4uoy - Revision history

OCA at 10:32, 10 January 2024

2024-01-10T10:32:10Z

←Older revision		Revision as of 10:32, 10 January 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4uoy]] 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=4UOY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4UOY FirstGlance]. <br>		<table><tr><td colspan='2'>[[4uoy]] 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=4UOY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4UOY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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]] 2.305Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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=4uoy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4uoy OCA], [https://pdbe.org/4uoy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4uoy RCSB], [https://www.ebi.ac.uk/pdbsum/4uoy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4uoy 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=4uoy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4uoy OCA], [https://pdbe.org/4uoy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4uoy RCSB], [https://www.ebi.ac.uk/pdbsum/4uoy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4uoy ProSAT]</span></td></tr>
	</table>		</table>

OCA at 07:30, 29 March 2023

2023-03-29T07:30:15Z

←Older revision		Revision as of 07:30, 29 March 2023
Line 3:		Line 3:
	<StructureSection load='4uoy' size='340' side='right'caption='[[4uoy]], [[Resolution\|resolution]] 2.31Å' scene=''>		<StructureSection load='4uoy' size='340' side='right'caption='[[4uoy]], [[Resolution\|resolution]] 2.31Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4uoy]] 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=4UOY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4UOY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4uoy]] 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=4UOY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4UOY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4uox\|4uox]]</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=4uoy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4uoy OCA], [https://pdbe.org/4uoy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4uoy RCSB], [https://www.ebi.ac.uk/pdbsum/4uoy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4uoy 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/Putrescine_aminotransferase Putrescine aminotransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.82 2.6.1.82] </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=4uoy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4uoy OCA], [~~http~~://pdbe.org/4uoy PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4uoy RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4uoy PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4uoy ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PAT_ECOLI PAT_ECOLI]] Catalyzes the aminotransferase reaction from putrescine to 2-oxoglutarate, leading to glutamate and 4-aminobutanal, which spontaneously cyclizes to form 1-pyrroline. Is also able to transaminate cadaverine and, in lower extent, spermidine, but not ornithine. Alpha-ketobutyrate and pyruvate can also act as amino acceptors, although much less efficiently.<ref>PMID:12617754</ref>	+	[https://www.uniprot.org/uniprot/PAT_ECOLI PAT_ECOLI] Catalyzes the aminotransferase reaction from putrescine to 2-oxoglutarate, leading to glutamate and 4-aminobutanal, which spontaneously cyclizes to form 1-pyrroline. Is also able to transaminate cadaverine and, in lower extent, spermidine, but not ornithine. Alpha-ketobutyrate and pyruvate can also act as amino acceptors, although much less efficiently.<ref>PMID:12617754</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 27:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Putrescine aminotransferase]]~~	+	[[Category: Jeong JH]]
-	[[Category: Jeong~~, J H~~]]	+	[[Category: Kim YG]]
-	[[Category: Kim~~, Y G]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 09:16, 21 May 2019

2019-05-21T09:16:53Z

←Older revision		Revision as of 09:16, 21 May 2019
Line 1:		Line 1:

	==Crystal structure of YgjG in complex with Pyridoxal-5'-phosphate==		==Crystal structure of YgjG in complex with Pyridoxal-5'-phosphate==
-	<StructureSection load='4uoy' size='340' side='right' caption='[[4uoy]], [[Resolution\|resolution]] 2.31Å' scene=''>	+	<StructureSection load='4uoy' size='340' side='right'caption='[[4uoy]], [[Resolution\|resolution]] 2.31Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4uoy]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UOY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4UOY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4uoy]] 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=4UOY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4UOY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4uox\|4uox]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4uox\|4uox]]</td></tr>
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 4uoy" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4uoy" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Aminotransferase 3D structures\|Aminotransferase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Putrescine aminotransferase]]		[[Category: Putrescine aminotransferase]]
	[[Category: Jeong, J H]]		[[Category: Jeong, J H]]
	[[Category: Kim, Y G]]		[[Category: Kim, Y G]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 04:58, 5 August 2016

2016-08-05T04:58:11Z

←Older revision		Revision as of 04:58, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of YgjG in complex with Pyridoxal-5'-phosphate==		==Crystal structure of YgjG in complex with Pyridoxal-5'-phosphate==
	<StructureSection load='4uoy' size='340' side='right' caption='[[4uoy]], [[Resolution\|resolution]] 2.31Å' scene=''>		<StructureSection load='4uoy' size='340' side='right' caption='[[4uoy]], [[Resolution\|resolution]] 2.31Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4uox\|4uox]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4uox\|4uox]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Putrescine_aminotransferase Putrescine aminotransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.82 2.6.1.82] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Putrescine_aminotransferase Putrescine aminotransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.82 2.6.1.82] </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=4uoy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4uoy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4uoy RCSB], [http://www.ebi.ac.uk/pdbsum/4uoy 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=4uoy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4uoy OCA], [http://pdbe.org/4uoy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4uoy RCSB], [http://www.ebi.ac.uk/pdbsum/4uoy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4uoy ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	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 4uoy" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 15:57, 25 December 2014

