3t8l - Revision history

OCA at 13:20, 14 March 2024

OCA — Thu, 14 Mar 2024 13:20:52 GMT

←Older revision		Revision as of 13:20, 14 March 2024
Line 10:		Line 10:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/ADEC2_AGRFC ADEC2_AGRFC]		[https://www.uniprot.org/uniprot/ADEC2_AGRFC ADEC2_AGRFC]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Adenine deaminase (ADE) from the amidohydrolase superfamily (AHS) of enzymes catalyzes the conversion of adenine to hypoxanthine and ammonia. Enzyme isolated from Escherichia coli was largely inactive toward the deamination of adenine. Molecular weight determinations by mass spectrometry provided evidence that multiple histidine and methionine residues were oxygenated. When iron was sequestered with a metal chelator and the growth medium supplemented with Mn(2+) before induction, the post-translational modifications disappeared. Enzyme expressed and purified under these conditions was substantially more active for adenine deamination. Apo-enzyme was prepared and reconstituted with two equivalents of FeSO(4). Inductively coupled plasma mass spectrometry and Mossbauer spectroscopy demonstrated that this protein contained two high-spin ferrous ions per monomer of ADE. In addition to the adenine deaminase activity, [Fe(II) /Fe(II) ]-ADE catalyzed the conversion of H(2)O(2) to O(2) and H(2)O. The values of k(cat) and k(cat)/K(m) for the catalase activity are 200 s(-1) and 2.4 x 10(4) M(-1) s(-1), respectively. [Fe(II)/Fe(II)]-ADE underwent more than 100 turnovers with H(2)O(2) before the enzyme was inactivated due to oxygenation of histidine residues critical for metal binding. The iron in the inactive enzyme was high-spin ferric with g(ave) = 4.3 EPR signal and no evidence of anti-ferromagnetic spin-coupling. A model is proposed for the disproportionation of H(2)O(2) by [Fe(II)/Fe(II)]-ADE that involves the cycling of the binuclear metal center between the di-ferric and di-ferrous oxidation states. Oxygenation of active site residues occurs via release of hydroxyl radicals. These findings represent the first report of redox reaction catalysis by any member of the AHS.
-
-	The catalase activity of diiron adenine deaminase.,Kamat SS, Holmes-Hampton GP, Bagaria A, Kumaran D, Tichy SE, Gheyi T, Zheng X, Bain K, Groshong C, Emtage S, Sauder JM, Burley SK, Swaminathan S, Lindahl PA, Raushel FM Protein Sci. 2011 Dec;20(12):2080-94. doi: 10.1002/pro.748. Epub 2011 Nov 9. PMID:21998098<ref>PMID:21998098</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3t8l" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Deaminase 3D structures\|Deaminase 3D structures]]		*[[Deaminase 3D structures\|Deaminase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 08:16, 6 December 2023

OCA — Wed, 06 Dec 2023 08:16:04 GMT

←Older revision		Revision as of 08:16, 6 December 2023
Line 1:		Line 1:

