Bossa, F., Bruno, S., Mozzarelli, A., Peneff, C., Silverman, R. B., and Schirmer, T. (2004) J. Biol. Chem. 279, 363-73.]. The binding of aminooxyacetate causes remarkably small changes in the active site structure, and no large domain movements are observed. Active site structure comparisons with pig gamma-aminobutyrate aminotransferase and dialkylglycine decarboxylase are discussed.

-	~~{{STRUCTURE_1sff\| PDB=1sff \| SCENE= }}~~	+	Crystal structures of unbound and aminooxyacetate-bound Escherichia coli gamma-aminobutyrate aminotransferase.,Liu W, Peterson PE, Carter RJ, Zhou X, Langston JA, Fisher AJ, Toney MD Biochemistry. 2004 Aug 31;43(34):10896-905. PMID:15323550<ref>PMID:15323550</ref>

-	~~===Structure~~ of ~~gamma-aminobutyrate aminotransferase complex with aminooxyacetate===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15323550}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1sff]] is a 4 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=1SFF OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:015323550<~~/~~ref~~><~~ref group="xtra">PMID:019146406</ref><references group="xtra"~~/>	+
	[[Category: 4-aminobutyrate transaminase]]		[[Category: 4-aminobutyrate transaminase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]

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

2013-01-04T10:41:20Z

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

←Older revision

Revision as of 10:41, 4 January 2013

OCA at 10:41, 4 January 2013

2013-01-04T10:41:17Z

←Older revision		Revision as of 10:41, 4 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1sff.png\|left\|200px]]		[[Image:1sff.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1sff", 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_1sff\| PDB=1sff \| SCENE= }}		{{STRUCTURE_1sff\| PDB=1sff \| SCENE= }}

	===Structure of gamma-aminobutyrate aminotransferase complex with aminooxyacetate===		===Structure of gamma-aminobutyrate aminotransferase complex with aminooxyacetate===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15323550}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15323550 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15323550}}		{{ABSTRACT_PUBMED_15323550}}

	==About this Structure==		==About this Structure==
-	~~1SFF~~ is a 4 ~~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=1SFF OCA].	+	[[1sff]] is a 4 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=1SFF OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15323550~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015323550</ref><ref group="xtra">PMID:019146406</ref><references group="xtra"/>
	[[Category: 4-aminobutyrate transaminase]]		[[Category: 4-aminobutyrate transaminase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
Line 35:		Line 23:
	[[Category: Aminotransferase]]		[[Category: Aminotransferase]]
	[[Category: Enzyme complex]]		[[Category: Enzyme complex]]
-		+	[[Category: Transferase]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 10:53:18 2009''~~	+

OCA at 08:53, 17 February 2009

2009-02-17T08:53:19Z

←Older revision		Revision as of 08:53, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1SFF 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=1SFF OCA].	+	1SFF is a 4 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=1SFF OCA].

	==Reference==		==Reference==
-	Crystal structures of unbound and aminooxyacetate-bound Escherichia coli gamma-aminobutyrate aminotransferase., Liu W, Peterson PE, Carter RJ, Zhou X, Langston JA, Fisher AJ, Toney MD, Biochemistry. 2004 Aug 31;43(34):10896-905. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/15323550 15323550]~~	+	<ref group="xtra">PMID:15323550</ref><references group="xtra"/>
	[[Category: 4-aminobutyrate transaminase]]		[[Category: 4-aminobutyrate transaminase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Single protein]]
	[[Category: Carter, R J.]]		[[Category: Carter, R J.]]
	[[Category: Fisher, A J.]]		[[Category: Fisher, A J.]]
Line 37:		Line 36:
	[[Category: Enzyme complex]]		[[Category: Enzyme complex]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Jul 28 14~~:51:~~57 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 10:53:18 2009''