2014-12-25T15:57:43Z

←Older revision		Revision as of 15:57, 25 December 2014
Line 8:		Line 8:
	<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=4uoy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4uoy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4uoy RCSB], [http://www.ebi.ac.uk/pdbsum/4uoy 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=4uoy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4uoy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4uoy RCSB], [http://www.ebi.ac.uk/pdbsum/4uoy PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PAT_ECOLI PAT_ECOLI]] Catalyzes the aminotransferase reaction from putrescine to 2-oxoglutarate, leading to glutamate and 4-aminobutanal, which spontaneously cyclizes to form 1-pyrroline. Is also able to transaminate cadaverine and, in lower extent, spermidine, but not ornithine. Alpha-ketobutyrate and pyruvate can also act as amino acceptors, although much less efficiently.<ref>PMID:12617754</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 16:09, 10 December 2014

2014-12-10T16:09:39Z

←Older revision		Revision as of 16:09, 10 December 2014
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal structure of YgjG in complex with Pyridoxal-5'-phosphate==
		+	<StructureSection load='4uoy' size='340' side='right' caption='[[4uoy]], [[Resolution\|resolution]] 2.31Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4uoy]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UOY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4UOY FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4uox\|4uox]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Putrescine_aminotransferase Putrescine aminotransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.82 2.6.1.82] </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=4uoy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4uoy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4uoy RCSB], [http://www.ebi.ac.uk/pdbsum/4uoy PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	YgjG is a putrescine aminotransferase enzyme that transfers amino groups from compounds with terminal primary amines to compounds with an aldehyde group using pyridoxal-5'-phosphate (PLP) as a cofactor. Previous biochemical data show that the enzyme prefers primary diamines, such as putrescine, over ornithine as a substrate. To better understand the enzyme's substrate specificity, crystal structures of YgjG from Escherichia coli were determined at 2.3 and 2.1 A resolutions for the free and putrescine-bound enzymes, respectively. Sequence and structural analyses revealed that YgjG forms a dimer that adopts a class III PLP-dependent aminotransferase fold. A structural comparison between YgjG and other class III aminotransferases revealed that their structures are similar. However, YgjG has an additional N-terminal helical structure that partially contributes to a dimeric interaction with the other subunit via a helix-helix interaction. Interestingly, the YgjG substrate-binding site entrance size and charge distribution are smaller and more hydrophobic than other class III aminotransferases, which suggest that YgjG has a unique substrate binding site that could accommodate primary aliphatic diamine substrates, including putrescine. The YgjG crystal structures provide structural clues to putrescine aminotransferase substrate specificity and binding.

-	~~The entry 4uoy is ON HOLD until Paper Publication~~	+	Structure of Putrescine Aminotransferase from Escherichia coli Provides Insights into the Substrate Specificity among Class III Aminotransferases.,Cha HJ, Jeong JH, Rojviriya C, Kim YG PLoS One. 2014 Nov 25;9(11):e113212. doi: 10.1371/journal.pone.0113212., eCollection 2014. PMID:25423189<ref>PMID:25423189</ref>

-	~~Authors~~: Jeong, J.H., Kim, Y.G.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Crystal structure of YgjG in complex with Pyridoxal-5'-phosphate~~	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Putrescine aminotransferase]]
		+	[[Category: Jeong, J H]]
		+	[[Category: Kim, Y G]]
		+	[[Category: Transferase]]

OCA at 06:06, 25 June 2014

2014-06-25T06:06:38Z

←Older revision		Revision as of 06:06, 25 June 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4uoy is ON HOLD	+	The entry 4uoy is ON HOLD until Paper Publication

	Authors: Jeong, J.H., Kim, Y.G.		Authors: Jeong, J.H., Kim, Y.G.

	Description: Crystal structure of YgjG in complex with Pyridoxal-5'-phosphate		Description: Crystal structure of YgjG in complex with Pyridoxal-5'-phosphate

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

2014-06-18T06:51:08Z

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

←Older revision

Revision as of 06:51, 18 June 2014

OCA: New page: '''Unreleased structure''' The entry 4uoy is ON HOLD Authors: Jeong, J.H., Kim, Y.G. Description: Crystal structure of YgjG in complex with Pyridoxal-5'-phosphate

2014-06-18T06:51:07Z

New page: '''Unreleased structure''' The entry 4uoy is ON HOLD Authors: Jeong, J.H., Kim, Y.G. Description: Crystal structure of YgjG in complex with Pyridoxal-5'-phosphate

New page

'''Unreleased structure'''

The entry 4uoy is ON HOLD

Authors: Jeong, J.H., Kim, Y.G.

Description: Crystal structure of YgjG in complex with Pyridoxal-5'-phosphate