	==Crystal Structure of adenine deaminase with Mn/Fe==		==Crystal Structure of adenine deaminase with Mn/Fe==
-	<StructureSection load='3t8l' size='340' side='right'caption='[[3t8l]]' scene=''>	+	<StructureSection load='3t8l' size='340' side='right'caption='[[3t8l]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T8L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3T8L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3t8l]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Agrobacterium_fabrum_str._C58 Agrobacterium fabrum str. C58]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T8L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3T8L FirstGlance]. <br>
-	</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=3t8l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t8l OCA], [https://pdbe.org/3t8l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3t8l RCSB], [https://www.ebi.ac.uk/pdbsum/3t8l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3t8l ProSAT]</span></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]] 2.8Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</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=3t8l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t8l OCA], [https://pdbe.org/3t8l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3t8l RCSB], [https://www.ebi.ac.uk/pdbsum/3t8l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3t8l ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/ADEC2_AGRFC ADEC2_AGRFC]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Adenine deaminase (ADE) from the amidohydrolase superfamily (AHS) of enzymes catalyzes the conversion of adenine to hypoxanthine and ammonia. Enzyme isolated from Escherichia coli was largely inactive toward the deamination of adenine. Molecular weight determinations by mass spectrometry provided evidence that multiple histidine and methionine residues were oxygenated. When iron was sequestered with a metal chelator and the growth medium supplemented with Mn(2+) before induction, the post-translational modifications disappeared. Enzyme expressed and purified under these conditions was substantially more active for adenine deamination. Apo-enzyme was prepared and reconstituted with two equivalents of FeSO(4). Inductively coupled plasma mass spectrometry and Mossbauer spectroscopy demonstrated that this protein contained two high-spin ferrous ions per monomer of ADE. In addition to the adenine deaminase activity, [Fe(II) /Fe(II) ]-ADE catalyzed the conversion of H(2)O(2) to O(2) and H(2)O. The values of k(cat) and k(cat)/K(m) for the catalase activity are 200 s(-1) and 2.4 x 10(4) M(-1) s(-1), respectively. [Fe(II)/Fe(II)]-ADE underwent more than 100 turnovers with H(2)O(2) before the enzyme was inactivated due to oxygenation of histidine residues critical for metal binding. The iron in the inactive enzyme was high-spin ferric with g(ave) = 4.3 EPR signal and no evidence of anti-ferromagnetic spin-coupling. A model is proposed for the disproportionation of H(2)O(2) by [Fe(II)/Fe(II)]-ADE that involves the cycling of the binuclear metal center between the di-ferric and di-ferrous oxidation states. Oxygenation of active site residues occurs via release of hydroxyl radicals. These findings represent the first report of redox reaction catalysis by any member of the AHS.
		+
		+	The catalase activity of diiron adenine deaminase.,Kamat SS, Holmes-Hampton GP, Bagaria A, Kumaran D, Tichy SE, Gheyi T, Zheng X, Bain K, Groshong C, Emtage S, Sauder JM, Burley SK, Swaminathan S, Lindahl PA, Raushel FM Protein Sci. 2011 Dec;20(12):2080-94. doi: 10.1002/pro.748. Epub 2011 Nov 9. PMID:21998098<ref>PMID:21998098</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 3t8l" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Deaminase 3D structures\|Deaminase 3D structures]]		*[[Deaminase 3D structures\|Deaminase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Agrobacterium fabrum str. C58]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Bagaria A]]		[[Category: Bagaria A]]

OCA at 16:47, 6 July 2022

OCA — Wed, 06 Jul 2022 16:47:30 GMT

←Older revision		Revision as of 16:47, 6 July 2022
Line 1:		Line 1:

	==Crystal Structure of adenine deaminase with Mn/Fe==		==Crystal Structure of adenine deaminase with Mn/Fe==
-	<StructureSection load='3t8l' size='340' side='right' caption='[[3t8l]]~~, [[Resolution\|resolution]] 2.80Å~~' scene=''>	+	<StructureSection load='3t8l' size='340' side='right'caption='[[3t8l]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>~~[[3t8l]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Agrt5 Agrt5].~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T8L OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3T8L FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T8L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3T8L FirstGlance]. <br>
-	</td></tr>~~<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></td></tr>~~	+	</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=3t8l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t8l OCA], [https://pdbe.org/3t8l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3t8l RCSB], [https://www.ebi.ac.uk/pdbsum/3t8l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3t8l ProSAT]</span></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>~~	+
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3nqb\|3nqb]], [[3t81\|3t81]]</td></tr>~~	+
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ade2, adeC, AGR_L_883, Atu4426 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=176299 AGRT5])</td></tr>	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenine_deaminase Adenine deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.2 3.5.4.2] </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=3t8l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t8l OCA], [~~http~~://pdbe.org/3t8l PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3t8l RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3t8l PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3t8l ProSAT]</span></td></tr>	+
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Adenine deaminase (ADE) from the amidohydrolase superfamily (AHS) of enzymes catalyzes the conversion of adenine to hypoxanthine and ammonia. Enzyme isolated from Escherichia coli was largely inactive toward the deamination of adenine. Molecular weight determinations by mass spectrometry provided evidence that multiple histidine and methionine residues were oxygenated. When iron was sequestered with a metal chelator and the growth medium supplemented with Mn(2+) before induction, the post-translational modifications disappeared. Enzyme expressed and purified under these conditions was substantially more active for adenine deamination. Apo-enzyme was prepared and reconstituted with two equivalents of FeSO(4). Inductively coupled plasma mass spectrometry and Mossbauer spectroscopy demonstrated that this protein contained two high-spin ferrous ions per monomer of ADE. In addition to the adenine deaminase activity, [Fe(II) /Fe(II) ]-ADE catalyzed the conversion of H(2)O(2) to O(2) and H(2)O. The values of k(cat) and k(cat)/K(m) for the catalase activity are 200 s(-1) and 2.4 x 10(4) M(-1) s(-1), respectively. [Fe(II)/Fe(II)]-ADE underwent more than 100 turnovers with H(2)O(2) before the enzyme was inactivated due to oxygenation of histidine residues critical for metal binding. The iron in the inactive enzyme was high-spin ferric with g(ave) = 4.3 EPR signal and no evidence of anti-ferromagnetic spin-coupling. A model is proposed for the disproportionation of H(2)O(2) by [Fe(II)/Fe(II)]-ADE that involves the cycling of the binuclear metal center between the di-ferric and di-ferrous oxidation states. Oxygenation of active site residues occurs via release of hydroxyl radicals. These findings represent the first report of redox reaction catalysis by any member of the AHS.
-
-	The catalase activity of diiron adenine deaminase.,Kamat SS, Holmes-Hampton GP, Bagaria A, Kumaran D, Tichy SE, Gheyi T, Zheng X, Bain K, Groshong C, Emtage S, Sauder JM, Burley SK, Swaminathan S, Lindahl PA, Raushel FM Protein Sci. 2011 Dec;20(12):2080-94. doi: 10.1002/pro.748. Epub 2011 Nov 9. PMID:21998098<ref>PMID:21998098</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3t8l" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
-	*[[Deaminase\|Deaminase]]	+	*[[Deaminase 3D structures\|Deaminase 3D structures]]
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Adenine deaminase]]~~	+	[[Category: Large Structures]]
-	~~[[Category: Agrt5~~]]	+	[[Category: Bagaria A]]
-	[[Category: Bagaria, A]]	+	[[Category: Burley SK]]
-	[[Category: Burley~~, S K~~]]	+	[[Category: Kumaran D]]
-	[[Category: Kumaran, D]]	+	[[Category: Swaminathan S]]
-	~~[[Category: Structural genomic~~]]	+
-	[[Category: Swaminathan, S]]	+
-	~~[[Category: Adenine]]~~	+
-	~~[[Category: Alpha/beta]]~~	+
-	~~[[Category: Amidohydrolase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Nucleotide binding]]~~	+
-	~~[[Category: NYSGXRC, New York SGX Research Center for Structural Genomics]]~~	+
-	~~[[Category: PSI, Protein structure initiative]]~~	+
-	~~[[Category: Tim barrel~~]]	+

OCA at 07:16, 11 August 2016

OCA — Thu, 11 Aug 2016 07:16:56 GMT

←Older revision		Revision as of 07:16, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal Structure of adenine deaminase with Mn/Fe==		==Crystal Structure of adenine deaminase with Mn/Fe==
	<StructureSection load='3t8l' size='340' side='right' caption='[[3t8l]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='3t8l' size='340' side='right' caption='[[3t8l]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3t8l]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Agrobacterium_tumefaciens_str._c58 Agrobacterium tumefaciens str. c58~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T8L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3T8L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3t8l]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Agrt5 Agrt5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T8L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3T8L FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3nqb\|3nqb]], [[3t81\|3t81]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3nqb\|3nqb]], [[3t81\|3t81]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ade2, adeC, AGR_L_883, Atu4426 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=176299 ~~Agrobacterium tumefaciens str. C58~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ade2, adeC, AGR_L_883, Atu4426 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=176299 AGRT5])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenine_deaminase Adenine deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.2 3.5.4.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenine_deaminase Adenine deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.2 3.5.4.2] </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=3t8l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t8l OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3t8l RCSB], [http://www.ebi.ac.uk/pdbsum/3t8l 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=3t8l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t8l OCA], [http://pdbe.org/3t8l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3t8l RCSB], [http://www.ebi.ac.uk/pdbsum/3t8l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3t8l ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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 3t8l" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 26:		Line 28:
	</StructureSection>		</StructureSection>
	[[Category: Adenine deaminase]]		[[Category: Adenine deaminase]]
-	[[Category: ~~Agrobacterium tumefaciens str. c58~~]]	+	[[Category: Agrt5]]
	[[Category: Bagaria, A]]		[[Category: Bagaria, A]]
	[[Category: Burley, S K]]		[[Category: Burley, S K]]

OCA at 12:24, 6 November 2014

OCA — Thu, 06 Nov 2014 12:24:26 GMT

←Older revision		Revision as of 12:24, 6 November 2014
Line 26:		Line 26:
	</StructureSection>		</StructureSection>
	[[Category: Adenine deaminase]]		[[Category: Adenine deaminase]]
		+	[[Category: Agrobacterium tumefaciens str. c58]]
		+	[[Category: Bagaria, A]]
		+	[[Category: Burley, S K]]
	[[Category: Kumaran, D]]		[[Category: Kumaran, D]]
		+	[[Category: Structural genomic]]
		+	[[Category: Swaminathan, S]]
	[[Category: Adenine]]		[[Category: Adenine]]
	[[Category: Alpha/beta]]		[[Category: Alpha/beta]]
	[[Category: Amidohydrolase]]		[[Category: Amidohydrolase]]
		+	[[Category: Hydrolase]]
	[[Category: Nucleotide binding]]		[[Category: Nucleotide binding]]
		+	[[Category: NYSGXRC, New York SGX Research Center for Structural Genomics]]
		+	[[Category: PSI, Protein structure initiative]]
	[[Category: Tim barrel]]		[[Category: Tim barrel]]

OCA at 11:21, 6 November 2014

OCA — Thu, 06 Nov 2014 11:21:49 GMT

←Older revision		Revision as of 11:21, 6 November 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3t8l~~\| ~~PDB~~=3t8l \| ~~SCENE~~= }}	+	==Crystal Structure of adenine deaminase with Mn/Fe==
-	===~~Crystal Structure of adenine~~ deaminase with Mn/Fe===	+	<StructureSection load='3t8l' size='340' side='right' caption='[[3t8l]], [[Resolution\|resolution]] 2.80Å' scene=''>
-	~~{{ABSTRACT_PUBMED_21998098}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3t8l]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Agrobacterium_tumefaciens_str._c58 Agrobacterium tumefaciens str. c58]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T8L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3T8L FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3nqb\|3nqb]], [[3t81\|3t81]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ade2, adeC, AGR_L_883, Atu4426 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=176299 Agrobacterium tumefaciens str. C58])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenine_deaminase Adenine deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.2 3.5.4.2] </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=3t8l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t8l OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3t8l RCSB], [http://www.ebi.ac.uk/pdbsum/3t8l PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Adenine deaminase (ADE) from the amidohydrolase superfamily (AHS) of enzymes catalyzes the conversion of adenine to hypoxanthine and ammonia. Enzyme isolated from Escherichia coli was largely inactive toward the deamination of adenine. Molecular weight determinations by mass spectrometry provided evidence that multiple histidine and methionine residues were oxygenated. When iron was sequestered with a metal chelator and the growth medium supplemented with Mn(2+) before induction, the post-translational modifications disappeared. Enzyme expressed and purified under these conditions was substantially more active for adenine deamination. Apo-enzyme was prepared and reconstituted with two equivalents of FeSO(4). Inductively coupled plasma mass spectrometry and Mossbauer spectroscopy demonstrated that this protein contained two high-spin ferrous ions per monomer of ADE. In addition to the adenine deaminase activity, [Fe(II) /Fe(II) ]-ADE catalyzed the conversion of H(2)O(2) to O(2) and H(2)O. The values of k(cat) and k(cat)/K(m) for the catalase activity are 200 s(-1) and 2.4 x 10(4) M(-1) s(-1), respectively. [Fe(II)/Fe(II)]-ADE underwent more than 100 turnovers with H(2)O(2) before the enzyme was inactivated due to oxygenation of histidine residues critical for metal binding. The iron in the inactive enzyme was high-spin ferric with g(ave) = 4.3 EPR signal and no evidence of anti-ferromagnetic spin-coupling. A model is proposed for the disproportionation of H(2)O(2) by [Fe(II)/Fe(II)]-ADE that involves the cycling of the binuclear metal center between the di-ferric and di-ferrous oxidation states. Oxygenation of active site residues occurs via release of hydroxyl radicals. These findings represent the first report of redox reaction catalysis by any member of the AHS.

-	~~==About this Structure==~~	+	The catalase activity of diiron adenine deaminase.,Kamat SS, Holmes-Hampton GP, Bagaria A, Kumaran D, Tichy SE, Gheyi T, Zheng X, Bain K, Groshong C, Emtage S, Sauder JM, Burley SK, Swaminathan S, Lindahl PA, Raushel FM Protein Sci. 2011 Dec;20(12):2080-94. doi: 10.1002/pro.748. Epub 2011 Nov 9. PMID:21998098<ref>PMID:21998098</ref>
-	~~[[3t8l]] is a 2 chain structure with sequence from [http~~:~~//en~~.~~wikipedia~~.~~org/wiki~~/~~Agrobacterium_tumefaciens_str~~.~~_c58 Agrobacterium tumefaciens str~~. ~~c58]~~. ~~Full crystallographic information is available from [http~~://~~oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=3T8L OCA].~~	+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

	==See Also==		==See Also==
	*[[Deaminase\|Deaminase]]		*[[Deaminase\|Deaminase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:021998098</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Adenine deaminase]]		[[Category: Adenine deaminase]]
-	~~[[Category: Agrobacterium tumefaciens str. c58]]~~	+	[[Category: Kumaran, D]]
-	~~[[Category: Bagaria, A.]]~~	+
-	~~[[Category: Burley, S K.]]~~	+
-	[[Category: Kumaran, D~~.]]~~	+
-	~~[[Category: NYSGXRC, New York SGX Research Center for Structural Genomics.]]~~	+
-	~~[[Category: Swaminathan, S.~~]]	+
	[[Category: Adenine]]		[[Category: Adenine]]
-	[[Category: Adenine deaminase]]
	[[Category: Alpha/beta]]		[[Category: Alpha/beta]]
	[[Category: Amidohydrolase]]		[[Category: Amidohydrolase]]
-	[[Category: Hydrolase]]
-	[[Category: New york sgx research center for structural genomic]]
	[[Category: Nucleotide binding]]		[[Category: Nucleotide binding]]
-	[[Category: Nysgxrc]]
-	[[Category: Protein structure initiative]]
-	[[Category: Psi-2]]
-	[[Category: Structural genomic]]
	[[Category: Tim barrel]]		[[Category: Tim barrel]]

OCA at 02:49, 20 September 2013

OCA — Fri, 20 Sep 2013 02:49:57 GMT

←Older revision		Revision as of 02:49, 20 September 2013
Line 1:		Line 1:
-	[[Image:3t8l.jpg\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_3t8l", 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_3t8l\| PDB=3t8l \| SCENE= }}		{{STRUCTURE_3t8l\| PDB=3t8l \| SCENE= }}
-
	===Crystal Structure of adenine deaminase with Mn/Fe===		===Crystal Structure of adenine deaminase with Mn/Fe===
		+	{{ABSTRACT_PUBMED_21998098}}

		+	==About this Structure==
		+	[[3t8l]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Agrobacterium_tumefaciens_str._c58 Agrobacterium tumefaciens str. c58]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T8L OCA].

-	==~~About this Structure~~==	+	==See Also==
-	[[~~3t8l~~]] ~~is a 2 chain structure with sequence from [http~~://~~en.wikipedia.org~~/~~wiki/Agrobacterium_tumefaciens Agrobacterium tumefaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T8L OCA].~~	+	*[[Deaminase\|Deaminase]]
		+
		+	==Reference==
		+	<ref group="xtra">PMID:021998098</ref><references group="xtra"/><references/>
	[[Category: Adenine deaminase]]		[[Category: Adenine deaminase]]
-	[[Category: Agrobacterium tumefaciens]]	+	[[Category: Agrobacterium tumefaciens str. c58]]
	[[Category: Bagaria, A.]]		[[Category: Bagaria, A.]]
	[[Category: Burley, S K.]]		[[Category: Burley, S K.]]

OCA at 08:36, 2 November 2011

OCA — Wed, 02 Nov 2011 08:36:27 GMT

←Older revision		Revision as of 08:36, 2 November 2011
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-	~~'''Unreleased structure'''~~	+	[[Image:3t8l.jpg\|left\|200px]]

-	The ~~entry 3t8l~~ is ~~ON HOLD~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3t8l", 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_3t8l\| PDB=3t8l \| SCENE= }}

-	~~Authors: Bagaria, A., Kumaran, D., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)~~	+	===Crystal Structure of adenine deaminase with Mn/Fe===

-	~~Description: Crystal~~ Structure ~~of adenine deaminase~~ with Mn/Fe	+
		+	==About this Structure==
		+	[[3t8l]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Agrobacterium_tumefaciens Agrobacterium tumefaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T8L OCA].
		+	[[Category: Adenine deaminase]]
		+	[[Category: Agrobacterium tumefaciens]]
		+	[[Category: Bagaria, A.]]
		+	[[Category: Burley, S K.]]
		+	[[Category: Kumaran, D.]]
		+	[[Category: NYSGXRC, New York SGX Research Center for Structural Genomics.]]
		+	[[Category: Swaminathan, S.]]
		+	[[Category: Adenine]]
		+	[[Category: Adenine deaminase]]
		+	[[Category: Alpha/beta]]
		+	[[Category: Amidohydrolase]]
		+	[[Category: Hydrolase]]
		+	[[Category: New york sgx research center for structural genomic]]
		+	[[Category: Nucleotide binding]]
		+	[[Category: Nysgxrc]]
		+	[[Category: Protein structure initiative]]
		+	[[Category: Psi-2]]
		+	[[Category: Structural genomic]]
		+	[[Category: Tim barrel]]

OCA at 05:54, 17 August 2011

OCA — Wed, 17 Aug 2011 05:54:49 GMT

←Older revision		Revision as of 05:54, 17 August 2011
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	The entry 3t8l is ON HOLD		The entry 3t8l is ON HOLD

-	Authors: Bagaria, A., Kumaran, D., Burley, S. K., Swaminathan, S., New York Structural Genomics ~~Research Consortium~~ (~~NYSGRC~~)	+	Authors: Bagaria, A., Kumaran, D., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

	Description: Crystal Structure of adenine deaminase with Mn/Fe		Description: Crystal Structure of adenine deaminase with Mn/Fe

OCA: Protected "3t8l" [edit=sysop:move=sysop]

OCA — Wed, 10 Aug 2011 05:37:13 GMT

Protected "3t8l" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:37, 10 August 2011